### 2018

- J. Lipková, G. Arampatzis, P. Chatelain, B. Menze, and P. Koumoutsakos, “S-leaping: an adaptive, accelerated stochastic simulation algorithm, bridging τ-leaping and r-leaping," Bulletin of mathematical biology, 2018.

[BibTeX] [PDF] [DOI]`@article{lipkova2018a, author = {Jana Lipkov{\'{a}} and Georgios Arampatzis and Philippe Chatelain and Bjoern Menze and Petros Koumoutsakos}, doi = {10.1007/s11538-018-0464-9}, journal = {Bulletin of Mathematical Biology}, month = {jul}, publisher = {Springer Nature}, title = {S-Leaping: An Adaptive, Accelerated Stochastic Simulation Algorithm, Bridging -Leaping and R-Leaping}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/lipkova2018a.pdf}, year = {2018} }`

- F. Wermelinger, U. Rasthofer, P. E. Hadjidoukas, and P. Koumoutsakos, “Petascale simulations of compressible flows with interfaces," Journal of computational science, vol. 26, pp. 217-225, 2018.

[BibTeX] [Abstract] [PDF] [DOI]

We demonstrate a high throughput software for the efficient simulation of compressible multicomponent flow on high performance computing platforms. The discrete problem is represented on structured three-dimensional grids with non-uniform resolution. Discontinuous flow features are captured using a diffuse interface method. A distinguishing characteristic of the method is the proper treatment of the interface zone as a mixing region of liquid and gas. The governing equations are discretized by a Godunov-type finite volume method with explicit time stepping using a low-storage Runge-Kutta scheme. The presented flow solver Cubism-MPCF is based on our Cubism library which enables a highly optimized framework for the efficient treatment of stencil based problems on multicore architectures. The framework is general and not limited to applications in fluid dynamics. We validate our solver by classical benchmark examples. Furthermore, we examine a highly-resolved shock-induced bubble collapse and a cloud of collapsing bubbles, which demonstrate the high potential of the proposed framework and solver.

`@article{wermelinger2018a, author = {F. Wermelinger and U. Rasthofer and P.E. Hadjidoukas and P. Koumoutsakos}, doi = {10.1016/j.jocs.2018.01.008}, journal = {Journal of Computational Science}, month = {may}, pages = {217--225}, publisher = {Elsevier {BV}}, title = {Petascale simulations of compressible flows with interfaces}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/wermelinger2018a.pdf}, volume = {26}, year = {2018} }`

- Z. Y. Wan, P. R. Vlachas, P. Koumoutsakos, and T. P. Sapsis, “Data-assisted reduced-order modeling of extreme events in complex dynamical systems," PLoS ONE, vol. 13, iss. 5, pp. 1-22, 2018.

[BibTeX] [PDF] [DOI]`@article{wan2018a, author = {Zhong Y. Wan and Pantelis R. Vlachas and Petros Koumoutsakos and Themistoklis P. Sapsis}, doi = {10.1371/journal.pone.0197704}, journal = {{PL}o{S} {ONE}}, month = {may}, number = {5}, pages = {1-22}, publisher = {Public Library of Science}, title = {Data-assisted reduced-order modeling of extreme events in complex dynamical systems}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/wan2018a.pdf}, volume = {13}, year = {2018} }`

- S. Verma, G. Novati, and P. Koumoutsakos, “Efficient collective swimming by harnessing vortices through deep reinforcement learning," Proceedings of the national academy of sciences, p. 201800923, 2018.

[BibTeX] [PDF] [DOI]`@article{verma2018a, author = {Siddhartha Verma and Guido Novati and Petros Koumoutsakos}, doi = {10.1073/pnas.1800923115}, journal = {Proceedings of the National Academy of Sciences}, month = {may}, pages = {201800923}, publisher = {Proceedings of the National Academy of Sciences}, title = {Efficient collective swimming by harnessing vortices through deep reinforcement learning}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/verma2018a.pdf}, year = {2018} }`

- P. R. Vlachas, W. Byeon, Z. Y. Wan, T. P. Sapsis, and P. Koumoutsakos, “Data-driven forecasting of high-dimensional chaotic systems with long short-term memory networks," Proceedings of the royal society a: mathematical, physical and engineering science, vol. 474, iss. 2213, p. 20170844, 2018.

[BibTeX] [PDF] [DOI]`@article{vlachas2018a, author = {Pantelis R. Vlachas and Wonmin Byeon and Zhong Y. Wan and Themistoklis P. Sapsis and Petros Koumoutsakos}, doi = {10.1098/rspa.2017.0844}, journal = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Science}, month = {may}, number = {2213}, pages = {20170844}, publisher = {The Royal Society}, title = {Data-driven forecasting of high-dimensional chaotic systems with long short-term memory networks}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/vlachas2018a.pdf}, volume = {474}, year = {2018} }`

- G. Arampatzis, D. Wälchli, P. Angelikopoulos, S. Wu, P. Hadjidoukas, and P. Koumoutsakos, “Langevin diffusion for population based sampling with an application in bayesian inference for pharmacodynamics," SIAM journal on scientific computing, vol. 40, iss. 3, p. B788–B811, 2018.

[BibTeX] [PDF] [DOI]`@article{arampatzis2018a, author = {Georgios Arampatzis and Daniel W\"alchli and Panagiotis Angelikopoulos and Stephen Wu and Panagiotis Hadjidoukas and Petros Koumoutsakos}, doi = {10.1137/16m1107401}, journal = {{SIAM} Journal on Scientific Computing}, month = {jan}, number = {3}, pages = {B788--B811}, publisher = {Society for Industrial {\&} Applied Mathematics ({SIAM})}, title = {Langevin Diffusion for Population Based Sampling with an Application in Bayesian Inference for Pharmacodynamics}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/arampatzis2018a.pdf}, volume = {40}, year = {2018} }`

### 2017

- E. R. Cruz-Chú, E. Papadopoulou, J. H. Walther, A. Popadić, G. Li, M. Praprotnik, and P. Koumoutsakos, “On phonons and water flow enhancement in carbon nanotubes," Nature nanotechnology, vol. 12, iss. 12, pp. 1106-1108, 2017.

[BibTeX] [PDF] [DOI]`@article{cruzchu2017a, author = {Eduardo R. Cruz-Ch{\'{u}} and Ermioni Papadopoulou and Jens H. Walther and Aleksandar Popadi{\'{c}} and Gengyun Li and Matej Praprotnik and Petros Koumoutsakos}, doi = {10.1038/nnano.2017.234}, journal = {Nature Nanotechnology}, month = {dec}, number = {12}, pages = {1106--1108}, publisher = {Springer Nature}, title = {On phonons and water flow enhancement in carbon nanotubes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/cruzchu2017a.pdf}, volume = {12}, year = {2017} }`

- B. Mosimann, G. Arampatzis, S. Amylidi-Mohr, A. Bessire, M. Spinelli, P. Koumoutsakos, D. Surbek, and L. Raio, “Reference ranges for fetal atrioventricular and ventriculoatrial time intervals and their ratios during normal pregnancy," Fetal diagnosis and therapy, 2017.

[BibTeX] [PDF] [DOI]`@article{mosimann2017a, author = {Beatrice Mosimann and Georgios Arampatzis and Sofia Amylidi-Mohr and Anice Bessire and Marialuigia Spinelli and Petros Koumoutsakos and Daniel Surbek and Luigi Raio}, doi = {10.1159/000481349}, journal = {Fetal Diagnosis and Therapy}, month = {oct}, publisher = {S. Karger {AG}}, title = {Reference Ranges for Fetal Atrioventricular and Ventriculoatrial Time Intervals and Their Ratios during Normal Pregnancy}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/mosimann2017a.pdf}, year = {2017} }`

- S. Wu, P. Angelikopoulos, C. Papadimitriou, and P. Koumoutsakos, “Bayesian annealed sequential importance sampling (BASIS): an unbiased version of transitional markov chain Monte Carlo," ASCE-ASME j. risk and uncert. in engrg. sys., part b: mech. engrg., 2017.

[BibTeX] [PDF] [DOI]`@article{wu2017a, author = {Stephen Wu and Panagiotis Angelikopoulos and Costas Papadimitriou and Petros Koumoutsakos}, doi = {10.1115/1.4037450}, journal = {{ASCE}-{ASME} J. Risk and Uncert. in Engrg. Sys., Part B: Mech. Engrg.}, month = {aug}, publisher = {{ASME} International}, title = {{B}ayesian Annealed Sequential Importance Sampling ({BASIS}): an unbiased version of Transitional Markov Chain {M}onte {C}arlo}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/wu2017a.pdf}, year = {2017} }`

- S. Verma, G. Abbati, G. Novati, and P. Koumoutsakos, “Computing the force distribution on the surface of complex, deforming geometries using vortex methods and Brinkman penalization," International journal for numerical methods in fluids, 2017.

[BibTeX] [PDF] [DOI]`@article{verma2017a, author = {Siddhartha Verma and Gabriele Abbati and Guido Novati and Petros Koumoutsakos}, doi = {10.1002/fld.4392}, journal = {International Journal for Numerical Methods in Fluids}, month = {jun}, publisher = {Wiley-Blackwell}, title = {Computing the force distribution on the surface of complex, deforming geometries using vortex methods and {B}rinkman penalization}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/verma2017a.pdf}, year = {2017} }`

- G. Novati, S. Verma, D. Alexeev, D. Rossinelli, W. M. van Rees, and P. Koumoutsakos, “Synchronisation through learning for two self-propelled swimmers," Bioinspiration & biomimetics, vol. 12, iss. 3, p. 36001, 2017.

[BibTeX] [PDF] [DOI]`@article{novati2017a, author = {Guido Novati and Siddhartha Verma and Dmitry Alexeev and Diego Rossinelli and Wim M van Rees and Petros Koumoutsakos}, doi = {10.1088/1748-3190/aa6311}, journal = {Bioinspiration {\&} Biomimetics}, month = {mar}, number = {3}, pages = {036001}, publisher = {{IOP} Publishing}, title = {Synchronisation through learning for two self-propelled swimmers}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/novati2017a.pdf}, volume = {12}, year = {2017} }`

- N. Karathanasopoulos, P. Angelikopoulos, C. Papadimitriou, and P. Koumoutsakos, “Bayesian identification of the tendon fascicle’s structural composition using finite element models for helical geometries," Computer methods in applied mechanics and engineering, vol. 313, pp. 744-758, 2017.

[BibTeX] [PDF] [DOI]`@article{karathanasopoulos2017a, author = {N. Karathanasopoulos and P. Angelikopoulos and C. Papadimitriou and P. Koumoutsakos}, doi = {10.1016/j.cma.2016.10.024}, journal = {Computer Methods in Applied Mechanics and Engineering}, month = {jan}, pages = {744--758}, publisher = {Elsevier {BV}}, title = {{B}ayesian identification of the tendon fascicle's structural composition using finite element models for helical geometries}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/karathanasopoulos2017a.pdf}, volume = {313}, year = {2017} }`

- L. Kulakova, G. Arampatzis, P. Angelikopoulos, P. Hadjidoukas, C. Papadimitriou, and P. Koumoutsakos, “Data driven inference for the repulsive exponent of the Lennard-Jones potential in molecular dynamics simulations," Scientific reports, vol. 7, iss. 1, p. 16576, 2017.

[BibTeX] [Abstract] [PDF] [DOI]

The Lennard-Jones (LJ) potential is a cornerstone of Molecular Dynamics (MD) simulations and among the most widely used computational kernels in science. The LJ potential models atomistic attraction and repulsion with century old prescribed parameters (, respectively), originally related by a factor of two for simplicity of calculations. We propose the inference of the repulsion exponent through Hierarchical Bayesian uncertainty quantification We use experimental data of the radial distribution function and dimer interaction energies from quantum mechanics simulations. We find that the repulsion exponent provides an excellent fit for the experimental data of liquid argon, for a range of thermodynamic conditions, as well as for saturated argon vapour. Calibration using the quantum simulation data did not provide a good fit in these cases. However, values obtained by dimer quantum simulations are preferred for the argon gas while lower values are promoted by experimental data. These results show that the proposed LJ 6-p potential applies to a wider range of thermodynamic conditions, than the classical LJ 6-12 potential. We suggest that calibration of the repulsive exponent in the LJ potential widens the range of applicability and accuracy of MD simulations.

`@article{kulakova2017a, author = {Kulakova, Lina and Arampatzis, Georgios and Angelikopoulos, Panagiotis and Hadjidoukas, Panagiotis and Papadimitriou, Costas and Koumoutsakos, Petros}, doi = {10.1038/s41598-017-16314-4}, issn = {2045-2322}, journal = {Scientific Reports}, number = {1}, pages = {16576}, title = {Data driven inference for the repulsive exponent of the {L}ennard-{J}ones potential in molecular dynamics simulations}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/kulakova2017a.pdf}, volume = {7}, year = {2017} }`

- W. Byeon, Q. Wang, R. K. Srivastava, and P. Koumoutsakos, “Fully context-aware video prediction," Corr, vol. abs/1710.08518, 2017.

[BibTeX] [PDF]`@article{byeon2017a, archiveprefix = {arXiv}, arxiv = {http://arxiv.org/abs/1710.08518}, author = {Wonmin Byeon and Qin Wang and Rupesh Kumar Srivastava and Petros Koumoutsakos}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/bib/journals/corr/abs-1710-08518}, eprint = {1710.08518}, journal = {CoRR}, title = {Fully Context-Aware Video Prediction}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/byeon2017a.pdf}, volume = {abs/1710.08518}, year = {2017} }`

### 2016

- S. Wu, P. Angelikopoulos, G. Tauriello, C. Papadimitriou, and P. Koumoutsakos, “Fusing heterogeneous data for the calibration of molecular dynamics force fields using hierarchical Bayesian models," The journal of chemical physics, vol. 145, iss. 24, p. 244112, 2016.

[BibTeX] [PDF] [DOI]`@article{wu2016a, author = {Stephen Wu and Panagiotis Angelikopoulos and Gerardo Tauriello and Costas Papadimitriou and Petros Koumoutsakos}, doi = {10.1063/1.4967956}, journal = {The Journal of Chemical Physics}, month = {dec}, number = {24}, pages = {244112}, publisher = {{AIP} Publishing}, title = {Fusing heterogeneous data for the calibration of molecular dynamics force fields using hierarchical {B}ayesian models}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/wu2016a.pdf}, volume = {145}, year = {2016} }`

- J. Chen, J. H. Walther, and P. Koumoutsakos, “Ultrafast cooling by covalently bonded graphene-carbon nanotube hybrid immersed in water," Nanotechnology, vol. 27, iss. 46, p. 465705, 2016.

[BibTeX] [PDF] [DOI]`@article{chen2016a, author = {Jie Chen and Jens H Walther and Petros Koumoutsakos}, doi = {10.1088/0957-4484/27/46/465705}, journal = {Nanotechnology}, month = {oct}, number = {46}, pages = {465705}, publisher = {{IOP} Publishing}, title = {Ultrafast cooling by covalently bonded graphene-carbon nanotube hybrid immersed in water}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/chen2016a.pdf}, volume = {27}, year = {2016} }`

- M. Gazzola, A. A. Tchieu, D. Alexeev, A. de Brauer, and P. Koumoutsakos, “Learning to school in the presence of hydrodynamic interactions," Journal of fluid mechanics, vol. 789, pp. 726-749, 2016.

[BibTeX] [PDF] [DOI]`@article{gazzola2016a, author = {M. Gazzola and A. A. Tchieu and D. Alexeev and A. de Brauer and P. Koumoutsakos}, doi = {10.1017/jfm.2015.686}, journal = {Journal of Fluid Mechanics}, month = {jan}, pages = {726--749}, publisher = {Cambridge University Press ({CUP})}, title = {Learning to school in the presence of hydrodynamic interactions}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/gazzola2016a.pdf}, volume = {789}, year = {2016} }`

### 2015

- S. Wu, P. Angelikopoulos, C. Papadimitriou, R. Moser, and P. Koumoutsakos, “A hierarchical Bayesian framework for force field selection in molecular dynamics simulations," Philosophical transactions of the royal society a: mathematical, physical and engineering sciences, vol. 374, iss. 2060, p. 20150032, 2015.

[BibTeX] [Abstract] [PDF] [DOI]

We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different environmental conditions with the corresponding variability in experimental data. The high computational cost associated with the hierarchical Bayesian framework is reduced by orders of magnitude through a parallelized Transitional Markov Chain Monte Carlo method combined with the Laplace Asymptotic Approximation. The suitability of the hierarchical approach is demonstrated by performing MD simulations with prescribed parameters to obtain data for transport coefficients under different conditions, which are then used to infer and evaluate the parameters of the MD model. We demonstrate the selection of MD models based on experimental data and verify that the hierarchical model can accurately quantify the uncertainty across experiments; improve the posterior probability density function estimation of the parameters, thus, improve predictions on future experiments; identify the most plausible force field to describe the underlying structure of a given dataset. The framework and associated software are applicable to a wide range of nanoscale simulations associated with experimental data with a hierarchical structure.

`@article{wu2015a, author = {S. Wu and P. Angelikopoulos and C. Papadimitriou and R. Moser and P. Koumoutsakos}, doi = {10.1098/rsta.2015.0032}, journal = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences}, month = {dec}, number = {2060}, pages = {20150032}, publisher = {The Royal Society}, title = {A hierarchical {B}ayesian framework for force field selection in molecular dynamics simulations}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/wu2015a.pdf}, volume = {374}, year = {2015} }`

- C. Conti, D. Rossinelli, D. Alexeev, K. Lykov, P. Hadjidoukas, and P. Koumoutsakos, “Video: the in-silico lab-on-a-chip – catching a needle in a flowing haystack," in 68th annual meeting of the APS division of fluid dynamics – gallery of fluid motion, 2015.

[BibTeX] [Movie] [DOI]`@inproceedings{conti2015a, author = {Christian Conti and Diego Rossinelli and Dmitry Alexeev and Kirill Lykov and Panagiotis Hadjidoukas and Petros Koumoutsakos}, booktitle = {68th Annual Meeting of the {APS} Division of Fluid Dynamics - Gallery of Fluid Motion}, doi = {10.1103/aps.dfd.2015.gfm.v0008}, month = {nov}, movie = {https://www.youtube.com/watch?v=nVKjxqIP6I4}, publisher = {American Physical Society}, title = {Video: The In-Silico Lab-on-a-Chip - Catching a Needle in a Flowing Haystack}, year = {2015} }`

- J. Chen, J. H. Walther, and P. Koumoutsakos, “Covalently bonded graphene-carbon nanotube hybrid for high-performance thermal interfaces," Advanced functional materials, vol. 25, iss. 48, pp. 7539-7545, 2015.

[BibTeX] [Abstract] [PDF] [DOI]

The remarkable thermal properties of graphene and carbon nanotubes (CNTs) have been the subject of intensive investigations for the thermal management of integrated circuits. However, the small contact area of CNTs and the large anisotropic heat conduction of graphene have hindered their applications as effective thermal interface materials (TIMs). Here, a covalently bonded graphene{—}CNT (G-CNT) hybrid is presented that multiplies the axial heat transfer capability of individual CNTs through their parallel arrangement, while at the same time it provides a large contact area for efficient heat extraction. Through computer simulations, it is demonstrated that the G-CNT outperforms few-layer graphene by more than 2 orders of magnitude for the c-axis heat transfer, while its thermal resistance is 3 orders of magnitude lower than the state-of-the-art TIMs. We show that heat can be removed from the G-CNT by immersing it in a liquid. The heat transfer characteristics of G-CNT suggest that it has the potential to revolutionize the design of high-performance TIMs.

`@article{chen2015a, author = {Jie Chen and Jens H. Walther and Petros Koumoutsakos}, doi = {10.1002/adfm.201501593}, journal = {Advanced Functional Materials}, month = {nov}, number = {48}, pages = {7539--7545}, publisher = {Wiley-Blackwell}, title = {Covalently Bonded Graphene-Carbon Nanotube Hybrid for High-Performance Thermal Interfaces}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/chen2015a.pdf}, volume = {25}, year = {2015} }`

- G. Tauriello, H. M. Meyer, R. S. Smith, P. Koumoutsakos, and A. H. K. Roeder, “Variability and constancy in cellular growth of arabidopsis sepals," Plant physiology, p. pp.00839.2015, 2015.

[BibTeX] [Abstract] [PDF] [DOI]

Growth of tissues is highly reproducible; yet, growth of individual cells in a tissue is highly variable, and neighboring cells can grow at different rates. We analyzed the growth of epidermal cell lineages in the Arabidopsis (Arabidopsis thaliana) sepal to determine how the growth curves of individual cell lineages relate to one another in a developing tissue. To identify underlying growth trends, we developed a continuous displacement field to predict spatially averaged growth rates. We showed that this displacement field accurately describes the growth of sepal cell lineages and reveals underlying trends within the variability of in vivo cellular growth. We found that the tissue, individual cell lineages, and cell walls all exhibit growth rates that are initially low, accelerate to a maximum, and decrease again. Accordingly, these growth curves can be represented by sigmoid functions. We examined the relationships among the cell lineage growth curves and surprisingly found that all lineages reach the same maximum growth rate relative to their size. However, the cell lineages are not synchronized; each cell lineage reaches this same maximum relative growth rate but at different times. The heterogeneity in observed growth results from shifting the same underlying sigmoid curve in time and scaling by size. Thus, despite the variability in growth observed in our study and others, individual cell lineages in the developing sepal follow similarly shaped growth curves.

`@article{tauriello2015b, author = {Gerardo Tauriello and Heather M. Meyer and Richard S Smith and Petros Koumoutsakos and Adrienne H. K. Roeder}, doi = {10.1104/pp.15.00839}, journal = {Plant Physiology}, month = {oct}, pages = {pp.00839.2015}, publisher = {American Society of Plant Biologists ({ASPB})}, title = {Variability and constancy in cellular growth of Arabidopsis sepals}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/tauriello2015b.pdf}, year = {2015} }`

- S. Finley, P. Angelikopoulos, P. Koumoutsakos, and A. Popel, “Pharmacokinetics of anti-VEGF agent aflibercept in cancer predicted by data-driven, molecular-detailed model," CPT: pharmacometrics & systems pharmacology, vol. 4, iss. 11, pp. 641-649, 2015.

[BibTeX] [Abstract] [PDF] [DOI]

Mathematical models can support the drug development process by predicting the pharmacokinetic (PK) properties of the drug and optimal dosing regimens. We have developed a pharmacokinetic model that includes a biochemical molecular interaction network linked to a whole-body compartment model. We applied the model to study the PK of the anti-vascular endothelial growth factor (VEGF) cancer therapeutic agent, aflibercept. Clinical data is used to infer model parameters using a Bayesian approach, enabling a quantitative estimation of the contributions of specific transport processes and molecular interactions of the drug that cannot be examined in other PK modeling, and insight into the mechanisms of aflibercept’s antiangiogenic action. Additionally, we predict the plasma and tissue concentrations of unbound and VEGF-bound aflibercept. Thus, we present a computational framework that can serve as a valuable tool for drug development efforts.

`@article{finley2015a, author = {SD Finley and P Angelikopoulos and P Koumoutsakos and AS Popel}, doi = {10.1002/psp4.12040}, journal = {{CPT}: Pharmacometrics {\&} Systems Pharmacology}, month = {oct}, number = {11}, pages = {641--649}, publisher = {Wiley-Blackwell}, title = {Pharmacokinetics of Anti-{VEGF} Agent Aflibercept in Cancer Predicted by Data-Driven, Molecular-Detailed Model}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/finley2015a.pdf}, volume = {4}, year = {2015} }`

- D. Alexeev, J. Chen, J. H. Walther, K. P. Giapis, P. Angelikopoulos, and P. Koumoutsakos, “Kapitza resistance between few-layer graphene and water: liquid layering effects," Nano letters, vol. 15, iss. 9, pp. 5744-5749, 2015.

[BibTeX] [Abstract] [Supplemental] [PDF] [DOI]

The Kapitza resistance (R_K) between few-layer graphene (FLG) and water was studied using molecular dynamics simulations. The R_K was found to depend on the number of the layers in the FLG though, surprisingly, not on the water block thickness. This distinct size dependence is attributed to the large difference in the phonon mean free path between the FLG and water. Remarkably, R_K is strongly dependent on the layering of water adjacent to the FLG, exhibiting an inverse proportionality relationship to the peak density of the first water layer, which is consistent with better acoustic phonon matching between FLG and water. These findings suggest novel ways to engineer the thermal transport properties of solid{—}liquid interfaces by controlling and regulating the liquid layering at the interface.

`@article{alexeev2015a, author = {Dmitry Alexeev and Jie Chen and Jens H. Walther and Konstantinos P. Giapis and Panagiotis Angelikopoulos and Petros Koumoutsakos}, doi = {10.1021/acs.nanolett.5b03024}, journal = {Nano Letters}, month = {sep}, number = {9}, pages = {5744--5749}, publisher = {American Chemical Society ({ACS})}, supplemental = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/alexeev2015a_supplemental.pdf}, title = {Kapitza Resistance between Few-Layer Graphene and Water: Liquid Layering Effects}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/alexeev2015a.pdf}, volume = {15}, year = {2015} }`

- M. U. Baumann, M. Marti, L. Durrer, P. Koumoutsakos, P. Angelikopoulos, D. Bolla, G. Acharya, U. Bichsel, D. V. Surbek, and L. Raio, “Placental plasticity in monochorionic twins: impact on birth weight and placental weight," Placenta, vol. 36, iss. 9, pp. 1018-1023, 2015.

[BibTeX] [Abstract] [PDF] [DOI]

Introduction The knowledge about adaptive mechanisms of monochorionic placentas to fulfill the demands of two instead of one fetus is largely speculative. The aim of our study was to investigate the impact of chorionicity on birth weight and placental weight in twin pregnancies. Methods Forty Monochorionic (MC) and 43 dichorionic (DC) twin pregnancies were included in this retrospective study. Individual and total (sum of both twins) birth weights, placental weights ratios between placental and birth weights and observed-to-expected (O/E)-ratios were calculated and analyzed. Additionally, we investigated whether in twin pregnancies placental and birth weights follow the law of allometric metabolic scaling. Results MC pregnancies showed higher placental O/E-ratios than DC ones (2.25 {\pm} 0.85 versus 1.66 {\pm} 0.61; p < 0.05), whereas the total neonatal birth weight O/E-ratios were not different. In DC twins total placental weights correlated significantly with gestational age (r = 0.74, p < 0.001), but not in MC twins. Analysis of deliveries {\leq}32 weeks revealed that the placenta to birth weight ratio in MC twins was higher than in matched DC twins (0.49 {\pm} 0.3 versus 0.24 {\pm} 0.03; p = 0.03). Allometric metabolic scaling revealed that dichorionic twin placentas scale with birth weight, while the monochorionic ones do not. Discussion The weight of MC placentas compared to that of DC is not gestational age dependent in the third trimester. Therefore an early accelerated placental growth pattern has to be postulated which leads to an excess placental mass particularly below 32 weeks of gestation. The monochorionic twins do not follow allometric metabolic scaling principle making them more vulnerable to placental compromise. Keywords Twin pregnancy Monochorionic Dichorionic Birth weight Placental weight Fetal:placental ratio Allometric metabolic scaling

`@article{baumann2015a, author = {Marc U. Baumann and Michelle Marti and Lukas Durrer and Petros Koumoutsakos and Panagiotis Angelikopoulos and Daniele Bolla and Ganesh Acharya and Ursina Bichsel and Daniel V. Surbek and Luigi Raio}, doi = {10.1016/j.placenta.2015.07.120}, journal = {Placenta}, month = {sep}, number = {9}, pages = {1018--1023}, publisher = {Elsevier {BV}}, title = {Placental plasticity in monochorionic twins: Impact on birth weight and placental weight}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/baumann2015a.pdf}, volume = {36}, year = {2015} }`

- P. R. Jones, X. Hao, E. R. Cruz-Chu, K. Rykaczewski, K. Nandy, T. M. Schutzius, K. K. Varanasi, C. M. Megaridis, J. H. Walther, P. Koumoutsakos, H. D. Espinosa, and N. A. Patankar, “Sustaining dry surfaces under water," Scientific reports, vol. 5, iss. 1, 2015.

[BibTeX] [Abstract] [PDF] [DOI]

Rough surfaces immersed under water remain practically dry if the liquid-solid contact is on roughness peaks, while the roughness valleys are filled with gas. Mechanisms that prevent water from invading the valleys are well studied. However, to remain practically dry under water, additional mechanisms need consideration. This is because trapped gas (e.g. air) in the roughness valleys can dissolve into the water pool, leading to invasion. Additionally, water vapor can also occupy the roughness valleys of immersed surfaces. If water vapor condenses, that too leads to invasion. These effects have not been investigated, and are critically important to maintain surfaces dry under water. In this work, we identify the critical roughness scale, below which it is possible to sustain the vapor phase of water and/or trapped gases in roughness valleys {—} thus keeping the immersed surface dry. Theoretical predictions are consistent with molecular dynamics simulations and experiments.

`@article{jones2015a, author = {Paul R. Jones and Xiuqing Hao and Eduardo R. Cruz-Chu and Konrad Rykaczewski and Krishanu Nandy and Thomas M. Schutzius and Kripa K. Varanasi and Constantine M. Megaridis and Jens H. Walther and Petros Koumoutsakos and Horacio D. Espinosa and Neelesh A. Patankar}, doi = {10.1038/srep12311}, journal = {Scientific Reports}, month = {aug}, number = {1}, publisher = {Springer Nature}, title = {Sustaining dry surfaces under water}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/jones2015a.pdf}, volume = {5}, year = {2015} }`

- F. Huhn, W. M. van Rees, M. Gazzola, D. Rossinelli, G. Haller, and P. Koumoutsakos, “Quantitative flow analysis of swimming dynamics with coherent lagrangian vortices," Chaos: an interdisciplinary journal of nonlinear science, vol. 25, iss. 8, p. 87405, 2015.

[BibTeX] [PDF] [DOI]`@article{huhn2015a, author = {F. Huhn and W. M. van Rees and M. Gazzola and D. Rossinelli and G. Haller and P. Koumoutsakos}, doi = {10.1063/1.4919784}, journal = {Chaos: An Interdisciplinary Journal of Nonlinear Science}, month = {aug}, number = {8}, pages = {087405}, publisher = {{AIP} Publishing}, title = {Quantitative flow analysis of swimming dynamics with coherent Lagrangian vortices}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/huhn2015a.pdf}, volume = {25}, year = {2015} }`

- P. Angelikopoulos, C. Papadimitriou, and P. Koumoutsakos, “X-TMCMC: adaptive kriging for Bayesian inverse modeling," Computer methods in applied mechanics and engineering, vol. 289, pp. 409-428, 2015.

[BibTeX] [Abstract] [PDF] [DOI]

The Bayesian inference of models associated with large-scale simulations is prohibitively expensive even for massively parallel architectures. We demonstrate that we can drastically reduce this cost by combining adaptive kriging with the population-based Transitional Markov Chain Monte Carlo (TMCMC) techniques. For uni-modal posterior probability distribution functions (PDF), the proposed hybrid method can reduce the computational cost by an order of magnitude with the same computational resources. For complex posterior PDF landscapes we show that it is necessary to further extend the TMCMC by Langevin adjusted proposals. The proposed hybrid method exhibits high parallel efficiency. We demonstrate the capabilities of our method on test bed problems and on high fidelity simulations in structural dynamics.

`@article{angelikopoulos2015a, author = {Panagiotis Angelikopoulos and Costas Papadimitriou and Petros Koumoutsakos}, doi = {10.1016/j.cma.2015.01.015}, journal = {Computer Methods in Applied Mechanics and Engineering}, month = {jun}, pages = {409--428}, publisher = {Elsevier {BV}}, title = {{X-TMCMC}: Adaptive kriging for {B}ayesian inverse modeling}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/angelikopoulos2015a.pdf}, volume = {289}, year = {2015} }`

- W. M. van Rees, G. Novati, and P. Koumoutsakos, “Self-propulsion of a counter-rotating cylinder pair in a viscous fluid," Physics of fluids, vol. 27, iss. 6, p. 63102, 2015.

[BibTeX] [Abstract] [PDF] [DOI]

We study a self-propelling pair of steadily counter-rotating cylinders in simulations of a two-dimensional viscous fluid. We find two strikingly, opposite directions for the motion of the pair that is characterized by its width and rotational Reynolds number. At low Reynolds numbers and large widths, the cylinder pair moves similarly to an inviscid point vortex pair, while at higher Reynolds numbers and smaller widths, the pair moves in the opposite direction through a jet-like propulsion mechanism. Increasing further the Reynolds number, or decreasing the width, gives rise to non-polarised motion governed by the shedding direction and frequency of the boundary-layer vorticity. We discuss the fundamental physical mechanisms for these two types of motion and the transitions in the corresponding phase diagram. We discuss the fluid dynamics of each regime based on streamline plots, tracer particles, and the vorticity field. The counter rotating cylinder pair serves as a prototype for self-propelled bodies and suggests possible engineering devices composed of simple components and tunable by the rotation and width of the cylinder pair.

`@article{rees2015a, author = {Wim M. van Rees and Guido Novati and Petros Koumoutsakos}, doi = {10.1063/1.4922314}, journal = {Physics of Fluids}, month = {jun}, number = {6}, pages = {063102}, publisher = {{AIP} Publishing}, title = {Self-propulsion of a counter-rotating cylinder pair in a viscous fluid}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rees2015a.pdf}, volume = {27}, year = {2015} }`

- W. M. van Rees, M. Gazzola, and P. Koumoutsakos, “Optimal morphokinematics for undulatory swimmers at intermediate Reynolds numbers," Journal of fluid mechanics, vol. 775, pp. 178-188, 2015.

[BibTeX] [Abstract] [PDF] [DOI]

Undulatory locomotion is an archetypal mode of propulsion for natural swimmers across scales. Undulatory swimmers convert transverse body oscillations into forward velocity by a complex interplay between their flexural movements, morphological features and the fluid environment. Natural evolution has produced a wide range of morphokinematic examples of undulatory swimmers that often serve as inspiration for engineering devices. It is, however, unknown to what extent natural swimmers are optimized for hydrodynamic performance. In this work, we reverse-engineer the morphology and gait for fast and efficient swimmers by coupling an evolution strategy to three-dimensional direct numerical simulations of flows at intermediate Reynolds numbers. The fastest swimmer is slender with a narrow tail fin and performs a sequence of C-starts to maximize its average velocity. The most efficient swimmer combines moderate transverse movements with a voluminous head, tapering into a streamlined profile via a pronounced inflection point. These optimal solutions outperform anguilliform swimming zebrafish in both efficiency and speed. We investigate the transition between morphokinematic solutions in the speed{—}energy space, laying the foundations for the design of high-performance artificial swimming devices.

`@article{rees2015b, author = {Wim M. van Rees and Mattia Gazzola and Petros Koumoutsakos}, doi = {10.1017/jfm.2015.283}, journal = {Journal of Fluid Mechanics}, month = {jun}, pages = {178--188}, publisher = {Cambridge University Press ({CUP})}, title = {Optimal morphokinematics for undulatory swimmers at intermediate {R}eynolds numbers}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rees2015b.pdf}, volume = {775}, year = {2015} }`

- A. Popadić, M. Praprotnik, P. Koumoutsakos, and J. H. Walther, “Continuum simulations of water flow past fullerene molecules," The european physical journal special topics, vol. 224, iss. 12, pp. 2321-2330, 2015.

[BibTeX] [Abstract] [PDF] [DOI]

We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest as computed by the present model are in good agreement with results from atomistic and atomistic-continuum simulations at a fraction of the cost. We simulate the flow past a single fullerene and an array of fullerenes and demonstrate that such nanoscale flows can be computed efficiently by continuum flow solvers, allowing for investigations into spatiotemporal scales inaccessible to atomistic simulations.

`@article{popadic2015a, author = {A. Popadi{\'{c}} and M. Praprotnik and P. Koumoutsakos and J. H. Walther}, doi = {10.1140/epjst/e2015-02414-y}, journal = {The European Physical Journal Special Topics}, month = {jun}, number = {12}, pages = {2321--2330}, publisher = {Springer Nature}, title = {Continuum simulations of water flow past fullerene molecules}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/popadic2015a.pdf}, volume = {224}, year = {2015} }`

- P. B. de Reuille, A. Routier-Kierzkowska, D. Kierzkowski, G. W. Bassel, T. Schüpbach, G. Tauriello, N. Bajpai, S. Strauss, A. Weber, A. Kiss, A. Burian, H. Hofhuis, A. Sapala, M. Lipowczan, M. B. Heimlicher, S. Robinson, E. M. Bayer, K. Basler, P. Koumoutsakos, A. H. Roeder, T. Aegerter-Wilmsen, N. Nakayama, M. Tsiantis, A. Hay, D. Kwiatkowska, I. Xenarios, C. Kuhlemeier, and R. S. Smith, “MorphoGraphX: a platform for quantifying morphogenesis in 4D," Elife, vol. 4, 2015.

[BibTeX] [Abstract] [PDF] [DOI]

Morphogenesis emerges from complex multiscale interactions between genetic and mechanical processes. To understand these processes, the evolution of cell shape, proliferation and gene expression must be quantified. This quantification is usually performed either in full 3D, which is computationally expensive and technically challenging, or on 2D planar projections, which introduces geometrical artifacts on highly curved organs. Here we present MorphoGraphX (www.MorphoGraphX.org), a software that bridges this gap by working directly with curved surface images extracted from 3D data. In addition to traditional 3D image analysis, we have developed algorithms to operate on curved surfaces, such as cell segmentation, lineage tracking and fluorescence signal quantification. The software’s modular design makes it easy to include existing libraries, or to implement new algorithms. Cell geometries extracted with MorphoGraphX can be exported and used as templates for simulation models, providing a powerful platform to investigate the interactions between shape, genes and growth.

`@article{reuille2015a, author = {Pierre Barbier de Reuille and Anne-Lise Routier-Kierzkowska and Daniel Kierzkowski and George W Bassel and Thierry Sch{\"u}pbach and Gerardo Tauriello and Namrata Bajpai and S{\"o}ren Strauss and Alain Weber and Annamaria Kiss and Agata Burian and Hugo Hofhuis and Aleksandra Sapala and Marcin Lipowczan and Maria B Heimlicher and Sarah Robinson and Emmanuelle M Bayer and Konrad Basler and Petros Koumoutsakos and Adrienne HK Roeder and Tinri Aegerter-Wilmsen and Naomi Nakayama and Miltos Tsiantis and Angela Hay and Dorota Kwiatkowska and Ioannis Xenarios and Cris Kuhlemeier and Richard S Smith}, doi = {10.7554/elife.05864}, journal = {eLife}, month = {may}, publisher = {{eLife} Sciences Organisation, Ltd.}, title = {{MorphoGraphX}: A platform for quantifying morphogenesis in {4D}}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/reuille2015a.pdf}, volume = {4}, year = {2015} }`

- D. Rossinelli, B. Hejazialhosseini, W. van Rees, M. Gazzola, M. Bergdorf, and P. Koumoutsakos, “MRAG-i2d: multi-resolution adapted grids for remeshed vortex methods on multicore architectures," Journal of computational physics, vol. 288, pp. 1-18, 2015.

[BibTeX] [Abstract] [PDF] [DOI]

We present MRAG-I2D, an open source software framework, for multiresolution simulations of two-dimensional, incompressible, viscous flows on multicore architectures. The spatiotemporal scales of the flow field are captured by remeshed vortex methods enhanced by high order average-interpolating wavelets and local time-stepping. The multiresolution solver of the Poisson equation relies on the development of a novel, tree-based multipole method. MRAG-I2D implements a number of HPC strategies to map efficiently the irregular computational workload of wavelet-adapted grids on multicore nodes. The capabilities of the present software are compared to the current state-of-the-art in terms of accuracy, compression rates and time-to-solution. Benchmarks include the inviscid evolution of an elliptical vortex, flow past an impulsively started cylinder at Re = 40 – 40 000 and simulations of self-propelled anguilliform swimmers. The results indicate that the present software has the same or better accuracy than state-of-the-art solvers while it exhibits unprecedented performance in terms of time-to-solution.

`@article{rossinelli2015a, author = {Diego Rossinelli and Babak Hejazialhosseini and Wim van Rees and Mattia Gazzola and Michael Bergdorf and Petros Koumoutsakos}, doi = {10.1016/j.jcp.2015.01.035}, journal = {Journal of Computational Physics}, month = {may}, pages = {1--18}, publisher = {Elsevier {BV}}, title = {{MRAG}-I2D: Multi-resolution adapted grids for remeshed vortex methods on multicore architectures}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rossinelli2015a.pdf}, volume = {288}, year = {2015} }`

- G. Tauriello and P. Koumoutsakos, “A comparative study of penalization and phase field methods for the solution of the diffusion equation in complex geometries," Journal of computational physics, vol. 283, pp. 388-407, 2015.

[BibTeX] [Abstract] [PDF] [DOI]

We present a comparative study of penalization and phase field methods for the solution of the diffusion equation in complex geometries embedded using simple Cartesian meshes. The two methods have been widely employed to solve partial differential equations in complex and moving geometries for applications ranging from solid and fluid mechanics to biology and geophysics. Their popularity is largely due to their discretization on Cartesian meshes thus avoiding the need to create body-fitted grids. At the same time, there are questions regarding their accuracy and it appears that the use of each one is confined by disciplinary boundaries. Here, we compare penalization and phase field methods to handle problems with Neumann and Robin boundary conditions. We discuss extensions for Dirichlet boundary conditions and in turn compare with methods that have been explicitly designed to handle Dirichlet boundary conditions. The accuracy of all methods is analyzed using one and two dimensional benchmark problems such as the flow induced by an oscillating wall and by a cylinder performing rotary oscillations. This comparative study provides information to decide which methods to consider for a given application and their incorporation in broader computational frameworks. We demonstrate that phase field methods are more accurate than penalization methods on problems with Neumann boundary conditions and we present an error analysis explaining this result.

`@article{tauriello2015a, author = {Gerardo Tauriello and Petros Koumoutsakos}, doi = {10.1016/j.jcp.2014.11.033}, journal = {Journal of Computational Physics}, month = {feb}, pages = {388--407}, publisher = {Elsevier {BV}}, title = {A comparative study of penalization and phase field methods for the solution of the diffusion equation in complex geometries}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/tauriello2015a.pdf}, volume = {283}, year = {2015} }`

- M. M. Hejlesen, P. Koumoutsakos, A. Leonard, and J. H. Walther, “Iterative Brinkman penalization for remeshed vortex methods," Journal of computational physics, vol. 280, pp. 547-562, 2015.

[BibTeX] [Abstract] [PDF] [DOI]

We introduce an iterative Brinkman penalization method for the enforcement of the no-slip boundary condition in remeshed vortex methods. In the proposed method, the Brinkman penalization is applied iteratively only in the neighborhood of the body. This allows for using significantly larger time steps, than what is customary in the Brinkman penalization, thus reducing its computational cost while maintaining the capability of the method to handle complex geometries. We demonstrate the accuracy of our method by considering challenging benchmark problems such as flow past an impulsively started cylinder and normal to an impulsively started and accelerated flat plate. We find that the present method enhances significantly the accuracy of the Brinkman penalization technique for the simulations of highly unsteady flows past complex geometries.

`@article{hejlesen2015c, author = {Hejlesen, Mads M{\o}lholm and Koumoutsakos, Petros and Leonard, Anthony and Walther, Jens Honor{\'{e}}}, doi = {10.1016/j.jcp.2014.09.029}, journal = {Journal of Computational Physics}, month = {jan}, pages = {547--562}, publisher = {Elsevier {BV}}, title = {Iterative {B}rinkman penalization for remeshed vortex methods}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hejlesen2015c.pdf}, volume = {280}, year = {2015} }`

- P. E. Hadjidoukas, P. Angelikopoulos, C. Papadimitriou, and P. Koumoutsakos, “Π4U: a high performance computing framework for Bayesian uncertainty quantification of complex models," Journal of computational physics, vol. 284, pp. 1-21, 2015.

[BibTeX] [Abstract] [PDF] [DOI]

We present {Π}4U, an extensible framework, for non-intrusive Bayesian Uncertainty Quantification and Propagation (UQ+P) of complex and computationally demanding physical models, that can exploit massively parallel computer architectures. The framework incorporates Laplace asymptotic approximations as well as stochastic algorithms, along with distributed numerical differentiation and task-based parallelism for heterogeneous clusters. Sampling is based on the Transitional Markov Chain Monte Carlo (TMCMC) algorithm and its variants. The optimization tasks associated with the asymptotic approximations are treated via the Covariance Matrix Adaptation Evolution Strategy (CMA-ES). A modified subset simulation method is used for posterior reliability measurements of rare events. The framework accommodates scheduling of multiple physical model evaluations based on an adaptive load balancing library and shows excellent scalability. In addition to the software framework, we also provide guidelines as to the applicability and efficiency of Bayesian tools when applied to computationally demanding physical models. Theoretical and computational developments are demonstrated with applications drawn from molecular dynamics, structural dynamics and granular flow.

`@article{hadjidoukas2015b, author = {Hadjidoukas, Panagiotis E and Angelikopoulos, Panagiotis and Papadimitriou, Costas and Koumoutsakos, Petros}, doi = {https://doi.org/10.1016/j.jcp.2014.12.006}, journal = {Journal of Computational Physics}, pages = {1--21}, publisher = {Elsevier}, title = {{4U}: A high performance computing framework for {B}ayesian uncertainty quantification of complex models}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hadjidoukas2015b.pdf}, volume = {284}, year = {2015} }`

- P. E. Hadjidoukas, P. Angelikopoulos, L. Kulakova, C. Papadimitriou, and P. Koumoutsakos, “Exploiting task-based parallelism in Bayesian uncertainty quantification," in Lecture notes in computer science, Springer Berlin Heidelberg, 2015, pp. 532-544.

[BibTeX] [Abstract] [PDF] [DOI]

We introduce a task-parallel framework for non-intrusive Bayesian Uncertainty Quantification and Propagation of complex and computationally demanding physical models on massively parallel computing architectures. The framework incorporates Laplace asymptotic approximations and stochastic algorithms along with distributed numerical differentiation. Sampling is based on the Transitional Markov Chain Monte Carlo algorithm and its variants while the optimization tasks associated with the asymptotic approximations are treated via the Covariance Matrix Adaptation Evolution Strategy. Exploitation of task-based parallelism is based on a platform-agnostic adaptive load balancing library that orchestrates scheduling of multiple physical model evaluations on computing platforms that range from multicore systems to hybrid GPU clusters. Experimental results using representative applications demonstrate the flexibility and excellent scalability of the proposed framework.

`@incollection{hadjidoukas2015a, author = {Panagiotis E. Hadjidoukas and Panagiotis Angelikopoulos and Lina Kulakova and Costas Papadimitriou and Petros Koumoutsakos}, booktitle = {Lecture Notes in Computer Science}, doi = {10.1007/978-3-662-48096-0_41}, pages = {532--544}, publisher = {Springer Berlin Heidelberg}, title = {Exploiting Task-Based Parallelism in {B}ayesian Uncertainty Quantification}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hadjidoukas2015a.pdf}, year = {2015} }`

### 2014

- P. E. Hadjidoukas, P. Angelikopoulos, D. Rossinelli, D. Alexeev, C. Papadimitriou, and P. Koumoutsakos, “Bayesian uncertainty quantification and propagation for discrete element simulations of granular materials," Computer methods in applied mechanics and engineering, vol. 282, pp. 218-238, 2014.

[BibTeX] [Abstract] [PDF] [DOI]

Predictions in the behavior of granular materials using Discrete Element Methods (DEM) hinge on the employed interaction potentials. Here we introduce a data driven, Bayesian framework to quantify DEM predictions. Our approach relies on experimentally measured coefficients of restitution for single steel particle{—}wall collisions. The calibration data entail both tangential and normal coefficients of restitution, for varying impact angles and speeds of the bouncing particle. The parametric uncertainty in multiple Force{—}Displacement models is estimated using an enhanced Transitional Markov Chain Monte Carlo implemented efficiently on parallel computer architectures. In turn, the parametric model uncertainties are propagated to predict Quantities of Interest (QoI) for two testbed applications: silo discharge and vibration induced mass-segregation. This work demonstrates that the classical way of calibrating DEM potentials, through parameter optimization, is insufficient and it fails to provide robust predictions. The present Bayesian framework provides robust predictions for the behavior of granular materials using DEM simulations. Most importantly the results demonstrate the importance of including parametric and modeling uncertainties in the potentials employed in Discrete Element Methods.

`@article{hadjidoukas2014c, author = {P.E. Hadjidoukas and P. Angelikopoulos and D. Rossinelli and D. Alexeev and C. Papadimitriou and P. Koumoutsakos}, doi = {10.1016/j.cma.2014.07.017}, journal = {Computer Methods in Applied Mechanics and Engineering}, month = {dec}, pages = {218--238}, publisher = {Elsevier {BV}}, title = {{B}ayesian uncertainty quantification and propagation for discrete element simulations of granular materials}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hadjidoukas2014c.pdf}, volume = {282}, year = {2014} }`

- A. Popadić, J. H. Walther, P. Koumoutsakos, and M. Praprotnik, “Continuum simulations of water flow in carbon nanotube membranes," New journal of physics, vol. 16, iss. 8, p. 82001, 2014.

[BibTeX] [Abstract] [PDF] [DOI]

We propose the use of the Navier{—}Stokes equations subject to partial-slip boundary conditions to simulate water flows in Carbon NanoTube (CNT) membranes. The finite volume discretizations of the Navier{—}Stokes equations are combined with slip lengths extracted from molecular dynamics (MD) simulations to predict the pressure losses at the CNT entrance as well as the enhancement of the flow rate in the CNT. The flow quantities calculated from the present hybrid approach are in excellent agreement with pure MD results while they are obtained at a fraction of the computational cost. The method enables simulations of system sizes and times well beyond the present capabilities of MD simulations. Our simulations provide an asymptotic flow rate enhancement and indicate that the pressure losses at the CNT ends can be reduced by reducing their curvature. More importantly, our results suggest that flows at nanoscale channels can be described by continuum solvers with proper boundary conditions that reflect the molecular interactions of the liquid with the walls of the nanochannel.

`@article{popadic2014a, author = {A Popadi{\'{c}} and J H Walther and P Koumoutsakos and M Praprotnik}, doi = {10.1088/1367-2630/16/8/082001}, journal = {New Journal of Physics}, month = {aug}, number = {8}, pages = {082001}, publisher = {{IOP} Publishing}, title = {Continuum simulations of water flow in carbon nanotube membranes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/popadic2014a.pdf}, volume = {16}, year = {2014} }`

- F. Milde, G. Tauriello, H. Haberkern, and P. Koumoutsakos, “SEM++: a particle model of cellular growth, signaling and migration," Computational particle mechanics, vol. 1, iss. 2, pp. 211-227, 2014.

[BibTeX] [Abstract] [PDF] [DOI]

We present a discrete particle method to model biological processes from the sub-cellular to the inter-cellular level. Particles interact through a parametrized force field to model cell mechanical properties, cytoskeleton remodeling, growth and proliferation as well as signaling between cells. We discuss the guiding design principles for the selection of the force field and the validation of the particle model using experimental data. The proposed method is integrated into a multiscale particle framework for the simulation of biological systems.

`@article{milde2014a, author = {Florian Milde and Gerardo Tauriello and Hannah Haberkern and Petros Koumoutsakos}, doi = {10.1007/s40571-014-0017-4}, journal = {Computational Particle Mechanics}, month = {may}, number = {2}, pages = {211--227}, publisher = {Springer Nature}, title = {{SEM}: A particle model of cellular growth, signaling and migration}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/milde2014a.pdf}, volume = {1}, year = {2014} }`

- J. Chen, J. H. Walther, and P. Koumoutsakos, “Strain engineering of kapitza resistance in few-layer graphene," Nano letters, vol. 14, iss. 2, pp. 819-825, 2014.

[BibTeX] [Abstract] [PDF] [DOI]

We demonstrate through molecular dynamics simulations that the Kapitza resistance in few-layer graphene (FLG) can be controlled by applying mechanical strain. For unstrained FLG, the Kapitza resistance decreases with the increase of thickness and reaches an asymptotic value of 6 {\texttimes} 10{—}10 m{\^{}}2 K/W at a thickness about 16 nm. Uniaxial cross-plane strain is found to increase the Kapitza resistance in FLG monotonically, when the applied strain varies from compressive to tensile. Moreover, uniaxial strain couples the in-plane and out-of-plane strain/stress when the surface of FLG is buckled. We find that with a compressive cross-plane stress of 2 GPa, the Kapitza resistance is reduced by about 50%. On the other hand it is almost tripled with a tensile cross-plane stress of 1 GPa. Remarkably, compressive in-plane strain can either increase or reduce the Kapitza resistance, depending on the specific way it is applied. Our study suggests that graphene can be exploited for both heat dissipation and insulation through strain engineering.

`@article{chen2014a, author = {Jie Chen and Jens H. Walther and Petros Koumoutsakos}, doi = {10.1021/nl404182k}, journal = {Nano Letters}, month = {feb}, number = {2}, pages = {819--825}, publisher = {American Chemical Society ({ACS})}, title = {Strain Engineering of Kapitza Resistance in Few-Layer Graphene}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/chen2014a.pdf}, volume = {14}, year = {2014} }`

- E. R. Cruz-Chu, A. Malafeev, T. Pajarskas, I. V. Pivkin, and P. Koumoutsakos, “Structure and response to flow of the glycocalyx layer," Biophysical journal, vol. 106, iss. 1, pp. 232-243, 2014.

[BibTeX] [Abstract] [PDF] [DOI]

The glycocalyx is a sugar-rich layer located at the luminal part of the endothelial cells. It is involved in key metabolic processes and its malfunction is related to several diseases. To understand the function of the glycocalyx, a molecular level characterization is necessary. In this article, we present large-scale molecular-dynamics simulations that provide a comprehensive description of the structure and dynamics of the glycocalyx. We introduce the most detailed, to-date, all-atom glycocalyx model, composed of lipid bilayer, proteoglycan dimers, and heparan sulfate chains with realistic sequences. Our results reveal the folding of proteoglycan ectodomain and the extended conformation of heparan sulfate chains. Furthermore, we study the glycocalyx response under shear flow and its role as a flypaper for binding fibroblast growth factors (FGFs), which are involved in diverse functions related to cellular differentiation, including angiogenesis, morphogenesis, and wound healing. The simulations show that the glycocalyx increases the effective concentration of FGFs, leading to FGF oligomerization, and acts as a lever to transfer mechanical stimulus into the cytoplasmic side of endothelial cells.

`@article{cruzchu2014a, author = {Eduardo R. Cruz-Chu and Alexander Malafeev and Tautrimas Pajarskas and Igor V. Pivkin and Petros Koumoutsakos}, doi = {10.1016/j.bpj.2013.09.060}, journal = {Biophysical Journal}, month = {jan}, number = {1}, pages = {232--243}, publisher = {Elsevier {BV}}, title = {Structure and Response to Flow of the Glycocalyx Layer}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/cruzchu2014a.pdf}, volume = {106}, year = {2014} }`

- M. Gazzola, B. Hejazialhosseini, and P. Koumoutsakos, “Reinforcement learning and wavelet adapted vortex methods for simulations of self-propelled swimmers," SIAM journal on scientific computing, vol. 36, iss. 3, p. B622–B639, 2014.

[BibTeX] [Abstract] [PDF] [DOI]

We present a numerical method for the simulation of collective hydrodynamics in self-propelled swimmers. Swimmers in a viscous incompressible flow are simulated with a remeshed vortex method coupled with Brinkman penalization and projection approach. The remeshed vortex methods are enhanced via wavelet based adaptivity in space and time. The method is validated on benchmark swimming problems. Furthermore the flow solver is integrated with a reinforcement learning algorithm, such that swimmers can learn to adapt their motion so as to optimally achieve a specified goal, such as fish schooling. The computational efficiency of the wavelet adapted remeshed vortex method is a key aspect for the effective coupling with learning algorithms. The suitability of this approach for the identification of swimming behaviors is assessed on a set of learning tasks.

`@article{gazzola2014a, author = {Mattia Gazzola and Babak Hejazialhosseini and Petros Koumoutsakos}, doi = {10.1137/130943078}, journal = {{SIAM} Journal on Scientific Computing}, month = {jan}, number = {3}, pages = {B622--B639}, publisher = {Society for Industrial {\&} Applied Mathematics ({SIAM})}, title = {Reinforcement Learning and Wavelet Adapted Vortex Methods for Simulations of Self-propelled Swimmers}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/gazzola2014a.pdf}, volume = {36}, year = {2014} }`

- W. M. van Rees, D. Rossinelli, P. Hadjidoukas, and P. Koumoutsakos, “High performance CPU/GPU multiresolution poisson solver," Parallel computing: accelerating computational science and engineering (CSE), vol. 1, iss. 1, pp. 481-490, 2014.

[BibTeX] [Abstract] [PDF]

We present a multipole-based N-body solver for 3D multiresolution, block-structured grids. The solver is designed for a single heterogeneous CPU/GPU compute node, and evaluates the multipole expansions on the CPU while offloading the compute-heavy particle-particle interactions to the GPU. The regular structure of the destination points is exploited for data parallelism on the CPU, to reduce data transfer to the GPU and to minimize memory accesses during evaluation of the direct and indirect interactions. The algorithmic improvements together with HPC techniques lead to 81% and 96% of the upper bound performance for the CPU and GPU parts, respectively.

`@article{vanrees2014a, author = {van Rees, Wim M and Rossinelli, Diego and Hadjidoukas, Panagiotis and Koumoutsakos, Petros}, journal = {Parallel Computing: Accelerating Computational Science and Engineering {(CSE)}}, number = {1}, pages = {481--490}, title = {High performance {CPU/GPU} multiresolution Poisson solver}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/vanrees2014a.pdf}, volume = {1}, year = {2014} }`

### 2013

- P. Angelikopoulos, C. Papadimitriou, and P. Koumoutsakos, “Data driven, predictive molecular dynamics for nanoscale flow simulations under uncertainty," The journal of physical chemistry b, vol. 117, iss. 47, pp. 14808-14816, 2013.

[BibTeX] [Abstract] [PDF] [DOI]

For over five decades, molecular dynamics (MD) simulations have helped to elucidate critical mechanisms in a broad range of physiological systems and technological innovations. MD simulations are synergetic with experiments, relying on measurements to calibrate their parameters and probing {\textquotedblleft}what if scenarios{\textquotedblright} for systems that are difficult to investigate experimentally. However, in certain systems, such as nanofluidics, the results of experiments and MD simulations differ by several orders of magnitude. This discrepancy may be attributed to the spatiotemporal scales and structural information accessible by experiments and simulations. Furthermore, MD simulations rely on parameters that are often calibrated semiempirically, while the effects of their computational implementation on their predictive capabilities have only been sporadically probed. In this work, we show that experimental and MD investigations can be consolidated through a rigorous uncertainty quantification framework. We employ a Bayesian probabilistic framework for large scale MD simulations of graphitic nanostructures in aqueous environments. We assess the uncertainties in the MD predictions for quantities of interest regarding wetting behavior and hydrophobicity. We focus on three representative systems: water wetting of graphene, the aggregation of fullerenes in aqueous solution, and the water transport across carbon nanotubes. We demonstrate that the dominant mode of calibrating MD potentials in nanoscale fluid mechanics, through single values of water contact angle on graphene, leads to large uncertainties and fallible quantitative predictions. We demonstrate that the use of additional experimental data reduces uncertainty, improves the predictive accuracy of MD models, and consolidates the results of experiments and simulations.

`@article{angelikopoulos2013a, author = {Panagiotis Angelikopoulos and Costas Papadimitriou and Petros Koumoutsakos}, doi = {10.1021/jp4084713}, journal = {The Journal of Physical Chemistry B}, month = {nov}, number = {47}, pages = {14808--14816}, publisher = {American Chemical Society ({ACS})}, title = {Data Driven, Predictive Molecular Dynamics for Nanoscale Flow Simulations under Uncertainty}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/angelikopoulos2013a.pdf}, volume = {117}, year = {2013} }`

- B. Hejazialhosseini, D. Rossinelli, and P. Koumoutsakos, “Vortex dynamics in 3d shock-bubble interaction," Physics of fluids, vol. 25, iss. 11, p. 110816, 2013.

[BibTeX] [Abstract] [PDF] [DOI]

The dynamics of shock-bubble interaction involve an interplay of vortex stretching, dilation, and baroclinic vorticity generation. Here, we quantify the interplay of these contributions through high resolution 3D simulations for several Mach and Atwood numbers. We present a volume rendering of density and vorticity magnitude fields of shock-bubble interaction at M = 3 and air/helium density ratio {η} = 7.25 to elucidate the evolution of the flow structures. We distinguish the vorticity growth rates due to baroclinicity, stretching, and dilatation at low and high Mach numbers as well as the late time evolution of the circulation. The results demonstrate that a number of analytical models need to be revised in order to predict the late time circulation of shock-bubble interactions at high Mach numbers. To this effect, we propose a simple model for the dependence of the circulation to Mach number and ambient to bubble density ratio for air/helium shock-bubble interactions.

`@article{hejazialhosseini2013c, author = {Babak Hejazialhosseini and Diego Rossinelli and Petros Koumoutsakos}, doi = {10.1063/1.4819345}, journal = {Physics of Fluids}, month = {nov}, number = {11}, pages = {110816}, publisher = {{AIP} Publishing}, title = {Vortex dynamics in 3D shock-bubble interaction}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hejazialhosseini2013c.pdf}, volume = {25}, year = {2013} }`

- B. Hejazialhosseini, D. Rossinelli, and P. Koumoutsakos, “3d shock-bubble interaction," Physics of fluids, vol. 25, iss. 9, p. 91105, 2013.

[BibTeX] [Movie] [PDF] [DOI]`@article{hejazialhosseini2013b, author = {Babak Hejazialhosseini and Diego Rossinelli and Petros Koumoutsakos}, doi = {10.1063/1.4820017}, journal = {Physics of Fluids}, month = {sep}, movie = {https://www.youtube.com/watch?v=gnhbhpwTx1c}, number = {9}, pages = {091105}, publisher = {{AIP} Publishing}, title = {3D shock-bubble interaction}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hejazialhosseini2013b.pdf}, volume = {25}, year = {2013} }`

- P. Koumoutsakos and J. Feigelman, “Multiscale stochastic simulations of chemical reactions with regulated scale separation," Journal of computational physics, vol. 244, pp. 290-297, 2013.

[BibTeX] [Abstract] [PDF] [DOI]

We present a coupling of multiscale frameworks with accelerated stochastic simulation algorithms for systems of chemical reactions with disparate propensities. The algorithms regulate the propensities of the fast and slow reactions of the system, using alternating micro and macro sub-steps simulated with accelerated algorithms such as s and R-leaping. The proposed algorithms are shown to provide significant speedups in simulations of stiff systems of chemical reactions with a trade-off in accuracy as controlled by a regulating parameter. More importantly, the error of the methods exhibits a cutoff phenomenon that allows for optimal parameter choices. Numerical experiments demonstrate that hybrid algorithms involving accelerated stochastic simulations can be, in certain cases, more accurate while faster, than their corresponding stochastic simulation algorithm counterparts.

`@article{koumoutsakos2013b, author = {Petros Koumoutsakos and Justin Feigelman}, doi = {10.1016/j.jcp.2012.11.030}, journal = {Journal of Computational Physics}, month = {jul}, pages = {290--297}, publisher = {Elsevier {BV}}, title = {Multiscale stochastic simulations of chemical reactions with regulated scale separation}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos2013b.pdf}, volume = {244}, year = {2013} }`

- J. H. Walther, K. Ritos, E. R. Cruz-Chu, C. M. Megaridis, and P. Koumoutsakos, “Barriers to superfast water transport in carbon nanotube membranes," Nano letters, vol. 13, iss. 5, pp. 1910-1914, 2013.

[BibTeX] [Abstract] [PDF] [DOI]

Carbon nanotube (CNT) membranes hold the promise of extraordinary fast water transport for applications such as energy efficient filtration and molecular level drug delivery. However, experiments and computations have reported flow rate enhancements over continuum hydrodynamics that contradict each other by orders of magnitude. We perform large scale molecular dynamics simulations emulating for the first time the micrometer thick CNTs membranes used in experiments. We find transport enhancement rates that are length dependent due to entrance and exit losses but asymptote to 2 orders of magnitude over the continuum predictions. These rates are far below those reported experimentally. The results suggest that the reported superfast water transport rates cannot be attributed to interactions of water with pristine CNTs alone.

`@article{walther2013a, author = {Jens H. Walther and Konstantinos Ritos and Eduardo R. Cruz-Chu and Constantine M. Megaridis and Petros Koumoutsakos}, doi = {10.1021/nl304000k}, journal = {Nano Letters}, month = {may}, number = {5}, pages = {1910--1914}, publisher = {American Chemical Society ({ACS})}, title = {Barriers to Superfast Water Transport in Carbon Nanotube Membranes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther2013a.pdf}, volume = {13}, year = {2013} }`

- W. M. van Rees, M. Gazzola, and P. Koumoutsakos, “Optimal shapes for anguilliform swimmers at intermediate Reynolds numbers," Journal of fluid mechanics, vol. 722, 2013.

[BibTeX] [Abstract] [PDF] [DOI]

We investigate the optimal morphologies for fast and efficient anguilliform swimmers at intermediate Reynolds numbers, by combining an evolution strategy with three-dimensional viscous vortex methods. We show that anguilliform swimmer shapes enable the trapping and subsequent acceleration of regions of fluid transported along the entire body by the midline travelling wave. A sensitivity analysis of the optimal morphological traits identifies that the width thickness in the anterior of the body and the height of the caudal fin are critical factors for both speed and efficiency. The fastest swimmer without a caudal fin, however, still retains 80 % of its speed, showing that the entire body is used to generate thrust. The optimal shapes share several features with naturally occurring morphologies, but their overall appearances differ. This demonstrates that engineered swimmers can outperform biomimetic swimmers for the criteria considered here.

`@article{rees2013a, author = {Wim M. van Rees and Mattia Gazzola and Petros Koumoutsakos}, doi = {10.1017/jfm.2013.157}, journal = {Journal of Fluid Mechanics}, month = {apr}, publisher = {Cambridge University Press ({CUP})}, title = {Optimal shapes for anguilliform swimmers at intermediate {R}eynolds numbers}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rees2013a.pdf}, volume = {722}, year = {2013} }`

- D. Franco, F. Milde, M. Klingauf, F. Orsenigo, E. Dejana, D. Poulikakos, M. Cecchini, P. Koumoutsakos, A. Ferrari, and V. Kurtcuoglu, “Accelerated endothelial wound healing on microstructured substrates under flow," Biomaterials, vol. 34, iss. 5, pp. 1488-1497, 2013.

[BibTeX] [Abstract] [PDF] [DOI]

Understanding and accelerating the mechanisms of endothelial wound healing is of fundamental interest for biotechnology and of significant medical utility in repairing pathologic changes to the vasculature induced by invasive medical interventions. We report the fundamental mechanisms that determine the influence of substrate topography and flow on the efficiency of endothelial regeneration. We exposed endothelial monolayers, grown on topographically engineered substrates (gratings), to controlled levels of flow-induced shear stress. The wound healing dynamics were recorded and analyzed in various configurations, defined by the relative orientation of an inflicted wound, the topography and the flow direction. Under flow perpendicular to the wound, the speed of endothelial regeneration was signifi- cantly increased on substrates with gratings oriented in the direction of the flow when compared to flat substrates. This behavior is linked to the dynamic state of cell-to-cell adhesions in the monolayer. In particular, interactions with the substrate topography counteract Vascular Endothelial Cadherin phos- phorylation induced by the flow and the wounding. This effect contributes to modulating the mechanical connection between migrating cells to an optimal level, increasing their coordination and resulting in coherent cell motility and preservation of the monolayer integrity, thus accelerating wound healing. We further demonstrate that the reduction of vascular endothelial cadherin phosphorylation, through specific inhibition of Src activity, enhances endothelial wound healing in flows over flat substrates.

`@article{franco2013a, author = {Davide Franco and Florian Milde and Mirko Klingauf and Fabrizio Orsenigo and Elisabetta Dejana and Dimos Poulikakos and Marco Cecchini and Petros Koumoutsakos and Aldo Ferrari and Vartan Kurtcuoglu}, doi = {10.1016/j.biomaterials.2012.10.007}, journal = {Biomaterials}, month = {feb}, number = {5}, pages = {1488--1497}, publisher = {Elsevier {BV}}, title = {Accelerated endothelial wound healing on microstructured substrates under flow}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/franco2013a.pdf}, volume = {34}, year = {2013} }`

- G. Tauriello and P. Koumoutsakos, “Coupling remeshed particle and phase field methods for the simulation of reaction-diffusion on the surface and the interior of deforming geometries," SIAM journal on scientific computing, vol. 35, iss. 6, p. B1285–B1303, 2013.

[BibTeX] [Abstract] [PDF] [DOI]

Reaction-diffusion systems on the surface and the interior of complex domains are potent models of growth in living organisms. The simulation of these models requires numerical methods capable of handling large deformations and the accurate coupling of the evolution of substances in the lumen and on the surface of the deforming geometries. Here, we develop a novel computational method to handle such problems by combining a remeshed particle method with a phase field method. Remeshed particle methods are well suited to discretizing deforming geometries, while the phase field method is used to impose boundary conditions that effectuate the coupling of substances evolving in their lumen and on their surfaces. We demonstrate that this hybrid method enables for the first time the accurate coupling of reaction-diffusion on a deformable surface and its interior. The method is validated on benchmark problems and the effect of lumen diffusion to a pattern forming reaction-diffusion system on a deforming surface is discussed.

`@article{tauriello2013a, author = {Gerardo Tauriello and Petros Koumoutsakos}, doi = {10.1137/130906441}, journal = {{SIAM} Journal on Scientific Computing}, month = {jan}, number = {6}, pages = {B1285--B1303}, publisher = {Society for Industrial {\&} Applied Mathematics ({SIAM})}, title = {Coupling Remeshed Particle and Phase Field Methods for the Simulation of Reaction-Diffusion on the Surface and the Interior of Deforming Geometries}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/tauriello2013a.pdf}, volume = {35}, year = {2013} }`

- P. Koumoutsakos, I. Pivkin, and F. Milde, “The fluid mechanics of cancer and its therapy," Annual review of fluid mechanics, vol. 45, iss. 1, pp. 325-355, 2013.

[BibTeX] [Abstract] [PDF] [DOI]

Fluid mechanics is involved in the growth, progression, metastasis, and therapy of cancer. Blood vessels transport oxygen and nutrients to cancerous tissues, provide a route for metastasizing cancer cells to distant organs, and deliver drugs to tumors. The irregular and leaky tumor vasculature is responsible for increased interstitial pressure in the tumor microenvironment, whereas multiscale flow-structure interaction processes control tumor growth, metastasis, and nanoparticle-mediated drug delivery. We outline these flow-mediated processes, along with related experimental and computational methods for the diagnosis, predictive modeling, and therapy of cancer.

`@article{koumoutsakos2013a, author = {Petros Koumoutsakos and Igor Pivkin and Florian Milde}, doi = {10.1146/annurev-fluid-120710-101102}, journal = {Annual Review of Fluid Mechanics}, month = {jan}, number = {1}, pages = {325--355}, publisher = {Annual Reviews}, title = {The Fluid Mechanics of Cancer and Its Therapy}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos2013a.pdf}, volume = {45}, year = {2013} }`

- B. Hejazialhosseini, C. Conti, D. Rossinelli, and P. Koumoutsakos, “High performance CPU kernels for multiphase compressible flows," in Lecture notes in computer science, Springer Berlin Heidelberg, 2013, pp. 216-225.

[BibTeX] [Abstract] [PDF] [DOI]

We develop efficient CPU kernels for multiphase compressible flows and evaluate different optimization strategies. The presented software achieves up to 48% of the peak performance on shared memory architectures, outperforming by 9-14X what is considered to be state-of-the-art. On 48-core CPUs we observe speedups of 40-45X and measure up to 360 GFLOP/s over 840 GFLOP/s of the peak.

`@incollection{hejazialhosseini2013a, author = {Babak Hejazialhosseini and Christian Conti and Diego Rossinelli and Petros Koumoutsakos}, booktitle = {Lecture Notes in Computer Science}, doi = {10.1007/978-3-642-38718-0_22}, pages = {216--225}, publisher = {Springer Berlin Heidelberg}, title = {High Performance {CPU} Kernels for Multiphase Compressible Flows}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hejazialhosseini2013a.pdf}, year = {2013} }`

- F. Milde, S. Lauw, P. Koumoutsakos, and L. M. Iruela-Arispe, “The mouse retina in 3d: quantification of vascular growth and remodeling," Integrative biology, vol. 5, iss. 12, p. 1426, 2013.

[BibTeX] [Abstract] [PDF] [DOI]

The mouse retina has become a prominent model for studying angiogenesis. The easy access and well-known developmental progression have significantly propelled our ability to examine and manipulate blood vessels in vivo. Nonetheless, most studies have restricted their evaluations to the superficial plexus (an upper vascular layer in contact with the vitreous). Here we present experimental data and quantification for the developmental progression of the full retina including the intermediate and deeper plexus that sprouts from the superficial layer. We analyze the origin and advancement of vertical sprouting and present the progression of vascular perfusion within the tissue. Furthermore, we introduce the use of Minkowsky functionals to quantify remodeling in the superficial and deeper plexus. The work expands information on the retina towards a 3D structure. This is of particular interest, as recent data have demonstrated differential effects of gene deletion on the upper and deeper plexus, highlighting the concept of distinct operational pathways during sprouting angiogenesis.

`@article{milde2013a, author = {Florian Milde and Stephanie Lauw and Petros Koumoutsakos and M. Luisa Iruela-Arispe}, doi = {10.1039/c3ib40085a}, journal = {Integrative Biology}, number = {12}, pages = {1426}, publisher = {Royal Society of Chemistry ({RSC})}, title = {The mouse retina in 3D: quantification of vascular growth and remodeling}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/milde2013a.pdf}, volume = {5}, year = {2013} }`

### 2012

- M. Paolucci, D. Kossman, R. Conte, P. Lukowicz, P. Argyrakis, A. Blandford, G. Bonelli, S. Anderson, S. de Freitas, B. Edmonds, N. Gilbert, M. Gross, J. Kohlhammer, P. Koumoutsakos, A. Krause, B. -O. Linnér, P. Slusallek, O. Sorkine, R. W. Sumner, and D. Helbing, “Towards a living earth simulator," The european physical journal special topics, vol. 214, iss. 1, pp. 77-108, 2012.

[BibTeX] [Abstract] [PDF] [DOI]

The Living Earth Simulator (LES) is one of the core components of the FuturICT architecture. It will work as a federation of methods, tools, techniques and facilities supporting all of the FuturICT simulation-related activities to allow and encourage interactive exploration and understanding of societal issues. Society-relevant problems will be targeted by leaning on approaches based on complex systems theories and data science in tight interaction with the other components of FuturICT. The LES will evaluate and provide answers to real-world questions by taking into account multiple scenarios. It will build on present approaches such as agent-based simulation and modeling, multiscale modelling, statistical inference, and data mining, moving beyond disciplinary borders to achieve a new perspective on complex social systems.

`@article{paolucci2012a, author = {M. Paolucci and D. Kossman and R. Conte and P. Lukowicz and P. Argyrakis and A. Blandford and G. Bonelli and S. Anderson and S. de Freitas and B. Edmonds and N. Gilbert and M. Gross and J. Kohlhammer and P. Koumoutsakos and A. Krause and B. -O. Linn{\'{e}}r and P. Slusallek and O. Sorkine and R. W. Sumner and D. Helbing}, doi = {10.1140/epjst/e2012-01689-8}, journal = {The European Physical Journal Special Topics}, month = {nov}, number = {1}, pages = {77--108}, publisher = {Springer Nature}, title = {Towards a living earth simulator}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/paolucci2012a.pdf}, volume = {214}, year = {2012} }`

- P. Angelikopoulos, C. Papadimitriou, and P. Koumoutsakos, “Bayesian uncertainty quantification and propagation in molecular dynamics simulations: a high performance computing framework," The journal of chemical physics, vol. 137, iss. 14, p. 144103, 2012.

[BibTeX] [Abstract] [PDF] [DOI]

ent a Bayesian probabilistic framework for quantifying and propagating the uncertainties in the parameters of force fields employed in molecular dynamics (MD) simulations. We propose a highly parallel implementation of the transitional Markov chain Monte Carlo for populating the posterior probability distribution of the MD force-field parameters. Efficient scheduling algorithms are proposed to handle the MD model runs and to distribute the computations in clusters with heterogeneous architectures. Furthermore, adaptive surrogate models are proposed in order to reduce the computational cost associated with the large number of MD model runs. The effectiveness and computational efficiency of the proposed Bayesian framework is demonstrated in MD simulations of liquid and gaseous argon.

`@article{angelikopoulos2012a, author = {Panagiotis Angelikopoulos and Costas Papadimitriou and Petros Koumoutsakos}, doi = {10.1063/1.4757266}, journal = {The Journal of Chemical Physics}, month = {oct}, number = {14}, pages = {144103}, publisher = {{AIP} Publishing}, title = {{B}ayesian uncertainty quantification and propagation in molecular dynamics simulations: A high performance computing framework}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/angelikopoulos2012a.pdf}, volume = {137}, year = {2012} }`

- W. M. van Rees, F. Hussain, and P. Koumoutsakos, “Vortex tube reconnection at Re = 10^4," Physics of fluids, vol. 24, iss. 7, p. 75105, 2012.

[BibTeX] [Abstract] [PDF] [DOI]

We present simulations of the long-time dynamics of two anti-parallel vortex tubes with and without initial axial {fl}ow, at Reynolds number Re = {Γ}/{ν} = 104. Simulations were performed in a periodic domain with a remeshed vortex method using 785 {\texttimes} 106 particles. We quantify the vortex dynamics of the primary vortex reconnection that leads to the formation of elliptical rings with axial {fl}ow and report for the {fi}rst time a subsequent collision of these rings. In the absence of initial axial {fl}ow, a {-}5/3 slope of the energy spectrum is observed during the {fi}rst reconnection of the tubes. The resulting elliptical vortex rings experience a coiling of their vortex lines imparting an axial {fl}ow inside their cores. These rings eventually collide, exhibiting a {-}7/3 slope of the energy spectrum. Studies of vortex reconnection with an initial axial {fl}ow exhibit also the {-}7/3 slope during the initial collision as well as in the subsequent collision of the ensuing elliptical vortex rings. We quantify the detailed vortex dynamics of these collisions and examine the role of axial {fl}ow in the breakup of vortex structures.

`@article{rees2012a, author = {Wim M. van Rees and Fazle Hussain and Petros Koumoutsakos}, doi = {10.1063/1.4731809}, journal = {Physics of Fluids}, month = {jul}, number = {7}, pages = {075105}, publisher = {{AIP} Publishing}, title = {Vortex tube reconnection at }, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rees2012a.pdf}, volume = {24}, year = {2012} }`

- J. H. Walther, M. Praprotnik, E. M. Kotsalis, and P. Koumoutsakos, “Multiscale simulation of water flow past a c540 fullerene," Journal of computational physics, vol. 231, iss. 7, pp. 2677-2681, 2012.

[BibTeX] [Abstract] [PDF] [DOI]

We present a novel, three-dimensional, multiscale algorithm for simulations of water flow past a fullerene. We employ the Schwarz alternating overlapping domain method to couple molecular dynamics (MD) of liquid water around the C540 buckyball with a Lattice{—}Boltzmann (LB) description for the Navier{—}Stokes equations. The proposed method links the MD and LB domains using a fully three-dimensional interface and coupling of velocity gradients. The present overlapping domain method implicitly preserves the flux of mass and momentum and bridges flux-based and Schwarz domain decomposition algorithms. We use this method to determine the slip length and hydrodynamic radius for water flow past a buckyball.

`@article{walther2012a, author = {Jens H. Walther and Matej Praprotnik and Evangelos M. Kotsalis and Petros Koumoutsakos}, doi = {10.1016/j.jcp.2011.12.015}, journal = {Journal of Computational Physics}, month = {apr}, number = {7}, pages = {2677--2681}, publisher = {Elsevier {BV}}, title = {Multiscale simulation of water flow past a C540 fullerene}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther2012a.pdf}, volume = {231}, year = {2012} }`

- M. Gazzola, C. Mimeau, A. A. Tchieu, and P. Koumoutsakos, “Flow mediated interactions between two cylinders at finite re numbers," Physics of fluids, vol. 24, iss. 4, p. 43103, 2012.

[BibTeX] [Abstract] [PDF] [DOI]

We present simulations of two interacting moving cylinders immersed in a twodimensional incompressible, viscous flow. Simulations are performed by coupling a wavelet-adapted, remeshed vortex method with the Brinkman penalization and projection approach. This method is validated on benchmark problems and applied to simulations of a master-slave pair of cylinders. The master cylinder{‘}s motion is imposed and the slave cylinder is let free to respond to the flow.We study the relative role of viscous and inertia effects in the cylinders interactions and identify related sharp transitions in the response of the slave. The observed differences in the behavior of cylinders with respect to corresponding potential flow simulations are discussed. In addition, it is observed that in certain situations the finite size of the slave cylinders enhances the transport so that the cylinders are advected more effectively than passive tracers placed, respectively, at the same starting position.

`@article{gazzola2012b, author = {Mattia Gazzola and Chloe Mimeau and Andrew A. Tchieu and Petros Koumoutsakos}, doi = {10.1063/1.4704195}, journal = {Physics of Fluids}, month = {apr}, number = {4}, pages = {043103}, publisher = {{AIP} Publishing}, title = {Flow mediated interactions between two cylinders at finite Re numbers}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/gazzola2012b.pdf}, volume = {24}, year = {2012} }`

- C. Conti, D. Rossinelli, and P. Koumoutsakos, “GPU and APU computations of finite time lyapunov exponent fields," Journal of computational physics, vol. 231, iss. 5, pp. 2229-2244, 2012.

[BibTeX] [Abstract] [PDF] [DOI]

We present GPU and APU accelerated computations of Finite-Time Lyapunov Exponent (FTLE) fields. The calculation of FTLEs is a computationally intensive process, as in order to obtain the sharp ridges associated with the Lagrangian Coherent Structures an extensive resampling of the flow field is required. The computational performance of this resampling is limited by the memory bandwidth of the underlying computer architecture. The present technique harnesses data-parallel execution of many-core architectures and relies on fast and accurate evaluations of moment conserving functions for the mesh to particle interpolations. We demonstrate how the computation of FTLEs can be efficiently performed on a GPU and on an APU through OpenCL and we report over one order of magnitude improvements over multi-threaded executions in FTLE computations of bluff body flows.

`@article{conti2012a, author = {Christian Conti and Diego Rossinelli and Petros Koumoutsakos}, doi = {10.1016/j.jcp.2011.10.032}, journal = {Journal of Computational Physics}, month = {mar}, number = {5}, pages = {2229--2244}, publisher = {Elsevier {BV}}, title = {{GPU} and {APU} computations of Finite Time Lyapunov Exponent fields}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/conti2012a.pdf}, volume = {231}, year = {2012} }`

- M. Gazzola, V. W. M. Rees, and P. Koumoutsakos, “C-start: optimal start of larval fish," Journal of fluid mechanics, vol. 698, pp. 5-18, 2012.

[BibTeX] [Abstract] [PDF] [DOI]

We investigate the C-start escape response of larval fish by combining flow simulations using remeshed vortex methods with an evolutionary optimization. We test the hypothesis of the optimality of C-start of larval fish by simulations of larval-shaped, two- and three-dimensional self-propelled swimmers. We optimize for the distance travelled by the swimmer during its initial bout, bounding the shape deformation based on the larval mid-line curvature values observed experimentally. The best motions identified within these bounds are in good agreement with in vivo experiments and show that C-starts do indeed maximize escape distances. Furthermore we found that motions with curvatures beyond the ones experimentally observed for larval fish may result in even larger escape distances. We analyse the flow field and find that the effectiveness of the C-start escape relies on the ability of pronounced C-bent body configurations to trap and accelerate large volumes of fluid, which in turn correlates with large accelerations of the swimmer.

`@article{gazzola2012a, author = {M. Gazzola and W. M. Van Rees and P. Koumoutsakos}, doi = {10.1017/jfm.2011.558}, journal = {Journal of Fluid Mechanics}, month = {feb}, pages = {5--18}, publisher = {Cambridge University Press ({CUP})}, title = {C-start: optimal start of larval fish}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/gazzola2012a.pdf}, volume = {698}, year = {2012} }`

- F. Milde, D. Franco, A. Ferrari, V. Kurtcuoglu, D. Poulikakos, and P. Koumoutsakos, “Cell image velocimetry (CIV): boosting the automated quantification of cell migration in wound healing assays," Integrative biology, vol. 4, iss. 11, p. 1437, 2012.

[BibTeX] [Abstract] [PDF] [DOI]

Cell migration is commonly quantified by tracking the speed of the cell layer interface in wound healing assays. This quantification is often hampered by low signal to noise ratio, in particular when complex substrates are employed to emulate in vivo cell migration in geometrically complex environments. Moreover, information about the cell motion, readily available inside the migrating cell layers, is not usually harvested. We introduce Cell Image Velocimetry (CIV), a combination of cell layer segmentation and image velocimetry algorithms, to drastically enhance the quantification of cell migration by wound healing assays. The resulting software analyses the speed of the interface as well as the detailed velocity field inside the cell layers in an automated fashion. CIV is shown to be highly robust for images with low signal to noise ratio, low contrast and frame shifting and it is portable across various experimental settings. The modular design and parametrization of CIV is not restricted to wound healing assays and allows for the exploration and quantification of flow phenomena in any optical microscopy dataset. Here, we demonstrate the capabilities of CIV in wound healing assays over topographically engineered surfaces and quantify the relative merits of differently aligned gratings on cell migration.

`@article{milde2012a, author = {Florian Milde and Davide Franco and Aldo Ferrari and Vartan Kurtcuoglu and Dimos Poulikakos and Petros Koumoutsakos}, doi = {10.1039/c2ib20113e}, journal = {Integrative Biology}, number = {11}, pages = {1437}, publisher = {Royal Society of Chemistry ({RSC})}, title = {Cell Image Velocimetry ({CIV}): boosting the automated quantification of cell migration in wound healing assays}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/milde2012a.pdf}, volume = {4}, year = {2012} }`

### 2011

- M. Gazzola, P. Chatelain, W. M. van Rees, and P. Koumoutsakos, “Simulations of single and multiple swimmers with non-divergence free deforming geometries," Journal of computational physics, vol. 230, iss. 19, pp. 7093-7114, 2011.

[BibTeX] [Abstract] [PDF] [DOI]

We present a vortex particle method coupled with a penalization technique to simulate single and multiple swimmers in an incompressible, viscous flow in two and three dimensions. The proposed algorithm can handle arbitrarily deforming bodies and their corresponding non-divergence free deformation velocity fields. The method is validated on a number of benchmark problems with stationary and moving boundaries. Results include flows of tumbling objects and single and multiple self-propelled swimmers.

`@article{gazzola2011b, author = {Mattia Gazzola and Philippe Chatelain and Wim M. van Rees and Petros Koumoutsakos}, doi = {10.1016/j.jcp.2011.04.025}, journal = {Journal of Computational Physics}, month = {aug}, number = {19}, pages = {7093--7114}, publisher = {Elsevier {BV}}, title = {Simulations of single and multiple swimmers with non-divergence free deforming geometries}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/gazzola2011b.pdf}, volume = {230}, year = {2011} }`

- M. Gazzola, O. V. Vasilyev, and P. Koumoutsakos, “Shape optimization for drag reduction in linked bodies using evolution strategies," Computers & structures, vol. 89, iss. 11-12, pp. 1224-1231, 2011.

[BibTeX] [Abstract] [PDF] [DOI]

We present results from the shape optimization of linked bodies for drag reduction in simulations of incompressible flow at moderate Reynolds numbers. The optimization relies on the covariance matrix adaptation evolution strategy (CMA-ES) and the flow simulations use vortex methods with the Brinkman penalization to enforce boundary conditions in complex bodies. We exploit the inherent parallelism of CMA-ES, by implementing a multi-host framework which allows for the distribution of the expensive cost function evaluations across parallel architectures, without being limited to one computing facility. This study repeats in silico for the first time Ingo Rechenberg{‘}s pioneering wind tunnel experiments for drag reduction that led to the inception of evolution strategies. The simulations confirm that the results of these experimental studies indicate a flat plate is not the optimal solution for drag reduction in linked bodies. We present the vorticity field of the flow and identify the governing mechanisms for this drag reduction by the slightly corrugated linked plate configuration.

`@article{gazzola2011a, author = {Mattia Gazzola and Oleg V. Vasilyev and Petros Koumoutsakos}, doi = {10.1016/j.compstruc.2010.09.001}, journal = {Computers {\&} Structures}, month = {jun}, number = {11-12}, pages = {1224--1231}, publisher = {Elsevier {BV}}, title = {Shape optimization for drag reduction in linked bodies using evolution strategies}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/gazzola2011a.pdf}, volume = {89}, year = {2011} }`

- D. Rossinelli, C. Conti, and P. Koumoutsakos, “Mesh-particle interpolations on graphics processing units and multicore central processing units," Philosophical transactions of the royal society a: mathematical, physical and engineering sciences, vol. 369, iss. 1944, pp. 2164-2175, 2011.

[BibTeX] [Abstract] [PDF] [DOI]

Particle{—}mesh interpolations are fundamental operations for particle-in-cell codes, as implemented in vortex methods, plasma dynamics and electrostatics simulations. In these simulations, the mesh is used to solve the field equations and the gradients of the fields are used in order to advance the particles. The time integration of particle trajectories is performed through an extensive resampling of the flow field at the particle locations. The computational performance of this resampling turns out to be limited by the memory bandwidth of the underlying computer architecture. We investigate how mesh{—}particle interpolation can be efficiently performed on graphics processing units (GPUs) and multicore central processing units (CPUs), and we present two implementation techniques. The single-precision results for the multicore CPU implementation show an acceleration of 45{—}70{\texttimes}, depending on system size, and an acceleration of 85{—}155{\texttimes} for the GPU implementation over an efficient single-threaded C++ implementation. In double precision, we observe a performance improvement of 30{—}40{\texttimes} for the multicore CPU implementation and 20{—}45{\texttimes} for the GPU implementation. With respect to the 16-threaded standard C++ implementation, the present CPU technique leads to a performance increase of roughly 2.8{—}3.7{\texttimes} in single precision and 1.7{—}2.4{\texttimes} in double precision, whereas the GPU technique leads to an improvement of 9{\texttimes} in single precision and 2.2{—}2.8{\texttimes} in double precision.

`@article{rossinelli2011a, author = {D. Rossinelli and C. Conti and P. Koumoutsakos}, doi = {10.1098/rsta.2011.0074}, journal = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences}, month = {may}, number = {1944}, pages = {2164--2175}, publisher = {The Royal Society}, title = {Mesh-particle interpolations on graphics processing units and multicore central processing units}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rossinelli2011a.pdf}, volume = {369}, year = {2011} }`

- W. M. van Rees, A. Leonard, D. I. Pullin, and P. Koumoutsakos, “A comparison of vortex and pseudo-spectral methods for the simulation of periodic vortical flows at high Reynolds numbers," Journal of computational physics, vol. 230, iss. 8, pp. 2794-2805, 2011.

[BibTeX] [Abstract] [PDF] [DOI]

We present a validation study for the hybrid particle-mesh vortex method against a pseudo-spectral method for the Taylor{—}Green vortex at Re=1600 as well as in the collision of two antiparallel vortex tubes at Re=10,000. In this study we present diagnostics such as energy spectra and enstrophy as computed by both methods as well as point-wise comparisons of the vorticity field. Using a fourth order accurate kernel for interpolation between the particles and the mesh, the results of the hybrid vortex method and of the pseudo-spectral method agree well in both flow cases. For the Taylor{—}Green vortex, the vorticity contours computed by both methods around the time of the energy dissipation peak overlap. The energy spectrum shows that only the smallest length scales in the flow are not captured by the vortex method. In the second flow case, where we compute the collision of two anti-parallel vortex tubes at Reynolds number 10,000, the vortex method results and the pseudo-spectral method results are in very good agreement up to and including the first reconnection of the tubes. The maximum error in the effective viscosity is about 2.5% for the vortex method and about 1% for the pseudo-spectral method. At later times the flows computed with the different methods show the same qualitative features, but the quantitative agreement on vortical structures is lost.

`@article{rees2011a, author = {Wim M. van Rees and Anthony Leonard and D.I. Pullin and Petros Koumoutsakos}, doi = {10.1016/j.jcp.2010.11.031}, journal = {Journal of Computational Physics}, month = {apr}, number = {8}, pages = {2794--2805}, publisher = {Elsevier {BV}}, title = {A comparison of vortex and pseudo-spectral methods for the simulation of periodic vortical flows at high {R}eynolds numbers}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rees2011a.pdf}, volume = {230}, year = {2011} }`

- P. D. Koumoutsakos, B. Bayati, F. Milde, and G. Tauriello, “Particle simulations of morphogenesis," Mathematical models and methods in applied sciences, vol. 21, iss. supp01, pp. 955-1006, 2011.

[BibTeX] [Abstract] [PDF] [DOI]

The simulation of the creation and evolution of biological forms requires the development of computational methods that are capable of resolving their hierarchical, spatial and temporal complexity. Computations based on interacting particles, provide a unique computational tool for discrete and continuous descriptions of morphogenesis of systems ranging from the molecular to the organismal level. The capabilities of particle methods hinge on the simplicity of their formulation which enables the formulation of a unifying computational framework encom- passing deterministic and stochastic models. In this paper, we discuss recent advances in particle methods for the simulation of biological systems at the mesoscopic and the macroscale level. We present results from applications of particle methods including reaction-diffusion on deforming surfaces, deterministic and stochastic descriptions of tumor growth and angiogenesis and discuss successes and challenges of this approach.

`@article{koumoutsakos2011a, author = {Petros D. Koumoutsakos and Basil Bayati and Florian Milde and Gerardo Tauriello}, doi = {10.1142/s021820251100543x}, journal = {Mathematical Models and Methods in Applied Sciences}, month = {apr}, number = {supp01}, pages = {955--1006}, publisher = {World Scientific Pub Co Pte Lt}, title = {Particle Simulations of Morphogenesis}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos2011a.pdf}, volume = {21}, year = {2011} }`

- D. Rossinelli, B. Hejazialhosseini, D. G. Spampinato, and P. Koumoutsakos, “Multicore/multi-GPU accelerated simulations of multiphase compressible flows using wavelet adapted grids," SIAM journal on scientific computing, vol. 33, iss. 2, pp. 512-540, 2011.

[BibTeX] [Abstract] [PDF] [DOI]

We present a computational method of coupling average interpolating wavelets with high-order finite volume schemes and its implementation on heterogeneous computer architectures for the simulation of multiphase compressible flows. The method is implemented to take advantage of the parallel computing capabilities of emerging heterogeneous multicore/multi-GPU architectures. A highly efficient parallel implementation is achieved by introducing the concept of wavelet blocks, exploiting the task-based parallelism for CPU cores, and by managing asynchronously an array of GPUs by means of OpenCL. We investigate the comparative accuracy of the GPU and CPU based simulations and analyze their discrepancy for two-dimensional simulations of shock-bubble interaction and Richtmeyer{—}Meshkov instability. The results indicate that the accuracy of the GPU/CPU heterogeneous solver is competitive with the one that uses exclusively the CPU cores. We report the performance improvements by employing up to 12 cores and 6 GPUs compared to the single-core execution. For the simulation of the shock-bubble interaction at Mach 3 with two million grid points, we observe a 100-fold speedup for the heterogeneous part and an overall speedup of 34.

`@article{rossinelli2011b, author = {Diego Rossinelli and Babak Hejazialhosseini and Daniele G. Spampinato and Petros Koumoutsakos}, doi = {10.1137/100795930}, journal = {{SIAM} Journal on Scientific Computing}, month = {jan}, number = {2}, pages = {512--540}, publisher = {Society for Industrial {\&} Applied Mathematics ({SIAM})}, title = {Multicore/Multi-{GPU} Accelerated Simulations of Multiphase Compressible Flows Using Wavelet Adapted Grids}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rossinelli2011b.pdf}, volume = {33}, year = {2011} }`

- B. Bayati, P. Chatelain, and P. Koumoutsakos, “Adaptive mesh refinement for stochastic reaction—diffusion processes," Journal of computational physics, vol. 230, iss. 1, pp. 13-26, 2011.

[BibTeX] [Abstract] [PDF] [DOI]

We present an algorithm for Adaptive Mesh Refinement applied to mesoscopic stochastic simulations of spatially evolving reaction-diffusion processes. The transition rates for the diffusion process are derived on adaptive, locally refined structured meshes. Convergence of the diffusion process is presented and the fluctuations of the stochastic process are verified. Furthermore, a refinement criterion is proposed for the evolution of the adaptive mesh. The method is validated in simulations of reaction-diffusion processes as described by the Fisher-Kolmogorov and Gray-Scott equations.

`@article{bayati2011a, author = {Basil Bayati and Philippe Chatelain and Petros Koumoutsakos}, doi = {10.1016/j.jcp.2010.08.035}, journal = {Journal of Computational Physics}, month = {jan}, number = {1}, pages = {13--26}, publisher = {Elsevier {BV}}, title = {Adaptive mesh refinement for stochastic reaction{\textendash}diffusion processes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bayati2011a.pdf}, volume = {230}, year = {2011} }`

- G. Schwank, G. Tauriello, R. Yagi, E. Kranz, P. Koumoutsakos, and K. Basler, “Antagonistic growth regulation by dpp and fat drives uniform cell proliferation," Developmental cell, vol. 20, iss. 1, pp. 123-130, 2011.

[BibTeX] [Abstract] [PDF] [DOI]

We use the Dpp morphogen gradient in the Drosophila wing disc as a model to address the fundamental question of how a gradient of a growth factor can produce uniform growth. We first show that proper expression and subcellular localization of components in the Fat tumor-suppressor pathway, which have been argued to depend on Dpp activity differences, are not reliant on the Dpp gradient. We next analyzed cell proliferation in discs with uniformly high Dpp or uniformly low Fat signaling activity and found that these pathways regulate growth in a complementary manner. While the Dpp mediator Brinker inhibits growth in the primordium primarily in the lateral regions, Fat represses growth mostly in the medial region. Together, our results indicate that the activities of both signaling pathways are regulated in a parallel rather than sequential manner and that uniform proliferation is achieved by their complementary action on growth.

`@article{schwank2011a, author = {Gerald Schwank and Gerardo Tauriello and Ryohei Yagi and Elizabeth Kranz and Petros Koumoutsakos and Konrad Basler}, doi = {10.1016/j.devcel.2010.11.007}, journal = {Developmental Cell}, month = {jan}, number = {1}, pages = {123--130}, publisher = {Elsevier {BV}}, title = {Antagonistic Growth Regulation by Dpp and Fat Drives Uniform Cell Proliferation}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/schwank2011a.pdf}, volume = {20}, year = {2011} }`

- P. Chatelain, M. Gazzola, S. Kern, and P. Koumoutsakos, “Optimization of aircraft wake alleviation schemes through an evolution strategy," in Lecture notes in computer science, Springer Berlin Heidelberg, 2011, pp. 210-221.

[BibTeX] [Abstract] [PDF] [DOI]

We investigate schemes to accelerate the decay of aircraft trailing vortices. These structures are susceptible to several instabilities that lead to their eventual destruction. We employ an Evolution Strategy to design a lift distribution and a lift perturbation scheme that minimize the wake hazard as proposed in [6]. The performance of a scheme is mea- sured as the reduction of the mean rolling moment that would be induced on a following aircraft; it is computed by means of a Direct Numerical Simulation using a parallel vortex particle code. We find a configuration and a perturbation scheme characterized by an intermediate wavelength {λ} {\sim} 4.64, necessary to trigger medium wavelength instabilities between tail and flap vortices and subsequently amplify long wavelength modes.

`@incollection{chatelain2011a, author = {Philippe Chatelain and Mattia Gazzola and Stefan Kern and Petros Koumoutsakos}, booktitle = {Lecture Notes in Computer Science}, doi = {10.1007/978-3-642-19328-6_21}, pages = {210--221}, publisher = {Springer Berlin Heidelberg}, title = {Optimization of Aircraft Wake Alleviation Schemes through an Evolution Strategy}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/chatelain2011a.pdf}, year = {2011} }`

### 2010

- B. Bayati, H. Owhadi, and P. Koumoutsakos, “A cutoff phenomenon in accelerated stochastic simulations of chemical kinetics via flow averaging (FLAVOR-SSA)," The journal of chemical physics, vol. 133, iss. 24, p. 244117, 2010.

[BibTeX] [Abstract] [PDF] [DOI]

We present a simple algorithm for the simulation of stiff, discrete-space, continuous-time Markov processes. The algorithm is based on the concept of flow averaging for the integration of stiff ordinary and stochastic differential equations and ultimately leads to a straightforward variation of the well-known stochastic simulation algorithm (SSA). The speedup that can be achieved by the present algorithm [flow averaging integrator SSA (FLAVOR-SSA)] over the classical SSA comes naturally at the expense of its accuracy. The error of the proposed method exhibits a cutoff phenomenon as a function of its speed-up, allowing for optimal tuning. Two numerical examples from chemical kinetics are provided to illustrate the efficiency of the method.

`@article{bayati2010a, author = {Basil Bayati and Houman Owhadi and Petros Koumoutsakos}, doi = {10.1063/1.3518419}, journal = {The Journal of Chemical Physics}, month = {dec}, number = {24}, pages = {244117}, publisher = {{AIP} Publishing}, title = {A cutoff phenomenon in accelerated stochastic simulations of chemical kinetics via flow averaging ({FLAVOR}-{SSA})}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bayati2010a.pdf}, volume = {133}, year = {2010} }`

- I. Hanasaki, J. H. Walther, S. Kawano, and P. Koumoutsakos, “Coarse-grained molecular dynamics simulations of shear-induced instabilities of lipid bilayer membranes in water," Physical review e, vol. 82, iss. 5, 2010.

[BibTeX] [Abstract] [PDF] [DOI]

We study shear-induced instabilities of lipid bilayers immersed in water using coarse-grained molecular dynamics simulations. The shear imposed by the flow of the water induces initially microscopic structural changes of the membrane, starting with tilting of the molecules in the direction of the shear. The tilting propagates in the spanwise direction when the shear rate exceeds a critical value and the membrane undergoes a bucklinglike deformation in the direction perpendicular to the shear. The bucklinglike undulation continues until a localized Kelvin-Helmholtz-like instability leads to membrane rupture. We study the different modes of membrane undulation using membranes of different geometries and quantify the relative importance of the bucklinglike bending and the Kelvin-Helmholtz-like instability of the membrane.

`@article{hanasaki2010a, author = {Itsuo Hanasaki and Jens H. Walther and Satoyuki Kawano and Petros Koumoutsakos}, doi = {10.1103/physreve.82.051602}, journal = {Physical Review E}, month = {nov}, number = {5}, publisher = {American Physical Society ({APS})}, title = {Coarse-grained molecular dynamics simulations of shear-induced instabilities of lipid bilayer membranes in water}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hanasaki2010a.pdf}, volume = {82}, year = {2010} }`

- B. Hejazialhosseini, D. Rossinelli, M. Bergdorf, and P. Koumoutsakos, “High order finite volume methods on wavelet-adapted grids with local time-stepping on multicore architectures for the simulation of shock-bubble interactions," Journal of computational physics, vol. 229, iss. 22, pp. 8364-8383, 2010.

[BibTeX] [Abstract] [PDF] [DOI]

We present a space{—}time adaptive solver for single- and multi-phase compressible flows that couples average interpolating wavelets with high-order finite volume schemes. The solver introduces the concept of wavelet blocks, handles large jumps in resolution and employs local time-stepping for efficient time integration. We demonstrate that the inherently sequential wavelet-based adaptivity can be implemented efficiently in multicore computer architectures using task-based parallelism and introducing the concept of wavelet blocks. We validate our computational method on a number of benchmark problems and we present simulations of shock-bubble interaction at different Mach numbers, demonstrating the accuracy and computational performance of the method.

`@article{hejazialhosseini2010a, author = {Babak Hejazialhosseini and Diego Rossinelli and Michael Bergdorf and Petros Koumoutsakos}, doi = {10.1016/j.jcp.2010.07.021}, journal = {Journal of Computational Physics}, month = {nov}, number = {22}, pages = {8364--8383}, publisher = {Elsevier {BV}}, title = {High order finite volume methods on wavelet-adapted grids with local time-stepping on multicore architectures for the simulation of shock-bubble interactions}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hejazialhosseini2010a.pdf}, volume = {229}, year = {2010} }`

- D. Rossinelli, B. Hejazialhosseini, M. Bergdorf, and P. Koumoutsakos, “Wavelet-adaptive solvers on multi-core architectures for the simulation of complex systems," Concurrency and computation: practice and experience, vol. 23, iss. 2, pp. 172-186, 2010.

[BibTeX] [Abstract] [PDF] [DOI]

We build wavelet-based adaptive numerical methods for the simulation of advection-dominated flows that develop multiple spatial scales, with an emphasis on fluid mechanics problems. Wavelet-based adaptivity is inherently sequential and in this work we demonstrate that these numerical methods can be implemented in software that is capable of harnessing the capabilities of multi-core architectures while maintaining their computational efficiency. Recent designs in frameworks for multi-core software development allow us to rethink parallelism as task-based, where parallel tasks are specified and automatically mapped onto physical threads. This way of exposing parallelism enables the parallelization of algorithms that were considered inherently sequential, such as wavelet-based adaptive simulations. In this paper we present a framework that combines wavelet-based adaptivity with the task-based parallelism. We demonstrate the promising performance obtained by simulating various physical systems on different multi-core architectures using up to 16 cores.

`@article{rossinelli2010b, author = {Diego Rossinelli and Babak Hejazialhosseini and Michael Bergdorf and Petros Koumoutsakos}, doi = {10.1002/cpe.1639}, journal = {Concurrency and Computation: Practice and Experience}, month = {aug}, number = {2}, pages = {172--186}, publisher = {Wiley-Blackwell}, title = {Wavelet-adaptive solvers on multi-core architectures for the simulation of complex systems}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rossinelli2010b.pdf}, volume = {23}, year = {2010} }`

- G. Morra, D. A. Yuen, L. Boschi, P. Chatelain, P. Koumoutsakos, and P. J. Tackley, “The fate of the slabs interacting with a density/viscosity hill in the mid-mantle," Physics of the earth and planetary interiors, vol. 180, iss. 3-4, pp. 271-282, 2010.

[BibTeX] [Abstract] [PDF] [DOI]

In the last two decades it has been proposed several times that a non-monotonic profile might fit the average lower mantle radial viscosity. Most proposed profiles consist in a more or less broad viscosity hill in the middle of the mantle, at a depth roughly between 1200 km and 2000 km. Also many tomographic models display strong signals of the presence of {\textquotedblleft}fast{\textquotedblright} material lying at mid mantle depths and a recent spectral analysis of seismic tomography shows a very clear transition for degree up to around 16 at a less than 1500 km depth. Finally latest works, both theoretical and experimental, on the high-to-low-spin transition for periclase, have suggested that the high-spin to low-spin transition of Fe++ might lie at the heart of all these observations. To verify the dynamical compatibility between possible mantle profile and observed tomographic images and compare them with possible mineral physics scenarios, such as the spin transition, we employ here a recently developed Fast Multipole-accelerated Boundary Element Method (FMM-BEM), a numerical approach for solving the viscous momentum equation in a global spherical setting, for simulating the interaction of an individual slab with a mid mantle smooth discontinuity in density and viscosity. We have focused on the complexities induced to the behaviour of average and very large plates O (2000{—}10,000 km), characteristic of the Farallon, Tethys and Pacific plate subducting during the Cenozoic, demonstrating that the a mid mantle density and/or viscosity discontinuity produces a strong alteration of the sinking velocity and an intricate set of slab morphologies. We also employ the Kula{—}Farallon plate system subducting at 60 Ma as a paradigmatic case, which reveals the best high resolution tomography models and clearly suggests an interaction with a strong and/or denser layer in the mantle. Our 38 models show that a plate might or might not penetrate into the lowest mantle and might stall in the mid lower mantle for long periods, depending on the radial profiles of density and viscosity, within a realistic range (viscosity 1, 10 or 100 times more viscous of the rest of the mantle, and a change of differential density in the range {-}2% to 2%), of a transitional layer of 200 km or 500 km. We conclude that a layer with high viscosity or negative density would naturally trigger the observed geodynamic snapshot. We finally propose a scenario in which the long time accumulation of depleted slabs in the mid mantle would give rise to a partially chemically stratified mantle, starting from the less prominent high-spin to low-spin contribution on the basis of mantle density and rheology.

`@article{morra2010a, author = {G. Morra and D.A. Yuen and L. Boschi and P. Chatelain and P. Koumoutsakos and P.J. Tackley}, doi = {10.1016/j.pepi.2010.04.001}, journal = {Physics of the Earth and Planetary Interiors}, month = {jun}, number = {3-4}, pages = {271--282}, publisher = {Elsevier {BV}}, title = {The fate of the slabs interacting with a density/viscosity hill in the mid-mantle}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/morra2010a.pdf}, volume = {180}, year = {2010} }`

- D. Rossinelli, M. Bergdorf, G. Cottet, and P. Koumoutsakos, “GPU accelerated simulations of bluff body flows using vortex particle methods," Journal of computational physics, vol. 229, iss. 9, pp. 3316-3333, 2010.

[BibTeX] [Abstract] [PDF] [DOI]

We present a GPU accelerated solver for simulations of bluff body flows in 2D using a remeshed vortex particle method and the vorticity formulation of the Brinkman penalization technique to enforce boundary conditions. The efficiency of the method relies on fast and accurate particle-grid interpolations on GPUs for the remeshing of the particles and the computation of the field operators. The GPU implementation uses OpenGL so as to perform efficient particle-grid operations and a CUFFT-based solver for the Poisson Equation with unbounded boundary conditions. The accuracy and performance of the GPU simulations and their relative advantages/drawbacks over CPU based computations are reported in simulations of flows past an impulsively started circular cylinder from Reynolds numbers between 40 and 9,500. The results indicate up to two orders of magnitude speed up of the GPU implementation over the respective CPU implementations. The accuracy of the GPU computations depends on the Re number of the flow. For Re up to 1000 there is little difference between GPU and CPU calculations but this agreement deteriorates (albeit remaining to within 5% in drag calculations) for higher Re numbers as the single precision of the GPU adversely affects the accuracy of the simulations.

`@article{rossinelli2010a, author = {Diego Rossinelli and Michael Bergdorf and Georges-Henri Cottet and Petros Koumoutsakos}, doi = {10.1016/j.jcp.2010.01.004}, journal = {Journal of Computational Physics}, month = {may}, number = {9}, pages = {3316--3333}, publisher = {Elsevier {BV}}, title = {{GPU} accelerated simulations of bluff body flows using vortex particle methods}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rossinelli2010a.pdf}, volume = {229}, year = {2010} }`

- E. M. Kotsalis, I. Hanasaki, J. H. Walther, and P. Koumoutsakos, “Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water," Computers & mathematics with applications, vol. 59, iss. 7, pp. 2370-2373, 2010.

[BibTeX] [Abstract] [PDF] [DOI]

We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.

`@article{kotsalis2010a, author = {E.M. Kotsalis and I. Hanasaki and J.H. Walther and P. Koumoutsakos}, doi = {10.1016/j.camwa.2009.08.054}, journal = {Computers {\&} Mathematics with Applications}, month = {apr}, number = {7}, pages = {2370--2373}, publisher = {Elsevier {BV}}, title = {Non-periodic Molecular Dynamics simulations of coarse grained lipid bilayer in water}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/kotsalis2010a.pdf}, volume = {59}, year = {2010} }`

- P. Chatelain and P. Koumoutsakos, “A fourier-based elliptic solver for vortical flows with periodic and unbounded directions," Journal of computational physics, vol. 229, iss. 7, pp. 2425-2431, 2010.

[BibTeX] [Abstract] [PDF] [DOI]

We present a computationally efficient, adaptive solver for the solution of the Poisson and Helmholtz equation used in flow simulations in domains with combinations of unbounded and periodic directions. The method relies on using FFTs on an extended domain and it is based on the method proposed by Hockney and Eastwood for plasma simulations. The method is well-suited to problems with dynamically growing domains and in particular flow simulations using vortex particle methods. The efficiency of the method is demonstrated in simulations of trailing vortices.

`@article{chatelain2010a, author = {Philippe Chatelain and Petros Koumoutsakos}, doi = {10.1016/j.jcp.2009.12.035}, journal = {Journal of Computational Physics}, month = {apr}, number = {7}, pages = {2425--2431}, publisher = {Elsevier {BV}}, title = {A Fourier-based elliptic solver for vortical flows with periodic and unbounded directions}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/chatelain2010a.pdf}, volume = {229}, year = {2010} }`

### 2009

- M. Bergdorf, I. F. Sbalzarini, and P. Koumoutsakos, “A lagrangian particle method for reaction—diffusion systems on deforming surfaces," Journal of mathematical biology, vol. 61, iss. 5, pp. 649-663, 2009.

[BibTeX] [Abstract] [PDF] [DOI]

Reaction-diffusion processes on complex deforming surfaces are fundamental to a number of biological processes ranging from embryonic development to cancer tumor growth and angiogenesis. The simulation of these processes using continuum reaction-diffusion models requires computational methods capable of accurately tracking the geometric deformations and discretizing on them the governing equations. We employ a Lagrangian level-set formulation to capture the deformation of the geometry and use an embedding formulation and an adaptive particle method to discretize both the level-set equations and the corresponding reaction-diffusion. We validate the proposed method and discuss its advantages and drawbacks through simulations of reaction-diffusion equations on complex and deforming geometries.

`@article{bergdorf2009a, author = {Michael Bergdorf and Ivo F. Sbalzarini and Petros Koumoutsakos}, doi = {10.1007/s00285-009-0315-2}, journal = {Journal of Mathematical Biology}, month = {dec}, number = {5}, pages = {649--663}, publisher = {Springer Nature}, title = {A Lagrangian particle method for reaction{\textendash}diffusion systems on deforming surfaces}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bergdorf2009a.pdf}, volume = {61}, year = {2009} }`

- M. Gazzola, C. J. Burckhardt, B. Bayati, M. Engelke, U. F. Greber, and P. Koumoutsakos, “A stochastic model for microtubule motors describes the in vivo cytoplasmic transport of human adenovirus," PLoS computational biology, vol. 5, iss. 12, p. e1000623, 2009.

[BibTeX] [Abstract] [PDF] [DOI]

Cytoplasmic transport of organelles, nucleic acids and proteins on microtubules is usually bidirectional with dynein and kinesin motors mediating the delivery of cargoes in the cytoplasm. Here we combine live cell microscopy, single virus tracking and trajectory segmentation to systematically identify the parameters of a stochastic computational model of cargo transport by molecular motors on microtubules. The model parameters are identified using an evolutionary optimization algorithm to minimize the Kullback-Leibler divergence between the in silico and the in vivo run length and velocity distributions of the viruses on microtubules. The present stochastic model suggests that bidirectional transport of human adenoviruses can be explained without explicit motor coordination. The model enables the prediction of the number of motors active on the viral cargo during microtubule-dependent motions as well as the number of motor binding sites, with the protein hexon as the binding site for the motors.

`@article{gazzola2009a, author = {Mattia Gazzola and Christoph J. Burckhardt and Basil Bayati and Martin Engelke and Urs F. Greber and Petros Koumoutsakos}, doi = {10.1371/journal.pcbi.1000623}, editor = {Herbert M. Sauro}, journal = {{PLoS} Computational Biology}, month = {dec}, number = {12}, pages = {e1000623}, publisher = {Public Library of Science ({PLoS})}, title = {A Stochastic Model for Microtubule Motors Describes the In Vivo Cytoplasmic Transport of Human Adenovirus}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/gazzola2009a.pdf}, volume = {5}, year = {2009} }`

- B. L. Falcón, H. Hashizume, P. Koumoutsakos, J. Chou, J. V. Bready, A. Coxon, J. D. Oliner, and D. M. McDonald, “Contrasting actions of selective inhibitors of angiopoietin-1 and angiopoietin-2 on the normalization of tumor blood vessels," The american journal of pathology, vol. 175, iss. 5, pp. 2159-2170, 2009.

[BibTeX] [Abstract] [PDF] [DOI]

Angiopoietin-1 (Ang1) and angiopoietin-2 (Ang2) have complex actions in angiogenesis and vascular remodeling due to their effects on Tie2 receptor signaling. Ang2 blocks Ang1-mediated activation of Tie2 in endothelial cells under certain conditions but is a Tie2 receptor agonist in others. We examined the effects of selective inhibitors of Ang1 (mL4-3) or Ang2 (L1-7[N]), alone or in combination, on the vasculature of human Colo205 tumors in mice. The Ang2 inhibitor decreased the overall abundance of tumor blood vessels by reducing tumor growth and keeping vascular density constant. After inhibition of Ang2, tumor vessels had many features of normal blood vessels (normalization), as evidenced by junctional accumulation of vascular endothelial-cadherin, junctional adhesion molecule-A, and platelet/endothelial cell adhesion molecule-1 in endothelial cells, increased pericyte coverage, reduced endothelial sprouting, and remodeling into smaller, more uniform vessels. The Ang1 inhibitor by itself had little noticeable effect on the tumor vasculature. However, when administered with the Ang2 inhibitor, the Ang1 inhibitor prevented tumor vessel normalization, but not the reduction in tumor vascularity produced by the Ang2 inhibitor. These findings are consistent with a model whereby inhibition of Ang2 leads to normalization of tumor blood vessels by permitting the unopposed action of Ang1, but decreases tumor vascularity primarily by blocking Ang2 actions.

`@article{falcon2009a, author = {Beverly L. Falc{\'{o}}n and Hiroya Hashizume and Petros Koumoutsakos and Jeyling Chou and James V. Bready and Angela Coxon and Jonathan D. Oliner and Donald M. McDonald}, doi = {10.2353/ajpath.2009.090391}, journal = {The American Journal of Pathology}, month = {nov}, number = {5}, pages = {2159--2170}, publisher = {Elsevier {BV}}, title = {Contrasting Actions of Selective Inhibitors of Angiopoietin-1 and Angiopoietin-2 on the Normalization of Tumor Blood Vessels}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/falcon2009a.pdf}, volume = {175}, year = {2009} }`

- B. Bayati, P. Chatelain, and P. Koumoutsakos, “D-leaping: accelerating stochastic simulation algorithms for reactions with delays," Journal of computational physics, vol. 228, iss. 16, pp. 5908-5916, 2009.

[BibTeX] [Abstract] [PDF] [DOI]

We propose a novel, accelerated algorithm for the approximate stochastic simulation of biochemical systems with delays. The present work extends existing accelerated algorithms by distributing, in a time adaptive fashion, the delayed reactions so as to minimize the computational effort while preserving their accuracy. The accuracy of the present algorithm is assessed by comparing its results to those of the corresponding delay differential equations for a representative biochemical system. In addition, the fluctuations produced from the present algorithm are comparable to those from an exact stochastic simulation with delays. The algorithm is used to simulate biochemical systems that model oscillatory gene expression. The results indicate that the present algorithm is competitive with existing works for several benchmark problems while it is orders of magnitude faster for certain systems of biochemical reactions.

`@article{bayati2009a, author = {Basil Bayati and Philippe Chatelain and Petros Koumoutsakos}, doi = {10.1016/j.jcp.2009.05.004}, journal = {Journal of Computational Physics}, month = {sep}, number = {16}, pages = {5908--5916}, publisher = {Elsevier {BV}}, title = {D-leaping: Accelerating stochastic simulation algorithms for reactions with delays}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bayati2009a.pdf}, volume = {228}, year = {2009} }`

- E. Mjolsness, D. Orendorff, P. Chatelain, and P. Koumoutsakos, “An exact accelerated stochastic simulation algorithm," The journal of chemical physics, vol. 130, iss. 14, p. 144110, 2009.

[BibTeX] [Abstract] [PDF] [DOI]

An exact method for stochastic simulation of chemical reaction networks, which accelerates the stochastic simulation algorithm SSA , is proposed. The present {\textquotedblleft}ER-leap{\textquotedblright} algorithm is derived from analytic upper and lower bounds on the multireaction probabilities sampled by SSA, together with rejection sampling and an adaptive multiplicity for reactions. The algorithm is tested on a number of well-quantified reaction networks and is found experimentally to be very accurate on test problems including a chaotic reaction network. At the same time ER-leap offers a substantial speedup over SSA with a simulation time proportional to the 2/3 power of the number of reaction events in a Galton{—}Watson process.

`@article{mjolsness2009a, author = {Eric Mjolsness and David Orendorff and Philippe Chatelain and Petros Koumoutsakos}, doi = {10.1063/1.3078490}, journal = {The Journal of Chemical Physics}, month = {apr}, number = {14}, pages = {144110}, publisher = {{AIP} Publishing}, title = {An exact accelerated stochastic simulation algorithm}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/mjolsness2009a.pdf}, volume = {130}, year = {2009} }`

- E. M. Kotsalis, J. H. Walther, E. Kaxiras, and P. Koumoutsakos, “Control algorithm for multiscale flow simulations of water," Physical review e, vol. 79, iss. 4, 2009.

[BibTeX] [Abstract] [PDF] [DOI]

We present a multiscale algorithm to couple atomistic water models with continuum incompressible flow simulations via a Schwarz domain decomposition approach. The coupling introduces an inhomogeneity in the description of the atomistic domain and prevents the use of periodic boundary conditions. The use of a mass conserving specular wall results in turn to spurious oscillations in the density profile of the atomistic description of water. These oscillations can be eliminated by using an external boundary force that effectively accounts for the virial component of the pressure. In this Rapid Communication, we extend a control algorithm, previously introduced for monatomic molecules, to the case of atomistic water and demonstrate the effectiveness of this approach. The proposed computational method is validated for the cases of equilibrium and Couette flow of water.

`@article{kotsalis2009a, author = {Evangelos M. Kotsalis and Jens H. Walther and Efthimios Kaxiras and Petros Koumoutsakos}, doi = {10.1103/physreve.79.045701}, journal = {Physical Review E}, month = {apr}, number = {4}, publisher = {American Physical Society ({APS})}, title = {Control algorithm for multiscale flow simulations of water}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/kotsalis2009a.pdf}, volume = {79}, year = {2009} }`

- P. Gonnet, J. H. Walther, and P. Koumoutsakos, “ϑ-SHAKE: an extension to SHAKE for the explicit treatment of angular constraints," Computer physics communications, vol. 180, iss. 3, pp. 360-364, 2009.

[BibTeX] [Abstract] [PDF] [DOI]

This paper presents {\textvartheta}-SHAKE, an extension to SHAKE, an algorithm for the resolution of holonomic constraints in molecular dynamics simulations, which allows for the explicit treatment of angular constraints. We show that this treatment is more efficient than the use of fictitious bonds, significantly reducing the overlap between the individual constraints and thus accelerating convergence. The new algorithm is compared with SHAKE, M-SHAKE, the matrix-based approach described by Ciccotti and Ryckaert and P-SHAKE for rigid water and octane.

`@article{gonnet2009a, author = {Pedro Gonnet and Jens H. Walther and Petros Koumoutsakos}, doi = {10.1016/j.cpc.2008.10.020}, journal = {Computer Physics Communications}, month = {mar}, number = {3}, pages = {360--364}, publisher = {Elsevier {BV}}, title = {{}-{SHAKE}: An extension to {SHAKE} for the explicit treatment of angular constraints}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/gonnet2009a.pdf}, volume = {180}, year = {2009} }`

- N. Hansen, A. S. P. Niederberger, L. Guzzella, and P. Koumoutsakos, “A method for handling uncertainty in evolutionary optimization with an application to feedback control of combustion," IEEE transactions on evolutionary computation, vol. 13, iss. 1, pp. 180-197, 2009.

[BibTeX] [Abstract] [PDF] [DOI]

We present a novel method for handling uncertainty in evolutionary optimization. The method entails quantification and treatment of uncertainty and relies on the rank based selection operator of evolutionary algorithms. The proposed uncertainty handling is implemented in the context of the covariance matrix adaptation evolution strategy (CMA-ES) and verified on test functions. The present method is independent of the uncertainty distribution, prevents premature convergence of the evolution strategy and is well suited for online optimization as it requires only a small number of additional function evaluations. The algorithm is applied in an experimental setup to the online optimization of feedback controllers of thermoacoustic instabilities of gas turbine combustors. In order to mitigate these instabilities, gain-delay or model-based controllers sense the pressure and command secondary fuel injectors. The parameters of these controllers are usually specified via a trial and error procedure. We demonstrate that their online optimization with the proposed methodology enhances, in an automated fashion, the online performance of the controllers, even under highly unsteady operating conditions, and it also compensates for uncertainties in the model-building and design process.

`@article{hansen2009a, author = {N. Hansen and A.S.P. Niederberger and L. Guzzella and P. Koumoutsakos}, doi = {10.1109/tevc.2008.924423}, journal = {{IEEE} Transactions on Evolutionary Computation}, month = {feb}, number = {1}, pages = {180--197}, publisher = {Institute of Electrical and Electronics Engineers ({IEEE})}, title = {A Method for Handling Uncertainty in Evolutionary Optimization With an Application to Feedback Control of Combustion}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hansen2009a.pdf}, volume = {13}, year = {2009} }`

- H. A. Zambrano, J. H. Walther, P. Koumoutsakos, and I. F. Sbalzarini, “Thermophoretic motion of water nanodroplets confined inside carbon nanotubes," Nano letters, vol. 9, iss. 1, pp. 66-71, 2009.

[BibTeX] [Abstract] [PDF] [DOI]

We study the thermophoretic motion of water nanodroplets confined inside carbon nanotubes using molecular dynamics simulations. We find that the nanodroplets move in the direction opposite the imposed thermal gradient with a terminal velocity that is linearly proportional to the gradient. The translational motion is associated with a solid body rotation of the water nanodroplet coinciding with the helical symmetry of the carbon nanotube. The thermal diffusion displays a weak dependence on the wetting of the water-carbon nanotube interface. We introduce the use of the moment scaling spectrum (MSS) in order to determine the characteristics of the motion of the nanoparticles inside the carbon nanotube. The MSS indicates that affinity of the nanodroplet with the walls of the carbon nanotubes is important for the isothermal diffusion and hence for the Soret coefficient of the system.

`@article{zambrano2009b, author = {Harvey A. Zambrano and Jens H. Walther and Petros Koumoutsakos and Ivo F. Sbalzarini}, doi = {10.1021/nl802429s}, journal = {Nano Letters}, month = {jan}, number = {1}, pages = {66--71}, publisher = {American Chemical Society ({ACS})}, title = {Thermophoretic Motion of Water Nanodroplets Confined inside Carbon Nanotubes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/zambrano2009b.pdf}, volume = {9}, year = {2009} }`

- D. Rossinelli, M. Bergdorf, B. Hejazialhosseini, and P. Koumoutsakos, “Wavelet-based adaptive solvers on multi-core architectures for the simulation of complex systems," in Lecture notes in computer science, Springer Berlin Heidelberg, 2009, pp. 721-734.

[BibTeX] [Abstract] [PDF] [DOI]

We build wavelet-based adaptive numerical methods for the simulation of advection dominated flows that develop multiple spatial scales, with an emphasis on fluid mechanics problems. Wavelet based adaptivity is inherently sequential and in this work we demonstrate that these numerical methods can be implemented in software that is capable of harnessing the capabilities of multi-core architectures while maintaining their computational efficiency. Recent designs in frameworks for multi-core software development allow us to rethink parallelism as task-based, where parallel tasks are specified and automatically mapped into physical threads. This way of exposing parallelism enables the parallelization of algorithms that were considered inherently sequential, such as wavelet-based adaptive simulations. In this paper we present a framework that combines wavelet-based adaptivity with the task-based parallelism. We demonstrate good scaling performance obtained by simulating diverse physical systems on different multi-core and SMP architectures using up to 16 cores.

`@incollection{rossinelli2009a, author = {Diego Rossinelli and Michael Bergdorf and Babak Hejazialhosseini and Petros Koumoutsakos}, booktitle = {Lecture Notes in Computer Science}, doi = {10.1007/978-3-642-03869-3_68}, pages = {721--734}, publisher = {Springer Berlin Heidelberg}, title = {Wavelet-Based Adaptive Solvers on Multi-core Architectures for the Simulation of Complex Systems}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rossinelli2009a.pdf}, year = {2009} }`

- T. Gebäck, M. Schulz, P. Koumoutsakos, and M. Detmar, “Tscratch: a novel and simple software tool for automated analysis of monolayer wound healing assays.," Biotechniques, vol. 46, iss. 4, pp. 265-274, 2009.

[BibTeX] [Abstract] [PDF] [DOI]

Cell migration plays a major role in development, physiology, and disease, and is frequently evaluated in vitro by the monolayer wound healing assay. The assay analysis, however, is a time-consuming task that is often performed manually. In order to accelerate this analysis, we have developed TScratch, a new, freely available image analysis technique and associated software tool that uses the fast discrete curvelet transform to automate the measurement of the area occupied by cells in the images. This tool helps to significantly reduce the time needed for analysis and enables objective and reproducible quantification of assays. The software also offers a graphical user interface which allows easy inspection of analysis results and, if desired, manual modification of analysis parameters. The automated analysis was validated by comparing its results with manual-analysis results for a range of different cell lines. The comparisons demonstrate a close agreement for the vast majority of images that were examined and indicate that the present computational tool can reproduce statistically significant results in experiments with well-known cell migration inhibitors and enhancers.

`@article{geback2009b, author = {Geb{\"a}ck, Tobias and Schulz, MM and Koumoutsakos, Petros and Detmar, Michael}, doi = {10.2144/000113083}, journal = {Biotechniques}, number = {4}, pages = {265--274}, title = {TScratch: a novel and simple software tool for automated analysis of monolayer wound healing assays.}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/geback2009b.pdf}, volume = {46}, year = {2009} }`

- T. Gebäck and P. Koumoutsakos, “Edge detection in microscopy images using curvelets," BMC bioinformatics, vol. 10, iss. 1, p. 75, 2009.

[BibTeX] [Abstract] [PDF] [DOI]

Despite significant progress in imaging technologies, the efficient detection of edges and elongated features in images of intracellular and multicellular structures acquired using light or electron microscopy is a challenging and time consuming task in many laboratories. We present a novel method, based on the discrete curvelet transform, to extract a directional field from the image that indicates the location and direction of the edges. This directional field is then processed using the non-maximal suppression and thresholding steps of the Canny algorithm to trace along the edges and mark them. Optionally, the edges may then be extended along the directions given by the curvelets to provide a more connected edge map. We compare our scheme to the Canny edge detector and an edge detector based on Gabor filters, and show that our scheme performs better in detecting larger, elongated structures possibly composed of several step or ridge edges. The proposed curvelet based edge detection is a novel and competitive approach for imaging problems. We expect that the methodology and the accompanying software will facilitate and improve edge detection in images available using light or electron microscopy.

`@article{geback2009a, author = {Tobias Geb{\"a}ck and Petros Koumoutsakos}, doi = {10.1186/1471-2105-10-75}, journal = {{BMC} Bioinformatics}, number = {1}, pages = {75}, publisher = {Springer Nature}, title = {Edge detection in microscopy images using curvelets}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/geback2009a.pdf}, volume = {10}, year = {2009} }`

### 2008

- S. E. Hieber and P. Koumoutsakos, “A lagrangian particle method for the simulation of linear and nonlinear elastic models of soft tissue," Journal of computational physics, vol. 227, iss. 21, pp. 9195-9215, 2008.

[BibTeX] [Abstract] [PDF] [DOI]

We present a novel Lagrangian particle method for the simulation of linear and nonlinear elastic models of soft tissue.Linear solids are represented by the Lagrangian formulation of the stress{—}strain relationship that is extended to nonlinear solids by using the Lagrangian evolution of the deformation gradient described in a moving framework. The present method introduces a level set description, along with the particles, to capture the body deformations and to enforce theboundary conditions. Furthermore, the accuracy of the method in cases of large deformations is ensured by implementinga particle remeshing procedure. The method is validated in several benchmark problems, in two and three dimensions andthe results compare well with the results of respective finite elements simulations. In simulations of large solid deformationunder plane strain compression, the finite element solver exhibits spurious structures that are not present in the Lagrangianparticle simulations. The particle simulations are compared with experimental results in an aspiration test of liver tissue.

`@article{hieber2008b, author = {Simone E. Hieber and Petros Koumoutsakos}, doi = {10.1016/j.jcp.2008.05.016}, journal = {Journal of Computational Physics}, month = {nov}, number = {21}, pages = {9195--9215}, publisher = {Elsevier {BV}}, title = {A Lagrangian particle method for the simulation of linear and nonlinear elastic models of soft tissue}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hieber2008b.pdf}, volume = {227}, year = {2008} }`

- S. E. Hieber and P. Koumoutsakos, “An immersed boundary method for smoothed particle hydrodynamics of self-propelled swimmers," Journal of computational physics, vol. 227, iss. 19, pp. 8636-8654, 2008.

[BibTeX] [Abstract] [PDF] [DOI]

We present a novel particle method, combining remeshed Smoothed Particle Hydrodynamics with Immersed Boundary and Level Set techniques for the simulation of flows past complex deforming geometries. The present method retains the Lagrangian adaptivity of particle methods and relies on the remeshing of particle locations in order to ensure the accuracy of the method. In fact this remeshing step enables the introduction of Immersed Boundary Techniques used in grid based methods. The method is applied to simulations of flows of isothermal and compressible fluids past steady and unsteady solid boundaries that are described using a particle Level Set formulation. The method is validated with two and three-dimensional benchmark problems of flows past cylinders and spheres and it is shown to be well suited to simulations of large scale simulations using tens of millions of particles, on flow-structure interaction problems as they pertain to self-propelled anguilliform swimmers.

`@article{hieber2008a, author = {S.E. Hieber and P. Koumoutsakos}, doi = {10.1016/j.jcp.2008.06.017}, journal = {Journal of Computational Physics}, month = {oct}, number = {19}, pages = {8636--8654}, publisher = {Elsevier {BV}}, title = {An immersed boundary method for smoothed particle hydrodynamics of self-propelled swimmers}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hieber2008a.pdf}, volume = {227}, year = {2008} }`

- F. Milde, M. Bergdorf, and P. Koumoutsakos, “A hybrid model for three-dimensional simulations of sprouting angiogenesis," Biophysical journal, vol. 95, iss. 7, pp. 3146-3160, 2008.

[BibTeX] [Abstract] [PDF] [DOI]

Recent advances in cancer research have identified critical angiogenic signaling pathways and the influence of the extracellular matrix on endothelial cell migration. These findings provide us with insight into the process of angiogenesis that can facilitate the development of effective computational models of sprouting angiogenesis. In this work, we present the first 3D model of sprouting angiogenesis that consider explicitly the effect of the extracellular matrix and of the soluble as well as matrix bound growth factors on capillary growth. The computational model relies on a hybrid particle-mesh representation of the blood vessels and it introduces an implicit representation of the vasculature that can accommodate detailed descriptions of nutrient transport. Extensive parametric studies reveal the role of the extracellular matrix structure and the distribution of the different VEGF isoforms on the dynamics and the morphology of the generated vascular networks.

`@article{milde2008b, author = {Florian Milde and Michael Bergdorf and Petros Koumoutsakos}, doi = {10.1529/biophysj.107.124511}, journal = {Biophysical Journal}, month = {oct}, number = {7}, pages = {3146--3160}, publisher = {Elsevier {BV}}, title = {A Hybrid Model for Three-Dimensional Simulations of Sprouting Angiogenesis}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/milde2008b.pdf}, volume = {95}, year = {2008} }`

- D. Rossinelli and P. Koumoutsakos, “Vortex methods for incompressible flow simulations on the GPU," The visual computer, vol. 24, iss. 7-9, pp. 699-708, 2008.

[BibTeX] [Abstract] [PDF] [DOI]

We present a remeshed vortex particle method for incompressible flow simulations on GPUs. The particles are convected in a Lagrangian frame and are periodically reinitialized on a regular grid. The grid is used in addition to solve for the velocity{—}vorticity Poisson equation and for the computation of the diffusion operators. In the present GPU implementation of particle methods, the remeshing and the solution of the Poisson equation rely on fast and efficient mesh-particle interpolations. We demonstrate that particle remeshing introduces minimal artificial dissipation, enables a faster computation of differential operators on particles over grid-free techniques and can be efficiently implemented on GPUs. The results demonstrate that, contrary to common practice in particle simulations, it is necessary to remesh the (vortex) particle locations in order to solve accurately the equations they discretize, without compromising the speed of the method. The present method leads to simulations of incompressible vortical flows on GPUs with unprecedented accuracy and efficiency.

`@article{rossinelli2008a, author = {Diego Rossinelli and Petros Koumoutsakos}, doi = {10.1007/s00371-008-0250-z}, journal = {The Visual Computer}, month = {may}, number = {7-9}, pages = {699--708}, publisher = {Springer Nature}, title = {Vortex methods for incompressible flow simulations on the {GPU}}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rossinelli2008a.pdf}, volume = {24}, year = {2008} }`

- G. Morra, P. Chatelain, P. Tackley, and P. Koumoutsakos, “Earth curvature effects on subduction morphology: modeling subduction in a spherical setting," Acta geotechnica, vol. 4, iss. 2, pp. 95-105, 2008.

[BibTeX] [Abstract] [PDF] [DOI]

{We present here the first application in Geodynamics of a (Fast ultipole) Accelerated Boundary Element Method (Accelerated-BEM) for tokes flow. The approach offers the advantages of a reduced number of computational elements and linear scaling with the problem size. We show that this numerical method can be fruitfully applied to the simulation of several geodynamic systems at the planetary scale in spherical coordinates and we suggest a general approach for modeling combined mantle convection and plate tectonics. The first part of the paper is devoted to the technical exposition of the new approach, while the second part focuses on the effect layed by Earth curvature on the subduction of a very wide oceanic ithosphere (W = 6000km and W = 9000km), comparing the effects of two different planetary radiuses (ER = 6371km

`@article{morra2008a, author = {Gabriele Morra and Philippe Chatelain and Paul Tackley and Petros Koumoutsakos}, doi = {10.1007/s11440-008-0060-5}, journal = {Acta Geotechnica}, month = {may}, number = {2}, pages = {95--105}, publisher = {Springer Nature}, title = {Earth curvature effects on subduction morphology: Modeling subduction in a spherical setting}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/morra2008a.pdf}, volume = {4}, year = {2008} }`

- U. Zimmerli and P. Koumoutsakos, “Simulations of electrophoretic RNA transport through transmembrane carbon nanotubes," Biophysical journal, vol. 94, iss. 7, pp. 2546-2557, 2008.

[BibTeX] [Abstract] [PDF] [DOI]

The study of interactions between carbon nanotubes and cellular components, such as membranes and biomolecules, is fundamental for the rational design of nanodevices interfacing with biological systems. In this work, we use molecular dynamics simulations to study the electrophoretic transport of RNA through carbon nanotubes, embedded in membranes. Decorated and naked carbon nanotubes are inserted into a dodecane membrane and a dimyristoylphosphatidylcholine lipid bilayer, and the system is subjected to electrostatic potential differences. The transport properties of this artificial pore are determined by the structural modifications of the membrane in the vicinity of the nanotube openings and they are quantified by the nonuniform electrostatic potential maps at the entrance and inside the nanotube. The pore is used to transport electrophoretically a short RNA segment and we find that the speed of translocation exhibits an exponential dependence on the applied potential differences. The RNA is transported while undergoing a repeated stacking and unstacking process, affected by steric interactions with the membrane headgroups and by hydrophobic interaction with the walls of the nanotube. The RNA is structurally reorganized inside the nanotube, with its backbone solvated by water molecules near the axis of the tube and its bases aligned with the nanotube walls. Upon exiting the pore, the RNA interacts with the membrane headgroups and remains attached to the dodecane membrane while it is expelled into the solvent in the case of the lipid bilayer. The results of the simulations detail processes of molecular transport into cellular compartments through manufactured nanopores and they are discussed in the context of applications in biotechnology and nanomedicine.

`@article{zimmerli2008a, author = {Urs Zimmerli and Petros Koumoutsakos}, doi = {10.1529/biophysj.106.102467}, journal = {Biophysical Journal}, month = {apr}, number = {7}, pages = {2546--2557}, publisher = {Elsevier {BV}}, title = {Simulations of Electrophoretic {RNA} Transport Through Transmembrane Carbon Nanotubes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/zimmerli2008a.pdf}, volume = {94}, year = {2008} }`

- A. Dupuis, P. Chatelain, and P. Koumoutsakos, “An immersed boundary—lattice-boltzmann method for the simulation of the flow past an impulsively started cylinder," Journal of computational physics, vol. 227, iss. 9, pp. 4486-4498, 2008.

[BibTeX] [Abstract] [PDF] [DOI]

We present a lattice-Boltzmann method coupled with an immersed boundary technique for the simulation of bluff body lows. The lattice-Boltzmann method for the modeling of the Navier{—}Stokes equations, is enhanced by a forcing term to ccount for the no-slip boundary condition on a non-grid conforming boundary. We investigate two alternatives of coupling he boundary forcing term with the grid nodes, namely the direct and the interpolated forcing techniques. The present B{—}IB methods are validated in simulations of the incompressible flow past an impulsively started cylinder at low and oderate Reynolds numbers. We present diagnostics such as the near wall vorticity field and the drag coefficient and comparisons ith previous computational and experimental works and assess the advantages and drawbacks of the two techniques. 2008 Elsevier Inc. All rights reserved.

`@article{dupuis2008a, author = {Alexandre Dupuis and Philippe Chatelain and Petros Koumoutsakos}, doi = {10.1016/j.jcp.2008.01.009}, journal = {Journal of Computational Physics}, month = {apr}, number = {9}, pages = {4486--4498}, publisher = {Elsevier {BV}}, title = {An immersed boundary{\textendash}lattice-Boltzmann method for the simulation of the flow past an impulsively started cylinder}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/dupuis2008a.pdf}, volume = {227}, year = {2008} }`

- P. Poncet, R. Hildebrand, G. -H. Cottet, and P. Koumoutsakos, “Spatially distributed control for optimal drag reduction of the flow past a circular cylinder," Journal of fluid mechanics, vol. 599, 2008.

[BibTeX] [Abstract] [PDF] [DOI]

We report high drag reduction in direct numerical simulations of controlled flows past ircular cylinders at Reynolds numbers of 300 and 1000. The flow is controlled by the zimuthal component of the tangential velocity of the cylinder surface. Starting from spanwise-uniform velocity profile that leads to high drag reduction, the optimization rocedure identifies, for the same energy input, spanwise-varying velocity profiles that ead to higher drag reduction. The three-dimensional variations of the velocity field, orresponding to modes A and B of three-dimensional wake instabilities, are largely esponsible for this drag reduction. The spanwise wall velocity variations introduce treamwise vortex braids in the wake that are responsible for reducing the drag nduced by the primary spanwise vortices shed by the cylinder. The results demonstrate hat extending two-dimensional controllers to three-dimensional flows is not optimal s three-dimensional control strategies can lead efficiently to higher drag reduction.

`@article{poncet2008a, author = {Poncet, P. and Hildebrand, R. and Cottet, G.-H. and Koumoutsakos, P.}, doi = {10.1017/s0022112008000177}, journal = {Journal of Fluid Mechanics}, month = {mar}, publisher = {Cambridge University Press ({CUP})}, title = {Spatially distributed control for optimal drag reduction of the flow past a circular cylinder}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/poncet2008a.pdf}, volume = {599}, year = {2008} }`

- P. Chatelain, A. Curioni, M. Bergdorf, D. Rossinelli, W. Andreoni, and P. Koumoutsakos, “Billion vortex particle direct numerical simulations of aircraft wakes," Computer methods in applied mechanics and engineering, vol. 197, iss. 13-16, pp. 1296-1304, 2008.

[BibTeX] [Abstract] [PDF] [DOI]

We present the Direct Numerical Simulations of high Reynolds numbers aircraft wakes employing vortex particle methods. The simulations involve a highly efficient implementation of vortex methods on massively parallel computers, enabling unprecedented simulations using billions of particles. The method relies on the Lagrangian discretization of the Navier-Stokes equations in vorticity-velocity form and relies on remeshing of the particles in order to ensure the convergence of the method. The remeshed particle locations are utilized for the computation of the field quantities, the discretization of the differential operators for diffusion and vortex stretching, and the solution of the Poisson equation for the advection velocity field. The method exhibits excellent scalability up to 16k BG/L nodes. The results include unprecedented Direct Numerical Simulations of the onset and the evolution of multiple wavelength instabilities induced by ambient noise in aircraft vortex wakes at Re = 6000. (c) 2007 Elsevier B.V. All rights reserved.

`@article{chatelain2008b, author = {Philippe Chatelain and Alessandro Curioni and Michael Bergdorf and Diego Rossinelli and Wanda Andreoni and Petros Koumoutsakos}, doi = {10.1016/j.cma.2007.11.016}, journal = {Computer Methods in Applied Mechanics and Engineering}, month = {feb}, number = {13-16}, pages = {1296--1304}, publisher = {Elsevier {BV}}, title = {Billion vortex particle direct numerical simulations of aircraft wakes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/chatelain2008b.pdf}, volume = {197}, year = {2008} }`

- D. Rossinelli, B. Bayati, and P. Koumoutsakos, “Accelerated stochastic and hybrid methods for spatial simulations of reaction—diffusion systems," Chemical physics letters, vol. 451, iss. 1-3, pp. 136-140, 2008.

[BibTeX] [Abstract] [PDF] [DOI]

Spatial distributions characterize the evolution of reaction-diffusion models of several physical, chemical, and biological systems. We present two novel algorithms for the efficient simulation of these models: Spatial tau-Leaping (S tau-Leaping), employing a unified acceleration of the stochastic simulation of reaction and diffusion, and Hybrid tau-Leaping (H tau-Leaping), combining a deterministic diffusion approximation with a tau-Leaping acceleration of the stochastic reactions. The algorithms are validated by solving Fisher’s equation and used to explore the role of the number of particles in pattern formation. The results indicate that the present algorithms have a nearly constant time complexity with respect to the number of events (reaction and diffusion), unlike the exact stochastic simulation algorithm which scales linearly.

`@article{rossinelli2008b, author = {Diego Rossinelli and Basil Bayati and Petros Koumoutsakos}, doi = {10.1016/j.cplett.2007.11.055}, journal = {Chemical Physics Letters}, month = {jan}, number = {1-3}, pages = {136--140}, publisher = {Elsevier {BV}}, title = {Accelerated stochastic and hybrid methods for spatial simulations of reaction{\textendash}diffusion systems}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rossinelli2008b.pdf}, volume = {451}, year = {2008} }`

- E. M. Kotsalis and P. Koumoutsakos, “A control algorithm for multiscale simulations of liquid water," in Computational science — ICCS 2008, Springer Berlin Heidelberg, 2008, pp. 234-241.

[BibTeX] [Abstract] [PDF] [DOI]

We present multiscale simulations of liquid water using a novel control algorithm to couple non-periodic molecular dynamics (MD) and continuum descriptions in the context of a Schwarz alternating method. In the present multiscale approach the non-periodic MD simulations are enhanced by an effective external boundary force that accounts for the virial component of the pressure and eliminates spurious density oscillations close to the boundary. This force is determined by a simple control algorithm that enables coupling of the atomistic description to a coarse grained or a continuum description of liquid water. The proposed computational method is validated in the case of equilibrium and parallel flow.

`@incollection{kotsalis2008a, author = {Evangelos M. Kotsalis and Petros Koumoutsakos}, booktitle = {Computational Science {\textendash} {ICCS} 2008}, doi = {10.1007/978-3-540-69387-1_26}, pages = {234--241}, publisher = {Springer Berlin Heidelberg}, title = {A Control Algorithm for Multiscale Simulations of Liquid Water}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/kotsalis2008a.pdf}, year = {2008} }`

- P. Chatelain, A. Curioni, M. Bergdorf, D. Rossinelli, W. Andreoni, and P. Koumoutsakos, “Vortex methods for massively parallel computer architectures," High performance computing for computational science-vecpar 2008, pp. 479-489, 2008.

[BibTeX] [Abstract] [PDF] [DOI]

We present Vortex Methods implemented in massively parallel computer architectures for the direct Numerical Simulations of high Reynolds numbers flows. Periodic and non-periodic domains are considered leading to unprecedented simulations using billions of particles. We discuss the implementation performance of the method up to 1.6k IBM BG/L nodes and the evolutionary optimization of long wavelength stabilities in aircraft wakes.

`@article{chatelain2008a, author = {Chatelain, Philippe and Curioni, Alessandro and Bergdorf, Michael and Rossinelli, Diego and Andreoni, Wanda and Koumoutsakos, Petros}, doi = {10.1007/978-3-540-92859-1_42}, journal = {High Performance Computing for Computational Science-VECPAR 2008}, pages = {479--489}, publisher = {Springer}, title = {Vortex methods for massively parallel computer architectures}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/chatelain2008a.pdf}, year = {2008} }`

- K. Fukagata, S. Kern, P. Chatelain, P. Koumoutsakos, and N. Kasagi, “Evolutionary optimization of an anisotropic compliant surface for turbulent friction drag reduction," Journal of turbulence, vol. 9, 2008.

[BibTeX] [Abstract] [PDF] [DOI]

Direct numerical simulation (DNS) of the channel {fl}ow with an anisotropic compliant surface is performed in order to investigate its drag reduction effect in a fully developed turbulent {fl}ow. The computational domain is set to be 3{δ} {\texttimes} 2{δ} {\texttimes} 3{δ} , where {δ} is the channel half-width. The surface is passively driven by the pressure and wall-shear stress {fl}uctuations, and the surface velocity provides a boundary condition for the {fl}uid velocity {fi}eld. An evolutionary optimization method (CMA-ES) is used to optimize the parameters of the anisotropic compliant surface. The optimization identi{fi}es several sets of parameters that result in a reduction of the friction drag with a maximum reduction rate of 8%. The primary mechanism for drag reduction is attributed to the decrease of the Reynolds shear stress (RSS) near the wall induced by the kinematics of the surface. The resultant wall motion is a uniform wave traveling downstream. The compliant wall, with the parameters found in the optimization study, is also tested in a computational domain that is doubled in the streamwise direction. The drag, however, is found to increase in the larger computational domain due to excessively large wall-normal velocity {fl}uctuations.

`@article{fukagata2008a, author = {Koji Fukagata and Stefan Kern and Philippe Chatelain and Petros Koumoutsakos and Nobuhide Kasagi}, doi = {10.1080/14685240802441126}, journal = {Journal of Turbulence}, publisher = {Informa {UK} Limited}, title = {Evolutionary optimization of an anisotropic compliant surface for turbulent friction drag reduction}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/fukagata2008a.pdf}, volume = {9}, year = {2008} }`

- B. Bayati, P. Chatelain, and P. Koumoutsakos, “Multiresolution stochastic simulations of reaction—diffusion processes," Physical chemistry chemical physics, vol. 10, iss. 39, p. 5963, 2008.

[BibTeX] [Abstract] [PDF] [DOI]

Stochastic simulations of reaction{—}diffusion processes are used extensively for the modeling of complex systems in areas ranging from biology and social sciences to ecosystems and materials processing. These processes often exhibit disparate scales that render their simulation prohibitive even for massive computational resources. The problem is resolved by introducing a novel stochastic multiresolution method that enables the efficient simulation of reaction{—}diffusion processes as modeled by many-particle systems. The proposed method quantifies and efficiently handles the associated stiffness in simulating the system dynamics and its computational efficiency and accuracy are demonstrated in simulations of a model problem described by the Fisher{—}Kolmogorov equation. The method is general and can be applied to other many-particle models of physical processes.

`@article{bayati2008a, author = {Basil Bayati and Philippe Chatelain and Petros Koumoutsakos}, doi = {10.1039/b810795e}, journal = {Physical Chemistry Chemical Physics}, number = {39}, pages = {5963}, publisher = {Royal Society of Chemistry ({RSC})}, title = {Multiresolution stochastic simulations of reaction{\textendash}diffusion processes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bayati2008a.pdf}, volume = {10}, year = {2008} }`

- P. Koumoutsakos, “Multiscale modeling and simulation for fluid mechanics at the nanoscale," Carbon nanotube devices: properties, modeling, integration and applications, pp. 229-290, 2008.

[BibTeX] [DOI]`@article{koumoutsakos2008a, author = {Koumoutsakos, Petros}, doi = {10.1002/9783527622597.ch6}, journal = {Carbon Nanotube Devices: Properties, Modeling, Integration and Applications}, pages = {229--290}, publisher = {Wiley Online Library}, title = {Multiscale Modeling and Simulation for Fluid Mechanics at the Nanoscale}, year = {2008} }`

- F. Milde, M. Bergdorf, and P. Koumoutsakos, “A hybrid model of sprouting angiogenesis," in Computational science — ICCS 2008, Springer Berlin Heidelberg, 2008, pp. 167-176.

[BibTeX] [Abstract] [PDF] [DOI]

We present a computational model of tumor induced sprouting angiogenesis that involves a novel coupling of particle-continuum descriptions. The present 3D model of sprouting angiogenesis accounts for the effect of the extracellular matrix on capillary growth and considers both soluble and matrix-bound growth factors. The results of the simulations emphasize the role of the extracellular matrix and the different VEGF isoforms on branching behavior and the morphology of generated vascular networks.

`@incollection{milde2008a, author = {Florian Milde and Michael Bergdorf and Petros Koumoutsakos}, booktitle = {Computational Science {\textendash} {ICCS} 2008}, doi = {10.1007/978-3-540-69387-1_19}, pages = {167--176}, publisher = {Springer Berlin Heidelberg}, title = {A Hybrid Model of Sprouting Angiogenesis}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/milde2008a.pdf}, year = {2008} }`

### 2007

- J. O. Ramsay, G. Hooker, D. Campbell, and J. Cao, “Parameter estimation for differential equations: a generalized smoothing approach," Journal of the royal statistical society: series b (statistical methodology), vol. 69, iss. 5, pp. 741-796, 2007.

[BibTeX] [DOI]`@article{ramsay2007a, author = {J. O. Ramsay and G. Hooker and D. Campbell and J. Cao}, doi = {10.1111/j.1467-9868.2007.00610.x}, journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)}, month = {oct}, number = {5}, pages = {741--796}, publisher = {Wiley-Blackwell}, title = {Parameter estimation for differential equations: a generalized smoothing approach}, volume = {69}, year = {2007} }`

- J. A. Helmuth, C. J. Burckhardt, P. Koumoutsakos, U. F. Greber, and I. F. Sbalzarini, “A novel supervised trajectory segmentation algorithm identifies distinct types of human adenovirus motion in host cells," Journal of structural biology, vol. 159, iss. 3, pp. 347-358, 2007.

[BibTeX] [Abstract] [PDF] [DOI]

Biological trajectories can be characterized by transient patterns that may provide insight into the interactions of the moving object with its immediate environment. The accurate and automated identification of trajectory motifs is important for the understanding of the underlying mechanisms. In this work, we develop a novel trajectory segmentation algorithm based on supervised support vector classification. The algorithm is validated on synthetic data and applied to the identification of trajectory fingerprints of fluorescently tagged human adenovirus particles in live cells. In virus trajectories on the cell surface, periods of confined motion, slow drift, and fast drift are efficiently detected. Additionally, directed motion is found for viruses in the cytoplasm. The algorithm enables the linking of microscopic observations to molecular phenomena that are critical in many biological processes, including infectious pathogen entry and signal transduction. (c) 2007 Elsevier Inc. All rights reserved.

`@article{helmuth2007a, author = {Jo A. Helmuth and Christoph J. Burckhardt and Petros Koumoutsakos and Urs F. Greber and Ivo F. Sbalzarini}, doi = {10.1016/j.jsb.2007.04.003}, journal = {Journal of Structural Biology}, month = {sep}, number = {3}, pages = {347--358}, publisher = {Elsevier {BV}}, title = {A novel supervised trajectory segmentation algorithm identifies distinct types of human adenovirus motion in host cells}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/helmuth2007a.pdf}, volume = {159}, year = {2007} }`

- S. Kern, P. Koumoutsakos, and K. Eschler, “Optimization of anguilliform swimming," Physics of fluids, vol. 19, iss. 9, p. 91102, 2007.

[BibTeX] [PDF] [DOI]`@article{kern2007a, author = {S. Kern and P. Koumoutsakos and Kristina Eschler}, doi = {10.1063/1.2774981}, journal = {Physics of Fluids}, month = {sep}, number = {9}, pages = {091102}, publisher = {{AIP} Publishing}, title = {Optimization of anguilliform swimming}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/kern2007a.pdf}, volume = {19}, year = {2007} }`

- A. M. Altenhoff, J. H. Walther, and P. Koumoutsakos, “A stochastic boundary forcing for dissipative particle dynamics," Journal of computational physics, vol. 225, iss. 1, pp. 1125-1136, 2007.

[BibTeX] [Abstract] [PDF] [DOI]

The method of dissipative particle dynamics (DPD) is an effective, coarse grained model of the hydrodynamics of complex fluids. DPD simulations of wall-bounded flows are however often associated with spurious fluctuations of the fluid properties near the wall. We present a novel stochastic boundary forcing for DPD simulations of wall-bounded flows, based on the identification of fluctuations in simulations of the corresponding homogeneous system at equilibrium. The present method is shown to enforce accurately the no-slip boundary condition, while minimizing spurious fluctuations of material properties, in a number of benchmark problems. (c) 2007 Elsevier Inc. All rights reserved.

`@article{altenhoff2007a, author = {Adrian M. Altenhoff and Jens H. Walther and Petros Koumoutsakos}, doi = {10.1016/j.jcp.2007.01.015}, journal = {Journal of Computational Physics}, month = {jul}, number = {1}, pages = {1125--1136}, publisher = {Elsevier {BV}}, title = {A stochastic boundary forcing for dissipative particle dynamics}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/altenhoff2007a.pdf}, volume = {225}, year = {2007} }`

- E. M. Kotsalis, J. H. Walther, and P. Koumoutsakos, “Control of density fluctuations in atomistic-continuum simulations of dense liquids," Physical review e, vol. 76, iss. 1, 2007.

[BibTeX] [Abstract] [PDF] [DOI]

We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system with a continuum solver for the simulation of the Navier-Stokes equations. The lack of periodic boundary conditions in the molecular dynamics simulations hinders the proper accounting for the virial pressure leading to spurious density fluctuations at the continuum-atomistic interface. An ad hoc boundary force is usually employed to remedy this situation. We propose the calculation of this boundary force using a control algorithm that explicitly cancels the density fluctuations. The results demonstrate that the present approach outperforms state-of-the-art algorithms. The conceptual and algorithmic simplicity of the method makes it suitable for any type of coupling between atomistic and continuum descriptions of dense fluids.

`@article{kotsalis2007a, author = {E. M. Kotsalis and J. H. Walther and P. Koumoutsakos}, doi = {10.1103/physreve.76.016709}, journal = {Physical Review E}, month = {jul}, number = {1}, publisher = {American Physical Society ({APS})}, title = {Control of density fluctuations in atomistic-continuum simulations of dense liquids}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/kotsalis2007a.pdf}, volume = {76}, year = {2007} }`

- P. A. E. Schoen, J. H. Walther, D. Poulikakos, and P. Koumoutsakos, “Phonon assisted thermophoretic motion of gold nanoparticles inside carbon nanotubes," Applied physics letters, vol. 90, iss. 25, p. 253116, 2007.

[BibTeX] [Abstract] [PDF] [DOI]

The authors investigate the thermally driven mass transport of gold nanoparticles confined inside carbon nanotubes using molecular dynamics simulations. The observed thermophoretic motion of the gold nanoparticles correlates with the phonon dispersion exhibited by a standard carbon nanotube and, in particular, with the breathing mode of the tube. Additionally, the results show an increased static friction for gold nanoparticles confines inside a zig-zag carbon nanotube when increasing the size (length) of the nanoparticles. However, an unexpected, opposite trend is observed for the same nanoparticles inside armchair tubes. (c) 2007 American Institute of Physics.

`@article{schoen2007a, author = {Philipp A. E. Schoen and Jens H. Walther and Dimos Poulikakos and Petros Koumoutsakos}, doi = {10.1063/1.2748367}, journal = {Applied Physics Letters}, month = {jun}, number = {25}, pages = {253116}, publisher = {{AIP} Publishing}, title = {Phonon assisted thermophoretic motion of gold nanoparticles inside carbon nanotubes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/schoen2007a.pdf}, volume = {90}, year = {2007} }`

- A. Dupuis, E. M. Kotsalis, and P. Koumoutsakos, “Coupling lattice boltzmann and molecular dynamics models for dense fluids," Physical review e, vol. 75, iss. 4, 2007.

[BibTeX] [Abstract] [PDF] [DOI]

We propose a hybrid model, coupling lattice Boltzmann (LB) and molecular dynamics (MD) models, for the simulation of dense fluids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The MD and LB formulations communicate via the exchange of velocities and velocity gradients at the interface. We validate the present LB-MD model in simulations of two- and three-dimensional flows of liquid argon past and through a carbon nanotube. Comparisons with existing hybrid algorithms and with reference MD solutions demonstrate the validity of the present approach.

`@article{dupuis2007b, author = {A. Dupuis and E. M. Kotsalis and P. Koumoutsakos}, doi = {10.1103/physreve.75.046704}, journal = {Physical Review E}, month = {apr}, number = {4}, publisher = {American Physical Society ({APS})}, title = {Coupling lattice Boltzmann and molecular dynamics models for dense fluids}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/dupuis2007b.pdf}, volume = {75}, year = {2007} }`

- A. Dupuis and P. Koumoutsakos, “Effects of atomistic domain size on hybrid lattice boltzmann—molecular dynamics simulations of dense fluids," International journal of modern physics c, vol. 18, iss. 04, pp. 644-651, 2007.

[BibTeX] [Abstract] [PDF] [DOI]

We present a convergence study for a hybrid Lattice Boltzmann-Molecular Dynamics model for the simulation of dense liquids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The velocity field from the atomistic domain is introduced as forcing terms to the Lattice Boltzmann model of the continuum while the mean field of the continuum imposes mean field conditions for the atomistic domain. In the present paper we investigate the effect of varying the size of the atomistic subdomain in simulations of two dimensional flows of liquid argon past carbon nanotubes and assess the efficiency of the method.

`@article{dupuis2007a, author = {Dupuis, A. and Koumoutsakos, P.}, doi = {10.1142/s0129183107010899}, journal = {International Journal of Modern Physics C}, month = {apr}, number = {04}, pages = {644--651}, publisher = {World Scientific Pub Co Pte Lt}, title = {Effects of Atomistic Domain Size on Hybrid Lattice Boltzmann{\textendash}Molecular Dynamics Simulations of Dense Fluids}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/dupuis2007a.pdf}, volume = {18}, year = {2007} }`

- P. Chatelain, G. -H. Cottet, and P. Koumoutsakos, “Particle mesh hydrodynamics for astrophysics simulations," International journal of modern physics c, vol. 18, iss. 04, pp. 610-618, 2007.

[BibTeX] [Abstract] [PDF] [DOI]

We present a particle method for the simulation of three dimensional compressible hydrodynamics based on a hybrid Particle-Mesh discretization of the governing equations. The method is rooted on the regularization of particle locations as in remeshed Smoothed Particle Hydrodynamics (rSPH). The rSPH method was recently introduced to remedy problems associated with the distortion of computational elements in SPH, by periodically re-initializing the particle positions and by using high order interpolation kernels. In the PMH formulation, the particles solely handle the convective part of the compressible Euler equations. The particle quantities are then interpolated onto a mesh, where the pressure terms are computed. PMH, like SPH, is free of the convection CFL condition while at the same time it is more efficient as derivatives are computed on a mesh rather than particle-particle interactions. PMH does not detract from the adaptive character of SPH and allows for control of its accuracy. We present simulations of a benchmark astrophysics problem demonstrating the capabilities of this approach.

`@article{chatelain2007a, author = {Chatelain, P. and Cottet, G.-H. and Koumoutsakos, P.}, doi = {10.1142/s0129183107010851}, journal = {International Journal of Modern Physics C}, month = {apr}, number = {04}, pages = {610--618}, publisher = {World Scientific Pub Co Pte Lt}, title = {Particle Mesh Hydrodynamics for Astrophysics Simulations}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/chatelain2007a.pdf}, volume = {18}, year = {2007} }`

- M. Bergdorf, P. Koumoutsakos, and A. Leonard, “Direct numerical simulations of vortex rings at Re_Γ= 7500," Journal of fluid mechanics, vol. 581, pp. 495-505, 2007.

[BibTeX] [Abstract] [PDF]

We present direct numerical simulations of the turbulent decay of vortex rings with Re-Gamma = 7500. We analyse the vortex dynamics during the nonlinear stage of the instability along with the structure of the vortex wake during the turbulent stage. These simulations enable the quantification of vorticity dynamics and their correlation with structures from dye visualization and the observations of circulation decay that have been reported in related experimental works. Movies are available with the online version of the paper.

`@article{bergdorf2007a, author = {Bergdorf, Michael and Koumoutsakos, Petros and Leonard, Anthony}, journal = {Journal of Fluid Mechanics}, pages = {495--505}, publisher = {Cambridge University Press}, title = {Direct numerical simulations of vortex rings at = 7500}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bergdorf2007a.pdf}, volume = {581}, year = {2007} }`

### 2006

- S. Kern and P. Koumoutsakos, “Simulations of optimized anguilliform swimming," Journal of experimental biology, vol. 209, iss. 24, pp. 4841-4857, 2006.

[BibTeX] [Abstract] [PDF] [DOI]

The hydrodynamics of anguilliform swimming motions was investigated using three-dimensional simulations of the fluid flow past a self-propelled body. The motion of the body is not specified a priori, but is instead obtained through an evolutionary algorithm used to optimize the swimming efficiency and the burst swimming speed. The results of the present simulations support the hypothesis that anguilliform swimmers modify their kinematics according to different objectives and provide a quantitative analysis of the swimming motion and the forces experienced by the body. The kinematics of burst swimming is characterized by the large amplitude of the tail undulations while the anterior part of the body remains straight. In contrast, during efficient swimming behavior significant lateral undulation occurs along the entire length of the body. In turn, during burst swimming, the majority of the thrust is generated at the tail, whereas in the efficient swimming mode, in addition to the tail, the middle of the body contributes significantly to the thrust. The burst swimming velocity is 42% higher and the propulsive efficiency is 15% lower than the respective values during efficient swimming. The wake, for both swimming modes, consists largely of a double row of vortex rings with an axis aligned with the swimming direction. The vortex rings are responsible for producing lateral jets of fluid, which has been documented in prior experimental studies. We note that the primary wake vortices are qualitatively similar in both swimming modes except that the wake vortex rings are stronger and relatively more elongated in the fast swimming mode. The present results provide quantitative information of three-dimensional fluid-body interactions that may complement related experimental studies. In addition they enable a detailed quantitative analysis, which may be difficult to obtain experimentally, of the different swimming modes linking the kinematics of the motion with the forces acting on the self-propelled body. Finally, the optimization procedure helps to identify, in a systematic fashion, links between swimming motion and biological function.

`@article{kern2006b, author = {S. Kern and P. Koumoutsakos}, doi = {10.1242/jeb.02526}, journal = {Journal of Experimental Biology}, month = {dec}, number = {24}, pages = {4841--4857}, publisher = {The Company of Biologists}, title = {Simulations of optimized anguilliform swimming}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/kern2006b.pdf}, volume = {209}, year = {2006} }`

- P. A. E. Schoen, J. H. Walther, S. Arcidiacono, D. Poulikakos, and P. Koumoutsakos, “Nanoparticle traffic on helical tracks: thermophoretic mass transport through carbon nanotubes," Nano letters, vol. 6, iss. 9, pp. 1910-1917, 2006.

[BibTeX] [Abstract] [PDF] [DOI]

Using molecular dynamics simulations, we demonstrate and quantify thermophoretic motion of solid gold nanoparticles inside carbon nanotubes subject to wall temperature gradients ranging from 0.4 to 25 K/nm. For temperature gradients below 1 K/nm, we find that the particles move “on tracks" in a predictable fashion as they follow unique helical orbits depending on the geometry of the carbon nanotubes. These findings markedly advance our knowledge of mass transport mechanisms relevant to nanoscale applications.

`@article{schoen2006a, author = {Philipp A. E. Schoen and Jens H. Walther and Salvatore Arcidiacono and Dimos Poulikakos and Petros Koumoutsakos}, doi = {10.1021/nl060982r}, journal = {Nano Letters}, month = {sep}, number = {9}, pages = {1910--1917}, publisher = {American Chemical Society ({ACS})}, title = {Nanoparticle Traffic on Helical Tracks: Thermophoretic Mass Transport through Carbon Nanotubes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/schoen2006a.pdf}, volume = {6}, year = {2006} }`

- A. Auger, P. Chatelain, and P. Koumoutsakos, “R-leaping: accelerating the stochastic simulation algorithm by reaction leaps," The journal of chemical physics, vol. 125, iss. 8, p. 84103, 2006.

[BibTeX] [Abstract] [PDF] [DOI]

A novel algorithm is proposed for the acceleration of the exact stochastic simulation algorithm by a predefined number of reaction firings (R-leaping) that may occur across several reaction channels. In the present approach, the numbers of reaction firings are correlated binomial distributions and the sampling procedure is independent of any permutation of the reaction channels. This enables the algorithm to efficiently handle large systems with disparate rates, providing substantial computational savings in certain cases. Several mechanisms for controlling the accuracy and the appearance of negative species are described. The advantages and drawbacks of R-leaping are assessed by simulations on a number of benchmark problems and the results are discussed in comparison with established methods.

`@article{auger2006a, author = {Anne Auger and Philippe Chatelain and Petros Koumoutsakos}, doi = {10.1063/1.2218339}, journal = {The Journal of Chemical Physics}, month = {aug}, number = {8}, pages = {084103}, publisher = {{AIP} Publishing}, title = {R-leaping: Accelerating the stochastic simulation algorithm by reaction leaps}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/auger2006a.pdf}, volume = {125}, year = {2006} }`

- I. F. Sbalzarini, J. H. Walther, M. Bergdorf, S. E. Hieber, E. M. Kotsalis, and P. Koumoutsakos, “PPM — a highly efficient parallel particle—mesh library for the simulation of continuum systems," Journal of computational physics, vol. 215, iss. 2, pp. 566-588, 2006.

[BibTeX] [Abstract] [PDF] [DOI]

This paper presents a highly efficient parallel particle-mesh (PPM) library, based on a unifying particle formulation for the simulation of continuous systems. In this formulation, the grid-free character of particle methods is relaxed by the introduction of a mesh for the reinitialization of the particles, the computation of the field equations, and the discretization of differential operators. The present utilization of the mesh does not detract from the adaptivity, the efficient handling of complex geometries, the minimal dissipation, and the good stability properties of particle methods. The coexistence of meshes and particles, allows for the development of a consistent and adaptive numerical method, but it presents a set of challenging parallelization issues that have hindered in the past the broader use of particle methods. The present library solves the key parallelization issues involving particle-mesh interpolations and the balancing of processor particle loading, using a novel adaptive tree for mixed domain decompositions along with a coloring scheme for the particle-mesh interpolation. The high parallel efficiency of the library is demonstrated in a series of benchmark tests on distributed memory and on a shared-memory vector architecture. The modularity of the method is shown by a range of simulations, from compressible vortex rings using a novel formulation of smooth particle hydrodynamics, to simulations of diffusion in real biological cell organelles. The present library enables large scale simulations of diverse physical problems using adaptive particle methods and provides a computational tool that is a viable alternative to mesh-based methods.

`@article{sbalzarini2006c, author = {I.F. Sbalzarini and J.H. Walther and M. Bergdorf and S.E. Hieber and E.M. Kotsalis and P. Koumoutsakos}, doi = {10.1016/j.jcp.2005.11.017}, journal = {Journal of Computational Physics}, month = {jul}, number = {2}, pages = {566--588}, publisher = {Elsevier {BV}}, title = {{PPM} {\textendash} A highly efficient parallel particle{\textendash}mesh library for the simulation of continuum systems}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/sbalzarini2006c.pdf}, volume = {215}, year = {2006} }`

- K. Fukagata, N. Kasagi, and P. Koumoutsakos, “A theoretical prediction of friction drag reduction in turbulent flow by superhydrophobic surfaces," Physics of fluids, vol. 18, iss. 5, p. 51703, 2006.

[BibTeX] [Abstract] [PDF] [DOI]

We present a theoretical prediction for the drag reduction rate achieved by superhydrophobic surfaces in a turbulent channel flow. The predicted drag reduction rate is in good agreement with results obtained from direct numerical simulations at Re-tau similar or equal to 180 and 400. The present theory suggests that large drag reduction is possible also at Reynolds numbers of practical interest (Re-tau similar to 10(5)-10(6)) by employing a hydrophobic surface, which induces a slip length on the order of ten wall units or more.

`@article{fukagata2006a, author = {Koji Fukagata and Nobuhide Kasagi and Petros Koumoutsakos}, doi = {10.1063/1.2205307}, journal = {Physics of Fluids}, month = {may}, number = {5}, pages = {051703}, publisher = {{AIP} Publishing}, title = {A theoretical prediction of friction drag reduction in turbulent flow by superhydrophobic surfaces}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/fukagata2006a.pdf}, volume = {18}, year = {2006} }`

- I. F. Sbalzarini, A. Hayer, A. Helenius, and P. Koumoutsakos, “Simulations of (an)isotropic diffusion on curved biological surfaces," Biophysical journal, vol. 90, iss. 3, pp. 878-885, 2006.

[BibTeX] [Abstract] [PDF] [DOI]

We present a computational particle method for the simulation of isotropic and anisotropic diffusion on curved biological surfaces that have been reconstructed from image data. The method is capable of handling surfaces of high curvature and complex shape, which are often encountered in biology. The method is validated on simple benchmark problems and is shown to be second-order accurate in space and time and of high parallel efficiency. It is applied to simulations of diffusion on the membrane of endoplasmic reticula ( ER) in live cells. Diffusion simulations are conducted on geometries reconstructed from real ER samples and are compared to fluorescence recovery after photobleaching experiments in the same ER samples using the transmembrane protein tsO45-VSV-G, C-terminally tagged with green fluorescent protein. Such comparisons allow derivation of geometry-corrected molecular diffusion constants for membrane components from fluorescence recovery after photobleaching data. The results of the simulations indicate that the diffusion behavior of molecules in the ER membrane differs significantly from the volumetric diffusion of soluble molecules in the lumen of the same ER. The apparent speed of recovery differs by a factor of similar to 4, even when the molecular diffusion constants of the two molecules are identical. In addition, the specific shape of the membrane affects the recovery half-time, which is found to vary by a factor of similar to 2 in different ER samples.

`@article{sbalzarini2006a, author = {Ivo F. Sbalzarini and Arnold Hayer and Ari Helenius and Petros Koumoutsakos}, doi = {10.1529/biophysj.105.073809}, journal = {Biophysical Journal}, month = {feb}, number = {3}, pages = {878--885}, publisher = {Elsevier {BV}}, title = {Simulations of (An)Isotropic Diffusion on Curved Biological Surfaces}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/sbalzarini2006a.pdf}, volume = {90}, year = {2006} }`

- M. Bergdorf and P. Koumoutsakos, “A lagrangian particle-wavelet method," Multiscale modeling & simulation, vol. 5, iss. 3, pp. 980-995, 2006.

[BibTeX] [Abstract] [PDF] [DOI]

This paper presents a novel, multiresolution Lagrangian particle method with enhanced, wavelet-based adaptivity. The method is formulated for transport problems and combines the efficiency of wavelet collocation with the inherent numerical stability of particle methods. The accuracy and efficiency of the present method is assessed on a number of benchmark problems pertaining to interface capturing and transport. The method is compared with existing techniques demonstrating its advantages and limitations. The present approach leads to a new generation of particle methods with multiresolution capabilities.

`@article{bergdorf2006a, author = {Michael Bergdorf and Petros Koumoutsakos}, doi = {10.1137/060652877}, journal = {Multiscale Modeling {\&} Simulation}, month = {jan}, number = {3}, pages = {980--995}, publisher = {Society for Industrial {\&} Applied Mathematics ({SIAM})}, title = {A Lagrangian Particle-Wavelet Method}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bergdorf2006a.pdf}, volume = {5}, year = {2006} }`

- I. F. Sbalzarini, J. H. Walther, B. Polasek, P. Chatelain, M. Bergdorf, S. E. Hieber, E. M. Kotsalis, and P. Koumoutsakos, “A software framework for the portable parallelization of particle-mesh simulations," in Euro-par 2006 parallel processing, Springer Berlin Heidelberg, 2006, pp. 730-739.

[BibTeX] [Abstract] [PDF] [DOI]

We present a software framework for the transparent and portable parallelization of simulations using particle-mesh methods. Particles are used to transport physical properties and a mesh is required in order to reinitialize the distorted particle locations, ensuring the convergence of the method. Field quantities are computed on the particles using fast multipole methods or by discretizing and solving the governing equations on the mesh. This combination of meshes and particles presents a challenging set of parallelization issues. The present library addresses these issues for a wide range of applications, and it enables orders of magnitude increase in the number of computational elements employed in particle methods. We demonstrate the performance and scalability of the library on several problems, including the first-ever billion particle simulation of diffusion in real biological cell geometries.

`@incollection{sbalzarini2006b, author = {I. F. Sbalzarini and J. H. Walther and B. Polasek and P. Chatelain and M. Bergdorf and S. E. Hieber and E. M. Kotsalis and P. Koumoutsakos}, booktitle = {Euro-Par 2006 Parallel Processing}, doi = {10.1007/11823285_76}, pages = {730--739}, publisher = {Springer Berlin Heidelberg}, title = {A Software Framework for the Portable Parallelization of Particle-Mesh Simulations}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/sbalzarini2006b.pdf}, year = {2006} }`

- P. Koumoutsakos and S. D. Müller, “Flow optimization using stochastic algorithms," in Control of fluid flow, Springer Berlin Heidelberg, 2006, pp. 213-229.

[BibTeX] [Abstract] [PDF] [DOI]

We present a set of stochastic optimization strategies and we discuss their applications to fluid mechanics problems. The optimization strategies are based on state-of-the-art stochastic algorithms and are extended for the application on fluid dynamics problems. The extensions address the question of parallelization, strategy parameter adaptation, robustness to noise, multiple objective optimization, and the use of empirical models. The applications range from burner design for gas turbines, cylinder drag minimization, aerodynamic profile design, micromixer, microchannel, jet mixing to aircraft trailing vortex destruction.

`@incollection{koumoutsakos2006a, author = {Petros Koumoutsakos and Sibylle D. M{\"u}ller}, booktitle = {Control of Fluid Flow}, doi = {10.1007/978-3-540-36085-8_10}, pages = {213--229}, publisher = {Springer Berlin Heidelberg}, title = {Flow Optimization Using Stochastic Algorithms}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos2006a.pdf}, year = {2006} }`

- S. Kern, N. Hansen, and P. Koumoutsakos, “Local meta-models for optimization using evolution strategies," in Parallel problem solving from nature – PPSN IX, Springer Berlin Heidelberg, 2006, pp. 939-948.

[BibTeX] [Abstract] [PDF] [DOI]

We employ local meta-models to enhance the efficiency of evolution strategies in the optimization of computationally expensive problems. The method involves the combination of second order local regression meta-models with the Covariance Matrix Adaptation Evolution Strategy. Experiments on benchmark problems demonstrate that the proposed meta-models have the potential to reliably account for the ranking of the offspring population resulting in significant computational savings. The results show that the use of local meta-models significantly increases the efficiency of already competitive evolution strategies.

`@incollection{kern2006a, author = {Stefan Kern and Nikolaus Hansen and Petros Koumoutsakos}, booktitle = {Parallel Problem Solving from Nature - {PPSN} {IX}}, doi = {10.1007/11844297_95}, pages = {939--948}, publisher = {Springer Berlin Heidelberg}, title = {Local Meta-models for Optimization Using Evolution Strategies}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/kern2006a.pdf}, year = {2006} }`

- N. Hansen, F. Gemperle, A. Auger, and P. Koumoutsakos, “When do heavy-tail distributions help?," in Parallel problem solving from nature – PPSN IX, Springer Berlin Heidelberg, 2006, pp. 62-71.

[BibTeX] [Abstract] [PDF] [DOI]

We examine the evidence for the widespread belief that heavy tail distributions enhance the search for minima on multimodal objective functions. We analyze isotropic and anisotropic heavy-tail Cauchy distributions and investigate the probability to sample a better solution, depending on the step length and the dimensionality of the search space. The probability decreases fast with increasing step length for isotropic Cauchy distributions and moderate search space dimension. The anisotropic Cauchy distribution maintains a large probability for sampling large steps along the coordinate axes, resulting in an exceptionally good performance on the separable multimodal Rastrigin function. In contrast, on a non-separable rotated Rastrigin function or for the isotropic Cauchy distribution the performance difference to a Gaussian search distribution is negligible.

`@incollection{hansen2006b, author = {Nikolaus Hansen and Fabian Gemperle and Anne Auger and Petros Koumoutsakos}, booktitle = {Parallel Problem Solving from Nature - {PPSN} {IX}}, doi = {10.1007/11844297_7}, pages = {62--71}, publisher = {Springer Berlin Heidelberg}, title = {When Do Heavy-Tail Distributions Help?}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hansen2006b.pdf}, year = {2006} }`

### 2005

- S. E. Hieber and P. Koumoutsakos, “A lagrangian particle level set method," Journal of computational physics, vol. 210, iss. 1, pp. 342-367, 2005.

[BibTeX] [Abstract] [PDF] [DOI]

We present a novel particle level set method for capturing interfaces. The level set equation is solved in a Lagrangian frame using particles that carry the level set information. A key aspect of the method involves a consistent remeshing procedure for the regularization of the particle locations when the particle map gets distorted by the advection field. The Lagrangian description of the level set method is inherently adaptive and exact in the case of solid body motions. The efficiency and accuracy of the method is demonstrated in several benchmark problems in two and three dimensions involving pure advection and curvature induced motion of the interface. The simplicity of the particle description is shown to be well suited for real time simulations of surfaces involving cutting and reconnection as in virtual surgery environments.

`@article{hieber2005a, author = {Simone E. Hieber and Petros Koumoutsakos}, doi = {10.1016/j.jcp.2005.04.013}, journal = {Journal of Computational Physics}, month = {nov}, number = {1}, pages = {342--367}, publisher = {Elsevier {BV}}, title = {A Lagrangian particle level set method}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hieber2005a.pdf}, volume = {210}, year = {2005} }`

- H. Ewers, A. E. Smith, I. F. Sbalzarini, H. Lilie, P. Koumoutsakos, and A. Helenius, “Single-particle tracking of murine polyoma virus-like particles on live cells and artificial membranes," Proceedings of the national academy of sciences, vol. 102, iss. 42, pp. 15110-15115, 2005.

[BibTeX] [Abstract] [PDF] [DOI]

The lateral mobility of individual murine polyoma virus-like particles (VLPs) bound to live cells and artificial lipid bilayers was studied by single fluorescent particle tracking using total internal reflection fluorescence microscopy. The particle trajectories were analyzed in terms of diffusion rates and modes of motion as described by the moment scaling spectrum. Although VLPs bound to their ganglioside receptor in lipid bilayers exhibited only free diffusion, analysis of trajectories on live 3T6 mouse fibroblasts revealed three distinct modes of mobility: rapid random motion, confined movement in small zones (30-60 nm in diameter), and confined movement in zones with a slow drift. After binding to the cell surface, particles typically underwent free diffusion for 5-10 s, and then they were confined in an actin filament-dependent manner without involvement of clathrin-coated pits or caveolae. Depletion of cholesterol dramatically reduced mobility of VLPs independently of actin, whereas inhibition of tyrosine kinases had no effect on confinement. The results suggested that clustering of ganglioside molecules by the multivalent VLPs induced transmembrane coupling that led to confinement of the virus/receptor complex by cortical actin filaments.

`@article{ewers2005a, author = {H. Ewers and A. E. Smith and I. F. Sbalzarini and H. Lilie and P. Koumoutsakos and A. Helenius}, doi = {10.1073/pnas.0504407102}, journal = {Proceedings of the National Academy of Sciences}, month = {oct}, number = {42}, pages = {15110--15115}, publisher = {Proceedings of the National Academy of Sciences}, title = {Single-particle tracking of murine polyoma virus-like particles on live cells and artificial membranes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/ewers2005a.pdf}, volume = {102}, year = {2005} }`

- I. F. Sbalzarini, A. Mezzacasa, A. Helenius, and P. Koumoutsakos, “Effects of organelle shape on fluorescence recovery after photobleaching," Biophysical journal, vol. 89, iss. 3, pp. 1482-1492, 2005.

[BibTeX] [Abstract] [PDF] [DOI]

The determination of diffusion coefficients from fluorescence recovery data is often complicated by geometric constraints imposed by the complex shapes of intracellular compartments. To address this issue, diffusion of proteins in the lumen of the endoplasmic reticulum (ER) is studied using cell biological and computational methods. Fluorescence recovery after photobleaching (FRAP) experiments are performed in tissue culture cells expressing GFP – KDEL, a soluble, fluorescent protein, in the ER lumen. The three-dimensional (3D) shape of the ER is determined by confocal microscopy and computationally reconstructed. Within these ER geometries diffusion of solutes is simulated using the method of particle strength exchange. The simulations are compared to experimental FRAP curves of GFP – KDEL in the same ER region. Comparisons of simulations in the 3D ER shapes to simulations in open 3D space show that the constraints imposed by the spatial confinement result in two-to fourfold underestimation of the molecular diffusion constant in the ER if the geometry is not taken into account. Using the same molecular diffusion constant in different simulations, the observed speed of fluorescence recovery varies by a factor of 2.5, depending on the particular ER geometry and the location of the bleached area. Organelle shape considerably influences diffusive transport and must be taken into account when relating experimental photobleaching data to molecular diffusion coefficients. This novel methodology combines experimental FRAP curves with high accuracy computer simulations of diffusion in the same ER geometry to determine the molecular diffusion constant of the solute in the particular ER lumen.

`@article{sbalzarini2005a, author = {Ivo F. Sbalzarini and Anna Mezzacasa and Ari Helenius and Petros Koumoutsakos}, doi = {10.1529/biophysj.104.057885}, journal = {Biophysical Journal}, month = {sep}, number = {3}, pages = {1482--1492}, publisher = {Elsevier {BV}}, title = {Effects of Organelle Shape on Fluorescence Recovery after Photobleaching}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/sbalzarini2005a.pdf}, volume = {89}, year = {2005} }`

- E. M. Kotsalis, E. Demosthenous, J. H. Walther, S. C. Kassinos, and P. Koumoutsakos, “Wetting of doped carbon nanotubes by water droplets," Chemical physics letters, vol. 412, iss. 4-6, pp. 250-254, 2005.

[BibTeX] [Abstract] [PDF] [DOI]

We study the wetting of doped single- and multi-walled carbon nanotubes by water droplets using molecular dynamics simulations. Chemisorbed hydrogen is considered as a model of surface impurities. We study systems with varying densities of surface impurities and we observe increased wetting, as compared to the pristine nanotube case, attributed to the surface dipole moment that changes the orientation of the interfacial water. We demonstrate that the nature of the impurity is important as here hydrogen induces the formation of an extended hydrogen bond network between the water molecules and the doping sites leading to enhanced wetting.

`@article{kotsalis2005a, author = {E.M. Kotsalis and E. Demosthenous and J.H. Walther and S.C. Kassinos and P. Koumoutsakos}, doi = {10.1016/j.cplett.2005.06.122}, journal = {Chemical Physics Letters}, month = {sep}, number = {4-6}, pages = {250--254}, publisher = {Elsevier {BV}}, title = {Wetting of doped carbon nanotubes by water droplets}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/kotsalis2005a.pdf}, volume = {412}, year = {2005} }`

- I. F. Sbalzarini and P. Koumoutsakos, “Feature point tracking and trajectory analysis for video imaging in cell biology," Journal of structural biology, vol. 151, iss. 2, pp. 182-195, 2005.

[BibTeX] [Abstract] [PDF] [DOI]

This paper presents a computationally efficient, two-dimensional, feature point tracking algorithm for the automated detection and quantitative analysis of particle trajectories as recorded by video imaging in cell biology. The tracking process requires no a priori mathematical modeling of the motion, it is self-initializing, it discriminates spurious detections, and it can handle temporary occlusion as well as particle appearance and disappearance from the image region. The efficiency of the algorithm is validated on synthetic video data where it is compared to existing methods and its accuracy and precision are assessed for a wide range of signal-to-noise ratios. The algorithm is well suited for video imaging in cell biology relying on low-intensity fluorescence microscopy. Its applicability is demonstrated in three case studies involving transport of low-density lipoproteins in endosomes, motion of fluorescently labeled Adenovirus-2 particles along microtubules, and tracking of quantum dots on the plasma membrane of live cells. The present automated tracking process enables the quantification of dispersive processes in cell biology using techniques such as moment scaling spectra.

`@article{sbalzarini2005b, author = {I.F. Sbalzarini and P. Koumoutsakos}, doi = {10.1016/j.jsb.2005.06.002}, journal = {Journal of Structural Biology}, month = {aug}, number = {2}, pages = {182--195}, publisher = {Elsevier {BV}}, title = {Feature point tracking and trajectory analysis for video imaging in cell biology}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/sbalzarini2005b.pdf}, volume = {151}, year = {2005} }`

- U. Zimmerli, P. G. Gonnet, J. H. Walther, and P. Koumoutsakos, “Curvature Induced L-defects in water conduction in carbon nanotubes," Nano letters, vol. 5, iss. 6, pp. 1017-1022, 2005.

[BibTeX] [Abstract] [PDF] [DOI]

We conduct molecular dynamics simulations to study the effect of the curvature induced static dipole moment of small open-ended single-walled carbon nanotubes (CNTs) immersed in water. This dipole moment generates a nonuniform electric field, changing the energy landscape in the CNT and altering the water conduction process. The CNT remains practically filled with water at all times, whereas intermittent filling is observed when the dipole term is not included. In addition, the dipole moment induces a preferential orientation of the water molecules near the end regions of the nanotube, which in turn causes a reorientation of the water chain in the middle of the nanotube. The most prominent feature of this reorientation is an L-defect in the chain of water molecules inside the CNT. The analysis of the water energetics and structural characteristics inside and in the vicinity of the CNT helps to identify the role of the dipole moment and to suggest possible mechanisms for controlled water and proton transport at the nanoscale.

`@article{zimmerli2005a, author = {Urs Zimmerli and Pedro G. Gonnet and Jens H. Walther and Petros Koumoutsakos}, doi = {10.1021/nl0503126}, journal = {Nano Letters}, month = {jun}, number = {6}, pages = {1017--1022}, publisher = {American Chemical Society ({ACS})}, title = {Curvature {Induced} {L}-Defects in Water Conduction in Carbon Nanotubes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/zimmerli2005a.pdf}, volume = {5}, year = {2005} }`

- T. Werder, J. H. Walther, and P. Koumoutsakos, “Hybrid atomistic—continuum method for the simulation of dense fluid flows," Journal of computational physics, vol. 205, iss. 1, pp. 373-390, 2005.

[BibTeX] [Abstract] [PDF] [DOI]

We present a hybrid atomistic-continuum method for multiscale simulations of dense fluids. In this method, the atomistic part is described using a molecular dynamics description, while the continuum flow is described by a finite volume discretization of the incompressible Navier-Stokes equations. The two descriptions are combined in a domain decomposition formulation using the Schwarz alternating method. A novel method has been proposed in order to impose non-periodic velocity boundary conditions from the continuum to the atomistic domain, based on an effective boundary potential, consistent body forces, a particle insertion algorithm and specular walls. The extraction of velocity boundary conditions for the continuum from the atomistic domain is formulated by taking into account the associated statistical errors. The advantages and drawbacks of the proposed Schwarz decomposition method as compared to related flux-based schemes are discussed. The efficiency and applicability of the method is demonstrated by considering hybrid and full molecular dynamics simulations of the flow of a Lennard-Jones fluid past a carbon nanotube.

`@article{werder2005a, author = {Thomas Werder and Jens H. Walther and Petros Koumoutsakos}, doi = {10.1016/j.jcp.2004.11.019}, journal = {Journal of Computational Physics}, month = {may}, number = {1}, pages = {373--390}, publisher = {Elsevier {BV}}, title = {Hybrid atomistic{\textendash}continuum method for the simulation of dense fluid flows}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/werder2005a.pdf}, volume = {205}, year = {2005} }`

- D. Buche, N. N. Schraudolph, and P. Koumoutsakos, “Accelerating evolutionary algorithms with gaussian process fitness function models," IEEE transactions on systems, man and cybernetics, part c (applications and reviews), vol. 35, iss. 2, pp. 183-194, 2005.

[BibTeX] [Abstract] [PDF] [DOI]

We present an overview of evolutionary algorithms that use empirical models of the fitness function to accelerate convergence, distinguishing between evolution control and the surrogate approach. We describe the Gaussian process model and propose using it as an inexpensive fitness function surrogate. Implementation issues such as efficient and numerically stable computation, exploration versus exploitation, local modeling, multiple objectives and constraints, and failed evaluations are addressed. Our resulting Gaussian process optimization procedure clearly outperforms other evolutionary strategies on standard test functions as well as on a real-world problem: the optimization of stationary gas turbine compressor profiles.

`@article{buche2005a, author = {D. Buche and N.N. Schraudolph and P. Koumoutsakos}, doi = {10.1109/tsmcc.2004.841917}, journal = {{IEEE} Transactions on Systems, Man and Cybernetics, Part C (Applications and Reviews)}, month = {may}, number = {2}, pages = {183--194}, publisher = {Institute of Electrical and Electronics Engineers ({IEEE})}, title = {Accelerating Evolutionary Algorithms With Gaussian Process Fitness Function Models}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/buche2005a.pdf}, volume = {35}, year = {2005} }`

- S. Arcidiacono, J. H. Walther, D. Poulikakos, D. Passerone, and P. Koumoutsakos, “Solidification of gold nanoparticles in carbon nanotubes," Physical review letters, vol. 94, iss. 10, 2005.

[BibTeX] [Abstract] [PDF] [DOI]

The structure and the solidification of gold nanoparticles in a carbon nanotube are investigated using molecular dynamics simulations. The simulations indicate that the predicted solidification temperature of the enclosed particle is lower than its bulk counterpart, but higher than that observed for clusters placed in vacuum. A comparison with a phenomenological model indicates that, in the considered range of tube radii (R-CNT) of 0.5 < R-CNT < 1.6 nm, the solidification temperature depends mainly on the length of the particle with a minor dependence on R-CNT.

`@article{arcidiacono2005a, author = {S. Arcidiacono and J. H. Walther and D. Poulikakos and D. Passerone and P. Koumoutsakos}, doi = {10.1103/physrevlett.94.105502}, journal = {Physical Review Letters}, month = {mar}, number = {10}, publisher = {American Physical Society ({APS})}, title = {Solidification of Gold Nanoparticles in Carbon Nanotubes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/arcidiacono2005a.pdf}, volume = {94}, year = {2005} }`

- T. Hou and P. Koumoutsakos, “Special section on multiscale modeling in materials and life sciences," Multiscale modeling & simulation, vol. 4, iss. 1, pp. 213-214, 2005.

[BibTeX] [Abstract] [PDF] [DOI]

This special section of Multiscale Modeling and Simulation: A SIAM Interdisci- plinary Journal, on multiscale modeling in life and materials sciences, is based on a summer program with the same theme, held August 4{—}30, 2003, at the Universita` della Svizzera Italiana in Lugano, Switzerland, and organized by the ETH Zurich Compu- tational Laboratory (CoLab). This workshop emphasized that multiscale modeling and simulation can serve as a common scientific language enabling cross-fertilization across disciplines and the definition of new scientific frontiers.

`@article{hou2005a, author = {Thomas Hou and Petros Koumoutsakos}, doi = {10.1137/mmsubt000004000001000213000001}, journal = {Multiscale Modeling {\&} Simulation}, month = {jan}, number = {1}, pages = {213--214}, publisher = {Society for Industrial {\&} Applied Mathematics ({SIAM})}, title = {Special Section on Multiscale Modeling in Materials and Life Sciences}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hou2005a.pdf}, volume = {4}, year = {2005} }`

- M. Bergdorf, G. Cottet, and P. Koumoutsakos, “Multilevel adaptive particle methods for convection-diffusion equations," Multiscale modeling & simulation, vol. 4, iss. 1, pp. 328-357, 2005.

[BibTeX] [Abstract] [PDF] [DOI]

We present novel multilevel particle methods with extended adaptivity in areas where increased resolution is required. We present two complementary approaches as inspired by r-adaptivity and adaptive mesh refinement (AMR) concepts introduced infinite difference and finite element schemes. For the r-adaptivity a new class of particle-based mapping functions is introduced, while the particle AMR method uses particle remeshing in overlapping domains as a key element. The advantages and drawbacks of the proposed particle methods are illustrated based on results from the solution of one-dimensional convection-diffusion equations, while the extension of the method to higher dimensions is demonstrated in simulations of the inviscid evolution of an elliptical vortex.

`@article{bergdorf2005a, author = {Michael Bergdorf and Georges-Henri Cottet and Petros Koumoutsakos}, doi = {10.1137/040602882}, journal = {Multiscale Modeling {\&} Simulation}, month = {jan}, number = {1}, pages = {328--357}, publisher = {Society for Industrial {\&} Applied Mathematics ({SIAM})}, title = {Multilevel Adaptive Particle Methods for Convection-Diffusion Equations}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bergdorf2005a.pdf}, volume = {4}, year = {2005} }`

- P. Poncet, G. Cottet, and P. Koumoutsakos, “Control of three-dimensional wakes using evolution strategies," Comptes rendus mécanique, vol. 333, iss. 1, pp. 65-77, 2005.

[BibTeX] [Abstract] [PDF] [DOI]

We investigate three-dimensional cylinder wakes of incompressible fully developed flows at Re = 300, resulting from control induced by tangential motions of the cylinder surface. The motion of the cylinder surface, in two dimensions, is optimized using evolution strategies, resulting in significant drag reduction and drastic modification of the wake as compared to the uncontrolled flow. The quasi-optimal velocity profile obtained in 2D is modified by spanwise harmonics and applied to 3D flows. The results indicate important differences in the flow physics induced by two and three dimensional control strategies.

`@article{poncet2005b, author = {Philippe Poncet and Georges-Henri Cottet and Petros Koumoutsakos}, doi = {10.1016/j.crme.2004.10.007}, journal = {Comptes Rendus M{\'{e}}canique}, month = {jan}, number = {1}, pages = {65--77}, publisher = {Elsevier {BV}}, title = {Control of three-dimensional wakes using evolution strategies}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/poncet2005b.pdf}, volume = {333}, year = {2005} }`

- P. Koumoutsakos, “Multicscale flow simulations using particles," Annual review of fluid mechanics, vol. 37, iss. 1, pp. 457-487, 2005.

[BibTeX] [Abstract] [PDF] [DOI]

Flow simulations are one of the archetypal multiscale problems. Simulations of turbulent and unsteady separated flows have to resolve a multitude of interacting scales, whereas molecular phenomena determine the structure of shocks and the validity of the no-slip boundary condition. Particle simulations of continuum and molecular phenomena can be formulated by following the motion of interacting particles that carry the physical properties of the flow. In this article we review Lagrangian, multiresolution, particle methods such as vortex methods and smooth particle hydrodynamics for the simulation of continuous flows and molecular dynamics for the simulation of flows at the atomistic scale. We review hybrid molecular-continuum simulations with an emphasis on the computational aspects of the problem. We identify the common computational characteristics of particle methods and discuss their properties that enable the formulation of a systematic framework for multiscale flow simulations.

`@article{koumoutsakos2005a, author = {Petros Koumoutsakos}, doi = {10.1146/annurev.fluid.37.061903.175753}, journal = {Annual Review of Fluid Mechanics}, month = {jan}, number = {1}, pages = {457--487}, publisher = {Annual Reviews}, title = {Multicscale Flow Simulations using Particles}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos2005a.pdf}, volume = {37}, year = {2005} }`

- P. Poncet and P. Koumoutsakos, “Optimization of vortex shedding in 3-D wakes using belt actuators," International journal of offshore and polar engineering, vol. 15, iss. 1, pp. 7-13, 2005.

[BibTeX] [Abstract] [PDF]

This paper discusses the control of cylinder wakes via tangential wall velocity modifications. The wall velocity is piecewise constant (corresponding to belt actuators), and its amplitude is optimized using a clustering real coded genetic algorithm. This type of control significantly affects the vortical structures being shed in the wake, and it is shown that the flow gets significantly modified, resulting in a 3-dimensional body shedding 2-dimensional vortical structures in the near wake of the body. Depending on the energy involved in the control, one can also obtain a dramatic decrease of shedding amplitude.

`@article{poncet2005a, author = {Poncet, P. and Koumoutsakos, P.}, journal = {International Journal of Offshore and Polar Engineering}, number = {1}, pages = {7--13}, title = {Optimization of Vortex Shedding In {3-D} Wakes Using Belt Actuators}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/poncet2005a.pdf}, volume = {15}, year = {2005} }`

### 2004

- E. M. Kotsalis, J. H. Walther, and P. Koumoutsakos, “Multiphase water flow inside carbon nanotubes," International journal of multiphase flow, vol. 30, iss. 7-8, pp. 995-1010, 2004.

[BibTeX] [Abstract] [PDF] [DOI]

We present nonequilibrium molecular dynamics simulations of the flow of liquid-vapour water mixtures and mixtures of water and nitrogen inside carbon nanotubes. A new adaptive forcing scheme is proposed to impose a mean flow through the system. The flow of liquid water is characterised by a distinct layering of the water molecules in the vicinity of the boundary and a slip length that is found to increase with the radius of the carbon nanotube. Increasing the temperature and pressure of the system furthermore results in a decrease in the slip length. For the flow of mixtures of nitrogen and water we find that the slip length is reduced as compared to the slip for the pure water. The shorter slip length is attributed to the fact that nitrogen forms droplets at the carbon surface, thus partially shielding the bulk flow from the hydrophobic carbon surface.

`@article{kotsalis2004a, author = {E.M. Kotsalis and J.H. Walther and P. Koumoutsakos}, doi = {10.1016/j.ijmultiphaseflow.2004.03.009}, journal = {International Journal of Multiphase Flow}, month = {jul}, number = {7-8}, pages = {995--1010}, publisher = {Elsevier {BV}}, title = {Multiphase water flow inside carbon nanotubes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/kotsalis2004a.pdf}, volume = {30}, year = {2004} }`

- J. H. Walther, T. Werder, R. L. Jaffe, and P. Koumoutsakos, “Hydrodynamic properties of carbon nanotubes," Physical review e, vol. 69, iss. 6, 2004.

[BibTeX] [Abstract] [PDF] [DOI]

We study water flowing past an array of single walled carbon nanotubes using nonequilibrium molecular dynamics simulations. For carbon nanotubes mounted with a tube spacing of 16.4×16.4 nm and diameters of 1.25 and 2.50 nm, respectively, we find drag coefficients in reasonable agreement with the macroscopic, Stokes-Oseen solution. The slip length is -0.11 nm for the 1.25 nm carbon nanotube, and 0.49 for the 2.50 nm tube for a flow speed of 50 m/s, respectively, and 0.28 nm for the 2.50 nm tube at 200 m/s. A slanted flow configuration with a stream- and spanwise velocity component of 100 ms(-1) recovers the two-dimensional results, but exhibits a significant 88 nm slip along the axis of the tube. These results indicate that slip depends on the particular flow configuration.

`@article{walther2004b, author = {J. H. Walther and T. Werder and R. L. Jaffe and P. Koumoutsakos}, doi = {10.1103/physreve.69.062201}, journal = {Physical Review E}, month = {jun}, number = {6}, publisher = {American Physical Society ({APS})}, title = {Hydrodynamic properties of carbon nanotubes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther2004b.pdf}, volume = {69}, year = {2004} }`

- S. D. Müller, I. Mezić, J. H. Walther, and P. Koumoutsakos, “Transverse momentum micromixer optimization with evolution strategies," Computers & fluids, vol. 33, iss. 4, pp. 521-531, 2004.

[BibTeX] [Abstract] [PDF] [DOI]

We conduct a numerical study of mixing in a transverse momentum micromixer. Good values for actuation frequencies can be determined using simple kinematic arguments, and evolution strategies are introduced for the optimization of mixing by adjusting the control parameters in micromixer devices. It is shown that the chosen optimization algorithm can identify, in an automated fashion, effective actuation parameters. We find that optimal frequencies for increasing number of transverse channels are superposable despite the non-linear nature of the mixing process.

`@article{muller2004a, author = {Sibylle D. M{\"u}ller and Igor Mezi{\'{c}} and Jens H. Walther and Petros Koumoutsakos}, doi = {10.1016/j.compfluid.2003.07.004}, journal = {Computers {\&} Fluids}, month = {may}, number = {4}, pages = {521--531}, publisher = {Elsevier {BV}}, title = {Transverse momentum micromixer optimization with evolution strategies}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/muller2004a.pdf}, volume = {33}, year = {2004} }`

- M. Milano, P. Koumoutsakos, and J. Schmidhuber, “Self-organizing nets for optimization," IEEE transactions on neural networks, vol. 15, iss. 3, pp. 758-765, 2004.

[BibTeX] [Abstract] [PDF] [DOI]

Given some optimization problem and a series of typically expensive trials of solution candidates sampled from a search space, how can we efficiently select the next candidate? We address this fundamental problem by embedding simple optimization strategies in learning algorithms inspired by Kohonen’s self-organizing maps and neural gas networks. Our adaptive nets or grids are used to identify and exploit search space regions that maximize the probability of generating points closer to the optima. Net nodes are attracted by candidates that lead to improved evaluations, thus, quickly biasing the active data selection process toward promising regions, without loss of ability to escape from local optima. On standard benchmark functions, our techniques perform more reliably than the widely used covariance matrix adaptation evolution strategy. The proposed algorithm is also applied to the problem of drag reduction in a flow past an actively controlled circular cylinder, leading to unprecedented drag reduction.

`@article{milano2004a, author = {M. Milano and P. Koumoutsakos and J. Schmidhuber}, doi = {10.1109/tnn.2004.826132}, journal = {{IEEE} Transactions on Neural Networks}, month = {may}, number = {3}, pages = {758--765}, publisher = {Institute of Electrical and Electronics Engineers ({IEEE})}, title = {Self-Organizing Nets for Optimization}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/milano2004a.pdf}, volume = {15}, year = {2004} }`

- R. L. Jaffe, P. Gonnet, T. Werder, J. H. Walther, and P. Koumoutsakos, “Water—carbon interactions 2: calibration of potentials using contact angle data for different interaction models," Molecular simulation, vol. 30, iss. 4, pp. 205-216, 2004.

[BibTeX] [Abstract] [PDF] [DOI]

Molecular dynamics simulations of water droplets on graphite are carried out to determine the contact angle for different water-carbon potential functions. Following the procedure of Werder et al. [ J. Phys. Chem. B , 107 (2003) 1345], the C-O Lennard-Jones well depth is varied to recover the experimental value for the contact angle (84-86degrees) using a 2000-molecule water droplet and compensating for the line tension effect that lowers the contact angle for increasing droplet size. For the discrete graphite surface model studied by Werder et al. , the effects of adding C-H Lennard-Jones interactions and changing the long-range cut-off distance are considered. In addition, a continuum graphite surface model is studied for which the water-graphite interaction energy depends only on the normal distance ( z ) from the water oxygen to the surface. This new model, with z(-10) repulsion and z(-4) attraction, is formulated in terms of the standard Lennard-Jones parameters, for which the recommended values are sigma(CO) =3.19 Angstrom and epsilon(CO) =0.3651 kJ/mol.

`@article{jaffe2004a, author = {Richard L. Jaffe and Pedro Gonnet and Thomas Werder and Jens H. Walther and Petros Koumoutsakos}, doi = {10.1080/08927020310001659124}, journal = {Molecular Simulation}, month = {apr}, number = {4}, pages = {205--216}, publisher = {Informa {UK} Limited}, title = {Water{\textendash}Carbon Interactions 2: Calibration of Potentials using Contact Angle Data for Different Interaction Models}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/jaffe2004a.pdf}, volume = {30}, year = {2004} }`

- U. Zimmerli, M. Parrinello, and P. Koumoutsakos, “Dispersion corrections to density functionals for water aromatic interactions," The journal of chemical physics, vol. 120, iss. 6, pp. 2693-2699, 2004.

[BibTeX] [Abstract] [PDF] [DOI]

We investigate recently published methods for extending density functional theory to the description of long-range dispersive interactions. In all schemes an empirical correction consisting of a C(6)r(-6) term is introduced that is damped at short range. The coefficient C-6 is calculated either from average molecular or atomic polarizabilities. We calculate geometry-dependent interaction energy profiles for the water benzene cluster and compare the results with second-order Moller-Plesset calculations. Our results indicate that the use of the B3LYP functional in combination with an appropriate mixing rule and damping function is recommended for the interaction of water with aromatics. (C) 2004 American Institute of Physics.

`@article{zimmerli2004a, author = {Urs Zimmerli and Michele Parrinello and Petros Koumoutsakos}, doi = {10.1063/1.1637034}, journal = {The Journal of Chemical Physics}, month = {feb}, number = {6}, pages = {2693--2699}, publisher = {{AIP} Publishing}, title = {Dispersion corrections to density functionals for water aromatic interactions}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/zimmerli2004a.pdf}, volume = {120}, year = {2004} }`

- J. H. Walther, R. L. Jaffe, E. M. Kotsalis, T. Werder, T. Halicioglu, and P. Koumoutsakos, “Hydrophobic hydration of c60 and carbon nanotubes in water," Carbon, vol. 42, iss. 5-6, pp. 1185-1194, 2004.

[BibTeX] [Abstract] [PDF] [DOI]

We perform molecular dynamics (MD) simulations to study the hydrophobic-hydrophilic behavior of pairs Of C-60 fullerene molecules and single wall carbon nanotubes in water. The interaction potentials involve a fully atomistic description of the fullerenes or carbon nanotubes and the water is modeled using the flexible SPC model. Both unconstrained and constrained MD simulations are carried out. We find that these systems display drying, as evidenced by expulsion of the interstitial water, when the C-60 and carbon nanotubes are separated by less than 12, and 9-10 Angstrom, respectively. From the constrained simulations, the computed mean force between two carbon nanotubes in water exhibits a maximum at a tube spacing of 5.0 Angstrom which corresponds to approximately one unstable layer of interstitial water molecules. The main contribution to the force stems from the van der Waals attraction between the carbon surfaces. The minimum in the potential of mean force has a value of – 17 kJ mol(-1) Angstrom(-1) at a tube spacing of 3.5 Angstrom.

`@article{walther2004c, author = {J.H. Walther and R.L. Jaffe and E.M. Kotsalis and T. Werder and T. Halicioglu and P. Koumoutsakos}, doi = {10.1016/j.carbon.2003.12.071}, journal = {Carbon}, month = {jan}, number = {5-6}, pages = {1185--1194}, publisher = {Elsevier {BV}}, title = {Hydrophobic hydration of C60 and carbon nanotubes in water}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther2004c.pdf}, volume = {42}, year = {2004} }`

- J. H. Walther, T. Werder, R. L. Jaffe, P. Gonnet, M. Bergdorf, U. Zimmerli, and P. Koumoutsakos, “Water—carbon interactions III: the influence of surface and fluid impurities," Phys. chem. chem. phys., vol. 6, iss. 8, pp. 1988-1995, 2004.

[BibTeX] [Abstract] [PDF] [DOI]

Molecular dynamics. simulations are performed to study the influence of surface and fluid impurities on water-carbon interactions. In order to quantify these interactions we consider the canonical problem of wetting of a doped flat graphitic surface by a water system with impurities. As model fluid impurities we consider aqueous solutions of potassium-chloride with molar concentrations up to 1.8 M. Quantum chemistry calculations are performed to derive pair potentials for the ion-graphite interactions. The contact angle is found to decrease weakly with increasing ionic concentration, from 90degrees at 0 M to 81degrees at 1.8 M concentration. The influence of solid impurities is found to be more significant. Thus, 10, 15, and 20% coverages of chemisorbed hydrogen result in contact angles of 90degrees, 74degrees and 60degrees, respectively.

`@article{walther2004a, author = {J. H. Walther and T. Werder and R. L. Jaffe and P. Gonnet and M. Bergdorf and U. Zimmerli and P. Koumoutsakos}, doi = {10.1039/b312740k}, journal = {Phys. Chem. Chem. Phys.}, number = {8}, pages = {1988--1995}, publisher = {Royal Society of Chemistry ({RSC})}, title = {Water{\textendash}carbon interactions {III}: The influence of surface and fluid impurities}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther2004a.pdf}, volume = {6}, year = {2004} }`

- S. Kern, S. D. Müller, N. Hansen, D. Büche, J. Ocenasek, and P. Koumoutsakos, “Learning probability distributions in continuous evolutionary algorithms — a comparative review," Natural computing, vol. 3, iss. 1, pp. 77-112, 2004.

[BibTeX] [Abstract] [PDF] [DOI]

We present a comparative review of Evolutionary Algorithms that generate new population members by sampling a probability distribution constructed during the optimization process. We present a unifying formulation for five such algorithms that enables us to characterize them based on the parametrization of the probability distribution, the learning methodology, and the use of historical information. The algorithms are evaluated on a number of test functions in order to assess their relative strengths and weaknesses. This comparative review helps to identify areas of applicability for the algorithms and to guide future algorithmic developments.

`@article{kern2004a, author = {Stefan Kern and Sibylle D. M{\"u}ller and Nikolaus Hansen and Dirk B{\"u}che and Jiri Ocenasek and Petros Koumoutsakos}, doi = {10.1023/b:naco.0000023416.59689.4e}, journal = {Natural Computing}, number = {1}, pages = {77--112}, publisher = {Springer Nature}, title = {Learning probability distributions in continuous evolutionary algorithms {\textendash} a comparative review}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/kern2004a.pdf}, volume = {3}, year = {2004} }`

- S. E. Hieber, J. H. Walther, and P. Koumoutsakos, “Remeshed smoothed particle hydrodynamics simulation of the mechanical behavior of human organs," Technology and health care, vol. 12, iss. 4, pp. 305-314, 2004.

[BibTeX] [Abstract] [PDF]

In computer aided surgery the accurate simulation of the mechanical behavior of human organs is essential for the development of surgical simulators. In this paper we introduce particle based simulations of two different human organ materials modeled as linear viscoelastic solids. The constitutive equations for the material behavior are discretized using a particle approach based on the smoothed particle hydrodynamics (SPH) method while the body surface is tracked using level sets. A key aspect of this approach is its flexibility which allows the simulation of complex time varying topologies with large deformations. The accuracy of the original formulation is significantly enhanced by using a particle reinitialization technique resulting in remeshed smoothed particle hydrodynamics (rSPH). The mechanical parameters of the systems used in the simulations are derived from experimental measurements on human cadaver organs. We compare the mechanical behavior of liver- and kidney-like materials based on the dynamic simulations of a tensile test case. Moreover, we present a particle based reconstruction of the liver topology and its strain distribution under a small local load. Finally, we demonstrate a unified formulation of fluid structure interaction based on particle method.

`@article{hieber2004a, author = {Hieber, S. E. and Walther, J. H. and Koumoutsakos, P.}, journal = {Technology and Health Care}, number = {4}, pages = {305--314}, title = {Remeshed smoothed particle hydrodynamics simulation of the mechanical behavior of human organs}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hieber2004a.pdf}, volume = {12}, year = {2004} }`

### 2003

- T. Werder, J. H. Walther, R. L. Jaffe, T. Halicioglu, and P. Koumoutsakos, “On the water-carbon interaction for use in molecular dynamics simulations of graphite and carbon nanotubes," The journal of physical chemistry b, vol. 112, iss. 44, pp. 14090-14090, 2003.

[BibTeX] [Abstract] [PDF] [DOI]

A systematic molecular dynamics study shows that the contact angle of a water droplet on graphite changes significantly as a function of the water-carbon interaction energy. Together with the observation that a linear relationship can be established between the contact angle and the water monomer binding energy on graphite, a new route to calibrate interaction potential parameters is presented. Through a variation of the droplet size in the range from 1000 to 17’500 water molecules, we determine the line tension to be positive and on the order of 2 {\texttimes} 10{\^{}}-10 J/m. To recover a macroscopic contact angle of 86{\textdegree}, a water monomer binding energy of -6.33 kJ mol{\^{}}-1 is required, which is obtained by applying a carbon-oxygen Lennard-Jones potential with the parameters eps_CO = 0.392 kJ mol{\^{}}-1 and sigma_CO = 3.19 {\AA}. For this new water-carbon interaction potential, we present density profiles and hydrogen bond distributions for a water droplet on graphite.

`@article{werder2003a, author = {T. Werder and J. H. Walther and R. L. Jaffe and T. Halicioglu and P. Koumoutsakos}, doi = {10.1021/jp8083106}, journal = {The Journal of Physical Chemistry B}, month = {nov}, number = {44}, pages = {14090--14090}, publisher = {American Chemical Society ({ACS})}, title = {On the Water-Carbon Interaction for Use in Molecular Dynamics Simulations of Graphite and Carbon Nanotubes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/werder2003a.pdf}, volume = {112}, year = {2003} }`

- N. Hansen, S. D. Müller, and P. Koumoutsakos, “Reducing the time complexity of the derandomized evolution strategy with covariance matrix adaptation (CMA-ES)," Evolutionary computation, vol. 11, iss. 1, pp. 1-18, 2003.

[BibTeX] [Abstract] [PDF] [DOI]

This paper presents a novel evolutionary optimization strategy based on the derandomized evolution strategy with covariance matrix adaptation (CMA-ES). This new approach is intended to reduce the number of generations required for convergence to the optimum. Reducing the number of generations, i.e., the time complexity of the algorithm, is important if a large population size is desired: (1) to reduce the effect of noise; (2) to improve global search properties; and (3) to implement the algorithm on (highly) parallel machines. Our method results in a highly parallel algorithm which scales favorably with large numbers of processors. This is accomplished by efficiently incorporating the available information from a large population, thus significantly reducing the number of generations needed to adapt the covariance matrix. The original version of the CMA-ES was designed to reliably adapt the covariance matrix in small populations but it cannot exploit large populations efficiently. Our modifications scale up the efficiency to population sizes of up to 10n, where n is the problem dimension. This method has been applied to a large number of test problems, demonstrating that in many cases the CMA-ES can be advanced from quadratic to linear time complexity.

`@article{hansen2003a, author = {Nikolaus Hansen and Sibylle D. M{\"u}ller and Petros Koumoutsakos}, doi = {10.1162/106365603321828970}, journal = {Evolutionary Computation}, month = {mar}, number = {1}, pages = {1--18}, publisher = {{MIT} Press - Journals}, title = {Reducing the Time Complexity of the Derandomized Evolution Strategy with Covariance Matrix Adaptation ({CMA}-{ES})}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hansen2003a.pdf}, volume = {11}, year = {2003} }`

### 2002

- D. Buche, P. Stoll, R. Dornberger, and P. Koumoutsakos, “Multi—objective evolutionary algorithm for the optimization of noisy combustion processes," IEEE transactions on systems, man and cybernetics, part c (applications and reviews), vol. 32, iss. 4, pp. 460-473, 2002.

[BibTeX] [Abstract] [PDF] [DOI]

Evolutionary Algorithms have been applied to single and multiple objectives optimization problems, with a strong emphasis on problems, solved through numerical simulations. However in several engineering problems, there is limited availability of suitable models and there is need for optimization of realistic or experimental configurations. The multiobjective optimization of an experimental set-up is addressed in this work. Experimental setups present a number of challenges to any optimization technique including: availability only of pointwise information, experimental noise in the objective function, uncontrolled changing of environmental conditions and measurement failure. This work introduces a multiobjective evolutionary algorithm capable of handling noisy problems with a particular emphasis on robustness against unexpected measurements (outliers). The algorithm is based on the Strength Pareto Evolutionary Algorithm (SPEA) of Zitzler and Thiele and includes the new concepts of domination dependent lifetime, reevaluation of solutions and modifi- cations in the update of the archive population. Several tests on prototypical functions underline the improvements in convergence speed and robustness of the extended algorithm. The proposed algorithm is implemented to the Pareto optimization of the combustion process of a stationary gas turbine in an industrial setup. The Pareto front is constructed for the objectives of minimization of NO emissions and reduction of the pressure fluctuations (pulsation) of the flame. Both objectives are conflicting affecting the environment and the lifetime of the turbine, respectively. The optimization leads a Pareto front corresponding to reduced emissions and pulsation of the burner. The physical implications of the solutions are discussed and the algorithm is evaluated.

`@article{buche2002a, author = {D. Buche and P. Stoll and R. Dornberger and P. Koumoutsakos}, doi = {10.1109/tsmcb.2002.804372}, journal = {{IEEE} Transactions on Systems, Man and Cybernetics, Part C (Applications and Reviews)}, month = {nov}, number = {4}, pages = {460--473}, publisher = {Institute of Electrical and Electronics Engineers ({IEEE})}, title = {Multi{\textendash}objective evolutionary algorithm for the optimization of noisy combustion processes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/buche2002a.pdf}, volume = {32}, year = {2002} }`

- M. Milano and P. Koumoutsakos, “Neural network modeling for near wall turbulent flow," Journal of computational physics, vol. 182, iss. 1, pp. 1-26, 2002.

[BibTeX] [Abstract] [PDF] [DOI]

A neural network methodology is developed in order to reconstruct the near wall field in a turbulent flow by exploiting flow fields provided by direct numerical simulations. The results obtained from the neural network methodology are compared with the results obtained from prediction and reconstruction using proper orthogonal decomposition (POD). Using the property that the POD is equivalent to a specific linear neural network, a nonlinear neural network extension is presented. It is shown that for a relatively small additional computational cost nonlinear neural networks provide us with improved reconstruction and prediction capabilities for the near wall velocity fields. Based on these results advantages and drawbacks of both approaches are discussed with an outlook toward the development of near wall models for turbulence modeling and control.

`@article{milano2002b, author = {Michele Milano and Petros Koumoutsakos}, doi = {10.1006/jcph.2002.7146}, journal = {Journal of Computational Physics}, month = {oct}, number = {1}, pages = {1--26}, publisher = {Elsevier {BV}}, title = {Neural Network Modeling for Near Wall Turbulent Flow}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/milano2002b.pdf}, volume = {182}, year = {2002} }`

- A. K. Chaniotis, D. Poulikakos, and P. Koumoutsakos, “Remeshed smoothed particle hydrodynamics for the simulation of viscous and heat conducting flows," Journal of computational physics, vol. 182, iss. 1, pp. 67-90, 2002.

[BibTeX] [Abstract] [PDF] [DOI]

We present an extension of the classical scheme of smoothed particle hydrodynamics (SPH) for the accurate handling of diffusion terms in the momentum and energy equation of viscous and heat conducting flows. A key aspect of the present SPH approach is the periodic reinitialization (remeshing) of the particle locations, which are being distorted by the flow map. High-order moment conserving kernels are being implemented for this remeshing procedure leading to accurate simulations. The accuracy of the proposed SPH methodology is tested for a number of benchmark problems involving flow and energy transport. The results demonstrate that the proposed SPH methodology is capable of DNS quality simulations while maintaining its robustness and adaptivity.

`@article{chaniotis2002a, author = {A.K. Chaniotis and D. Poulikakos and P. Koumoutsakos}, doi = {10.1006/jcph.2002.7152}, journal = {Journal of Computational Physics}, month = {oct}, number = {1}, pages = {67--90}, publisher = {Elsevier {BV}}, title = {Remeshed Smoothed Particle Hydrodynamics for the Simulation of Viscous and Heat Conducting Flows}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/chaniotis2002a.pdf}, volume = {182}, year = {2002} }`

- M. Milano and P. Koumoutsakos, “A clustering genetic algorithm for cylinder drag optimization," Journal of computational physics, vol. 175, iss. 1, pp. 79-107, 2002.

[BibTeX] [Abstract] [PDF] [DOI]

A real coded genetic algorithm is implemented for the optimization of actuator parameters for cylinder drag minimization. We consider two types of idealized actuators that are allowed either to move steadily and tangentially to the cylinder surface ({\textquotedblleft}belts{\textquotedblright}) or to steadily blow/suck with a zero net mass constraint. The genetic algorithm we implement has the property of identifying minima basins, rather than single optimum points. The knowledge of the shape of the minimum basin enables further insights into the system properties and provides a sensitivity analysis in a fully automated way. The drag minimization problem is formulated as an optimal regulation problem. By means of the clustering property of the present genetic algorithm, a set of solutions producing drag reduction of up to 50% is identified. A comparison between the two types of actuators, based on the clustering property of the algorithm, indicates that blowing/suction actuation parameters are associated with larger tolerances when compared to optimal parameters for the belt actuators. The possibility of using a few strategically placed actuators to obtain a significant drag reduction is explored using the clustering diagnostics of this method. The optimal belt-actuator parameters obtained by optimizing the two-dimensional case is employed in three-dimensional simulations, by extending the actuators across the span of the cylinder surface. The three-dimensional controlled flow exhibits a strong two-dimensional character near the cylinder surface, resulting in significant drag reduction.

`@article{milano2002a, author = {Michele Milano and Petros Koumoutsakos}, doi = {10.1006/jcph.2001.6882}, journal = {Journal of Computational Physics}, month = {jan}, number = {1}, pages = {79--107}, publisher = {Elsevier {BV}}, title = {A Clustering Genetic Algorithm for Cylinder Drag Optimization}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/milano2002a.pdf}, volume = {175}, year = {2002} }`

- S. D. Muller, J. Marchetto, S. Airaghi, and P. Kournoutsakos, “Optimization based on bacterial chemotaxis," IEEE transactions on evolutionary computation, vol. 6, iss. 1, pp. 16-29, 2002.

[BibTeX] [Abstract] [PDF] [DOI]

We present an optimization algorithm based on a model of bacterial chemotaxis. The original biological model is used to formulate a simple optimization algorithm, which is evaluated on a set of standard test problems. Based on this evaluation, several features are added to the basic algorithm using evolutionary concepts in order to obtain an improved optimization strategy, called the bacteria chemotaxis (BC) algorithm. This strategy is evaluated on a number of test functions for local and global optimization, compared with other optimization techniques, and applied to the problem of inverse airfoil design. The comparisons show that on average, BC performs similar to standard evolution strategies and worse than evolution strategies with enhanced convergence properties.

`@article{muller2002a, author = {S.D. Muller and J. Marchetto and S. Airaghi and P. Kournoutsakos}, doi = {10.1109/4235.985689}, journal = {{IEEE} Transactions on Evolutionary Computation}, number = {1}, pages = {16--29}, publisher = {Institute of Electrical and Electronics Engineers ({IEEE})}, title = {Optimization based on bacterial chemotaxis}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/muller2002a.pdf}, volume = {6}, year = {2002} }`

- R. Gämperle, S. D. Mueller, and P. Koumoutsakos, “A parameter study for differential evolution," in Proceedings of the international conference on advances in intelligent systems, fuzzy systems, evolutionary computation (WSEAS), 2002.

[BibTeX] [Abstract] [PDF]

We assess the selection of strategy parameters for Differential Evolution on a set of test problems. The original algorithm is analyzed with respect to its performance depending on the choice of strategy parameters. Although empirical rules are provided in the literature, choosing the proper strategy parameters for Differential Evolution is more difficult than expected.

`@inproceedings{gamperle2002a, author = {G{\"a}mperle, R. and Mueller, S. D. and Koumoutsakos, P.}, booktitle = {Proceedings of the International Conference on Advances in Intelligent Systems, Fuzzy Systems, Evolutionary Computation {(WSEAS)}}, title = {A parameter study for differential evolution}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/gamperle2002a.pdf}, year = {2002} }`

### 2001

- T. Werder, J. H. Walther, R. L. Jaffe, T. Halicioglu, F. Noca, and P. Koumoutsakos, “Molecular dynamics simulation of contact angles of water droplets in carbon nanotubes," Nano letters, vol. 1, iss. 12, pp. 697-702, 2001.

[BibTeX] [Abstract] [PDF] [DOI]

We examine the equilibrium shape of the water droplet and deduce its contact angle with the CNT surface. This is done using isochore line plots of the water following the algorithm suggested by Nijmeijer. Additionally, radial water density profiles and radial hydrogen bond distributions are reported. The systems considered include zigzag CNTs with diameters of 25.0, 50.0, and 75.0 {\AA} respectively and initially flat 23.7 {\AA} thick drops (this corresponds to 12 layers of water molecules). The simulations indicate that pure water does not wet pristine single wall carbon nanotubes.

`@article{werder2001b, author = {Thomas Werder and Jens H. Walther and Richard L. Jaffe and Timur Halicioglu and Flavio Noca and Petros Koumoutsakos}, doi = {10.1021/nl015640u}, journal = {Nano Letters}, month = {dec}, number = {12}, pages = {697--702}, publisher = {American Chemical Society ({ACS})}, title = {Molecular Dynamics Simulation of Contact Angles of Water Droplets in Carbon Nanotubes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/werder2001b.pdf}, volume = {1}, year = {2001} }`

- S. Zimmermann, P. Koumoutsakos, and W. Kinzelbach, “Simulation of pollutant transport using a particle method," Journal of computational physics, vol. 173, iss. 1, pp. 322-347, 2001.

[BibTeX] [Abstract] [PDF] [DOI]

A Lagrangian scheme is presented for the two-dimensional simulation of pollutant transport in a porous medium. The anisotropic extension of the particle strength exchange method is implemented to describe the diffusive{—}dispersive process. By applying the scheme to a benchmark problem with an analytical solution, the method is shown to be accurate and stable even in the limiting cases of vanishing diffusion{—} dispersion coefficients and high anisotropy ratios. The scheme is shown to perform well with spatially variable velocity fields also.

`@article{zimmermann2001a, author = {S. Zimmermann and P. Koumoutsakos and W. Kinzelbach}, doi = {10.1006/jcph.2001.6879}, journal = {Journal of Computational Physics}, month = {oct}, number = {1}, pages = {322--347}, publisher = {Elsevier {BV}}, title = {Simulation of Pollutant Transport Using a Particle Method}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/zimmermann2001a.pdf}, volume = {173}, year = {2001} }`

- J. H. Walther, R. Jaffe, T. Halicioglu, and P. Koumoutsakos, “Carbon nanotubes in water: structural characteristics and energetics," The journal of physical chemistry b, vol. 105, iss. 41, pp. 9980-9987, 2001.

[BibTeX] [Abstract] [PDF] [DOI]

We study the structural properties of water surrounding a carbon nanotube using molecular dynamics simulations. The interaction potentials involve a description of the carbon nanotube using Morse, harmonic bending, torsion, and Lennard-Jones potentials. The water is described by the flexible Simple Point Charge (SPC) model by Teleman et al., and the carbon-water interactions include a carbon-oxygen Lennard-Jones potential, and an electrostatic quadrupole moment acting between the carbon atoms and the charge sites of the water. Vibration of the breathing mode of the carbon nanotube in water is inferred from the oscillations in carbon-carbon van der Waals energy, and the inverse proportionality between the radius of the carbon nanotube and the breathing frequency is in good agreement with experimental values. The results indicate, that under the present conditions, the presence of the water has a negligible influence on the breathing frequency. The water at the carbon-water interface is found to have a HOH plane nearly tangential to the interface, and the water radial density profile exhibits the characteristic layering also found in the graphite-water system. The average number of hydrogen bonds decreases from a value of 3.73 in the bulk phase to a value of 2.89 at the carbon-water interface. The inclusion of the carbon quadrupole moment is found to have a negligible influence on the structural properties of the water. Energy changes that occur by the process of introducing a carbon nanotube in water are calculated. The creation of a cavity in the bulk water to accommodate the nanotube constitutes the largest energy contribution. Results include an analysis of surface structure and energy values for planar and for concave cylindrical surfaces of water.

`@article{walther2001b, author = {J. H. Walther and R. Jaffe and T. Halicioglu and P. Koumoutsakos}, doi = {10.1021/jp011344u}, journal = {The Journal of Physical Chemistry B}, month = {oct}, number = {41}, pages = {9980--9987}, publisher = {American Chemical Society ({ACS})}, title = {Carbon Nanotubes in Water: Structural Characteristics and Energetics}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther2001b.pdf}, volume = {105}, year = {2001} }`

- J. H. Walther and P. Koumoutsakos, “Three-dimensional vortex methods for particle-laden flows with two-way coupling," Journal of computational physics, vol. 167, iss. 1, pp. 39-71, 2001.

[BibTeX] [Abstract] [PDF] [DOI]

This paper presents a three-dimensional viscous vortex method for the simulation of particulate flows with two-way coupling. The flow is computed using Lagrangian vortex elements advected with the local velocity, while their strength is modified to account for viscous diffusion, vortex stretching, and generating vorticity induced by the particles. The solid particles move according to viscous drag and gravity, creating vorticity, which is discretised using vortex elements. This method adaptively tracks the evolution of the vorticity field and the generation of new computational elements to account for the vorticity source term. A key aspect of the present scheme is the remeshing of the computational elements to adaptively accommodate the production of vorticity induced by the solid particles, and to ensure sufficient support for the proper resolution of the diffusion equation. High-order moment-conserving formulas are implemented to maintain the adaptive character of the method while they remain local to minimize the computational cost. These formulas are also implemented in the particle{—}mesh interpolation of the field and particle quantities in the context of a Vortex-in-Cell algorithm. The method is validated against the results of a related finite-difference study for an axisymmetric swirling flow with particles. The method is then applied to the study of a three-dimensional particle blob falling under the effect of gravity. It is shown that drastically different behaviours are found depending on the presence of an initial vorticity field.

`@article{walther2001c, author = {J.H. Walther and P. Koumoutsakos}, doi = {10.1006/jcph.2000.6656}, journal = {Journal of Computational Physics}, month = {feb}, number = {1}, pages = {39--71}, publisher = {Elsevier {BV}}, title = {Three-Dimensional Vortex Methods for Particle-Laden Flows with Two-Way Coupling}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther2001c.pdf}, volume = {167}, year = {2001} }`

- P. Koumoutsakos, J. Freund, and D. Parekh, “Evolution strategies for automatic optimization of jet mixing," AIAA journal, vol. 39, pp. 967-969, 2001.

[BibTeX] [Abstract] [PDF] [DOI]

Evolution strategies (ES) are introduced for the optimization of active control parameters for enhancing jet mixing. It is shown that the evolution algorithms can identify, in an automated fashion, not only previously known effective actuations but also find good but previously unidentified parameters. In this study, simulations of model jets are used to demonstrate the feasibility of the methods. ES are robust, highly parallel, and portable algorithms that may be most useful in an experimental setting at realistic Reynolds numbers. Simulations of inviscid incompressible flows using vortex models, as well as direct numerical simulations (DNS) of very low-Reynolds-number compressible flows, are used in this study to evaluate different forcing parameters.

`@article{koumoutsakos2001a, author = {Petros Koumoutsakos and Jonathan Freund and David Parekh}, doi = {10.2514/3.14826}, journal = {{AIAA} Journal}, month = {jan}, pages = {967--969}, publisher = {American Institute of Aeronautics and Astronautics ({AIAA})}, title = {Evolution strategies for automatic optimization of jet mixing}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos2001a.pdf}, volume = {39}, year = {2001} }`

- S. D. Mueller, J. H. Walther, and P. D. Koumoutsakos, “Evolution strategies for film cooling optimization," AIAA journal, vol. 39, pp. 537-539, 2001.

[BibTeX] [Abstract] [PDF] [DOI]

An evolutionary algorithm is implemented in a realistic automated design cycle of turbine blade film cooling. This design cycle involves the use of empirical formulas for the flow calculation and the use of a commercial software package for the simulation of the heat transfer problem. The overall process consists of an engineering multiobjective optimization problem with constraints. In this work we consider the solution of this problem in the context of an automated optimization cycle using evolution strategies.

`@article{mueller2001a, author = {Sibylle D. Mueller and Jens H. Walther and Petros D. Koumoutsakos}, doi = {10.2514/3.14766}, journal = {{AIAA} Journal}, month = {jan}, pages = {537--539}, publisher = {American Institute of Aeronautics and Astronautics ({AIAA})}, title = {Evolution strategies for film cooling optimization}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/mueller2001a.pdf}, volume = {39}, year = {2001} }`

- J. H. Walther and P. Koumoutsakos, “Molecular dynamics simulation of nanodroplet evaporation," Journal of heat transfer, vol. 123, iss. 4, p. 741, 2001.

[BibTeX] [Abstract] [PDF] [DOI]

We conduct a series of high resolution simulations using several tens of thousands of computational molecules by efficiently employing tree data structures. We present a systematic convergence study to examine the influence of the different parameters imposed by the numerical method, including the size of the computational domain, cutoff radius, droplet diameter, heating frequency and size of heating region, initialisation period, and time step size. It is shown that molecular dynamics simulations converge to the D{\^{}}2 evaporation law to desired accuracy by using large number of computational molecules.

`@article{walther2001a, author = {J. H. Walther and P. Koumoutsakos}, doi = {10.1115/1.1370517}, journal = {Journal of Heat Transfer}, number = {4}, pages = {741}, publisher = {{ASME} International}, title = {Molecular Dynamics Simulation of Nanodroplet Evaporation}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther2001a.pdf}, volume = {123}, year = {2001} }`

### 2000

- F. Noca, M. Hoenk, B. Hunt, P. Koumoutsakos, J. Walther, and T. Werder, “Bio-inspired acoustic sensors based on artificial stereocilia," The journal of the acoustical society of america, vol. 108, iss. 5, pp. 2494-2494, 2000.

[BibTeX] [Abstract] [DOI]

A unique, biologically inspired acoustic transducer based on artificial stereocilia is being developed. This transducer will enable directional sensitivity and miniaturization of acoustic sensors while enhancing sensitivity, ultimately leading to revolutionary advances in acoustic detection and signal processing. The similarities between natural stereocilia and the proposed transducer array could allow for the first time the fabrication of an artificial cochlea that relies on biologically inspired signal{-}processing techniques. Other applications, such as measuring sounds generated by moving micro{-}organisms and nanoscale biological events (metabolic flows), may be enabled by this novel transducer. Finally, artificial stereocilia (functioning as actuators instead of sensors, analogous to stridulatory pegs in insects) will be capable of generating acoustic signals for applications in active acoustic instruments such as sonar. Before these advantages can be realized, fundamental developments are required in the design and fabrication of a transducer based on artificial stereocilia arrays. The potentially revolutionary nature of this transducer is being demonstrated by fabricating and characterizing acoustic sensors based on recently produced carbon nanotube arrays.

`@article{noca2000a, author = {Flavio Noca and Michael Hoenk and Brian Hunt and Petros Koumoutsakos and Jens Walther and Thomas Werder}, doi = {10.1121/1.4743209}, journal = {The Journal of the Acoustical Society of America}, month = {nov}, number = {5}, pages = {2494--2494}, publisher = {Acoustical Society of America ({ASA})}, title = {Bio-inspired acoustic sensors based on artificial stereocilia}, volume = {108}, year = {2000} }`

- J. H. Walther, S. -S. Lee, and P. Koumoutsakos, “Simulation of particle laden flows using particle methods," Physics of fluids, vol. 12, iss. 9, p. S13–S13, 2000.

[BibTeX] [Abstract] [PDF] [DOI]

We present simulations of an initially spherical suspension of solid particles falling due to gravity in a viscous incompressible fluid. The numerical simulations are performed using three-dimensional viscous, vortex methods with a two-way coupling between the fluid and the particles.

`@article{walther2000a, author = {J. H. Walther and S.-S. Lee and P. Koumoutsakos}, doi = {10.1063/1.4739174}, journal = {Physics of Fluids}, month = {sep}, number = {9}, pages = {S13--S13}, publisher = {{AIP} Publishing}, title = {Simulation of Particle Laden Flows Using Particle Methods}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther2000a.pdf}, volume = {12}, year = {2000} }`

- G. Cottet, P. Koumoutsakos, and M. L. O. Salihi, “Vortex methods with spatially varying cores," Journal of computational physics, vol. 162, iss. 1, pp. 164-185, 2000.

[BibTeX] [Abstract] [PDF] [DOI]

The accuracy of vortex methods employing smooth vortex particles/blobs is determined by the blob size, which can be viewed as a mollifier of the vorticity field. For computational efficiency, this core size needs to be spatially variable as particles are used to discretize different parts of the flow field, such as the boundary layer and the wake in bluff body flows. We derive here a consistent approximation for the viscous Navier{—}Stokes equations using variable size vortex particles. This derivation is based on the implementation of mappings that allow the consistent formulation of the diffusion and convection operators of the Navier{—}Stokes equations in the context of vortex methods. Several local mappings can be combined giving the capability of {\textquotedblleft}mesh-embedding{\textquotedblright} to vortex methods. It is shown that the proposed variable method offers a significant improvement on the computational efficiency of constant core size methods while maintaining the adaptive character of the method. The method is ideally suited to flows such as wakes and shear layers and the validity of the approach is illustrated by showing results from cylinder flows and wall-vortex interactions. Using this scheme, previously unattainable simulations of cylinders undergoing rotary oscillations at high Reynolds numbers reveal an interesting mechanism for drastic drag reduction.

`@article{cottet2000a, author = {Georges-Henri Cottet and Petros Koumoutsakos and Mohamed Lemine Ould Salihi}, doi = {10.1006/jcph.2000.6531}, journal = {Journal of Computational Physics}, month = {jul}, number = {1}, pages = {164--185}, publisher = {Elsevier {BV}}, title = {Vortex Methods with Spatially Varying Cores}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/cottet2000a.pdf}, volume = {162}, year = {2000} }`

### 1999

- T. Lundgren and P. Koumoutsakos, “On the generation of vorticity at a free surface," Journal of fluid mechanics, vol. 382, pp. 351-366, 1999.

[BibTeX] [Abstract] [PDF] [DOI]

The mechanism for the generation of vorticity at a viscous free surface is described. This is a free-surface analogue of Lighthill{‘}s strategy for determining the vorticity flux at solid boundaries. In this method the zero-shear-stress and pressure boundary conditions are transformed into a boundary integral formulation suitable for the velocity- vorticity description of the flow. A vortex sheet along the free surface is determined by the pressure boundary condition, while the condition of zero shear stress determines the vorticity at the surface. In general, vorticity is generated at free surfaces whenever there is flow past regions of surface curvature. It is shown that vorticity is conserved in free-surface viscous flows. Vorticity which flows out of the fluid across the free surface is gained by the vortex sheet; the integral of vorticity over the entire fluid region plus the integral of {`}surface vorticity{‘} over the free surface remains constant. The implications of the present strategy as an algorithm for numerical calculations are discussed.

`@article{lundgren1999a, author = {Thomas Lundgren and Petros Koumoutsakos}, doi = {10.1017/s0022112098003978}, journal = {Journal of Fluid Mechanics}, month = {mar}, pages = {351--366}, publisher = {Cambridge University Press ({CUP})}, title = {On the generation of vorticity at a free surface}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/lundgren1999a.pdf}, volume = {382}, year = {1999} }`

- P. Koumoutsakos, “Vorticity flux control for a turbulent channel flow," Physics of fluids, vol. 11, iss. 2, pp. 248-250, 1999.

[BibTeX] [Abstract] [PDF] [DOI]

A feedback control algorithm using wall only information has been applied in simulations of low Reynolds number (Re=180) turbulent channel flow. The present control scheme is based on the manipulation of the vorticity flux components, which can be obtained as a function of time by measuring the instantaneous pressure at the wall and calculating its gradient. The strength of the unsteady mass transpiration actuators can be derived explicitly by inverting a system of equations whose terms depend on the relative locations of the sensors and actuators. The results of the simulations indicate a large (up to 40%) drag reduction. Moreover it appears that using the present methodology open-loop control laws can be devised.

`@article{koumoutsakos1999a, author = {Petros Koumoutsakos}, doi = {10.1063/1.869874}, journal = {Physics of Fluids}, month = {feb}, number = {2}, pages = {248--250}, publisher = {{AIP} Publishing}, title = {Vorticity flux control for a turbulent channel flow}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos1999a.pdf}, volume = {11}, year = {1999} }`

- J. H. Walther, Y. Pan, D. Poulikakos, and P. Koumoutsakos, “Molecular dynamics simulations of evaporation and coalescence of nano size droplet," Journal of heat transfer, vol. 121, iss. 2, 1999.

[BibTeX]`@article{walther1999b, author = {Walther, J. H. and Pan, Y. and Poulikakos, D. and Koumoutsakos, P.}, journal = {Journal of Heat Transfer}, note = {Gallery Award}, number = {2}, title = {Molecular dynamics simulations of evaporation and coalescence of nano size droplet}, volume = {121}, year = {1999} }`

- J. H. Walther and P. Koumoutsakos, “Particle methods for incompressible flow simulations," Speedup journal, vol. 12, iss. 2, pp. 27-32, 1999.

[BibTeX] [Abstract] [PDF]

{}We report here results from the implementation of fast particle methods in parallel computer environments for micro and macroscale flow simulations involving three-dimensional vortex-wall interactions and droplet coalescence and evaporation.

`@article{walther1999a, author = {Walther, J. H. and Koumoutsakos, P.}, journal = {Speedup Journal}, number = {2}, pages = {27--32}, title = {Particle methods for incompressible flow simulations}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther1999a.pdf}, volume = {12}, year = {1999} }`

### 1997

- P. Koumoutsakos, “Active control of vortex—wall interactions," Physics of fluids, vol. 9, iss. 12, pp. 3808-3816, 1997.

[BibTeX] [Abstract] [PDF] [DOI]

A new simple and efficient methodology is presented for the active control of vortical wall bounded flows. The method is based on sensing of the wall pressure and the calculation of the wall vorticity flux. This information is used to determine explicitly the amount of unsteady, spatially varying mass transpiration, used as an actuating mechanism, necessary to achieve a desired wall vorticity flux. The present scheme is based on the physical mechanism of vorticity generation at solid boundaries. It has the advantage of implementing quantities that can be measured and manipulated at the wall, in computations as well as in experiments. It is shown to reproduce efficiently phenomena previously attained using off-wall information. An active control methodology is outlined and the practical implementation of the present scheme is discussed.

`@article{koumoutsakos1997b, author = {Petros Koumoutsakos}, doi = {10.1063/1.869515}, journal = {Physics of Fluids}, month = {dec}, number = {12}, pages = {3808--3816}, publisher = {{AIP} Publishing}, title = {Active control of vortex{\textendash}wall interactions}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos1997b.pdf}, volume = {9}, year = {1997} }`

- P. Koumoutsakos, “Inviscid axisymmetrization of an elliptical vortex," Journal of computational physics, vol. 138, iss. 2, pp. 821-857, 1997.

[BibTeX] [Abstract] [PDF] [DOI]

The inviscid evolution of elliptical, nonuniform vorticity distributions is studied computationally using a high resolution Lagrangian (vortex) method with minimal numerical dissipation. The simulations reveal that the vortices evolve, through a process of filamentation, to a configuration consisting of a vortex surrounded by weak filamentary structures. The shape of the final configuration depends on the profile of the initial vorticity distribution. For the same ellipticity, relatively smooth profiles evolve to axisymmetric vortical structures, whereas sharper initial vorticity distributions result in robust non- axisymmetric configurations. A systematic convergence study is conducted to establish the accuracy of the method for long time inviscid simulations. To further assess the issue of axisymmetrization we compare our results with related numerical and experimental studies.

`@article{koumoutsakos1997a, author = {P. Koumoutsakos}, doi = {10.1006/jcph.1997.5749}, journal = {Journal of Computational Physics}, month = {dec}, number = {2}, pages = {821--857}, publisher = {Elsevier {BV}}, title = {Inviscid Axisymmetrization of an Elliptical Vortex}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos1997a.pdf}, volume = {138}, year = {1997} }`

### 1996

- P. Koumoutsakos and D. Shiels, “Simulations of the viscous flow normal to an impulsively started and uniformly accelerated flat plate," Journal of fluid mechanics, vol. 328, iss. -1, p. 177, 1996.

[BibTeX] [Abstract] [PDF] [DOI]

The development of a two-dimensional viscous incompressible flow generated from an infinitesimally thin flat plate, impulsively started or uniformly accelerated normal to the free stream is studied computationally. An adaptive numerical scheme, based on vortex methods, is used to integrate the vorticity-velocity formulation of the Navier-Stokes equations. The results of the computations complement relevant experimental works while providing us with quantities such as the vorticity field and the unsteady forces experienced by the body. For the uniformly accelerated plate the present simulations capture the development of a number of centers of vorticity along the primary separating shear layer. This phenomenon has been observed in experimental works but has not been predicted by inviscid models. The present simulations suggest that this Kelvin-Helmholtz-type instability is driven by the interaction of primary and secondary vorticity near the tips of the plate and depends on the acceleration of the plate.

`@article{koumoutsakos1996a, author = {P. Koumoutsakos and D. Shiels}, doi = {10.1017/s0022112096008695}, journal = {Journal of Fluid Mechanics}, month = {dec}, number = {-1}, pages = {177}, publisher = {Cambridge University Press ({CUP})}, title = {Simulations of the viscous flow normal to an impulsively started and uniformly accelerated flat plate}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos1996a.pdf}, volume = {328}, year = {1996} }`

### 1995

- P. Koumoutsakos and A. Leonard, “High-resolution simulations of the flow around an impulsively started cylinder using vortex methods," Journal of fluid mechanics, vol. 296, iss. -1, p. 1, 1995.

[BibTeX] [Abstract] [PDF] [DOI]

The development of a two-dimensional viscous incompressible flow generated from a circular cylinder impulsively started into rectilinear motion is studied computationally. An adaptative numerical scheme, based on vortex methods, is used to integrate the vorticity/velocity formulation of the Navier-Stokes equations for a wide range of Reynolds numbers (Re = 40 to 9500). A novel technique is implemented to resolve diffusion effects and enforce the no-slip boundary condition. The Biot-Savart law is employed to compute the velocities, thus eliminating the need for imposing the far-field boundary conditions. An efficient fast summation algorithm was implemented that allows a large number of computational elements, thus producing unprecedented high- resolution simulations. Results are compared to those from other theoretical, experimental and computational works and the relation between the unsteady vorticity field and the forces experienced by the body is discussed

`@article{koumoutsakos1995a, author = {P. Koumoutsakos and A. Leonard}, doi = {10.1017/s0022112095002059}, journal = {Journal of Fluid Mechanics}, month = {aug}, number = {-1}, pages = {1}, publisher = {Cambridge University Press ({CUP})}, title = {High-resolution simulations of the flow around an impulsively started cylinder using vortex methods}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos1995a.pdf}, volume = {296}, year = {1995} }`

### 1994

- P. Koumoutsakos, A. Leonard, and F. Pépin, “Boundary conditions for viscous vortex methods," Journal of computational physics, vol. 113, iss. 1, pp. 52-61, 1994.

[BibTeX] [Abstract] [PDF] [DOI]

This paper presents a Neumann-type vorticity boundary condition for the vorticity formulation of the Navier-Stokes equations. The vorticity creation process at the boundary, due to the no-slip condition, is expressed in terms of a vorticity flux. The scheme is incorporated then into a Lagrangian vortex blob method that uses a particle strength exchange algorithm for viscous diffusion. The no-slip condition is not enforced by the generation of new vortices at the boundary but instead by modifying the strength of the vortices in the vicinity of the boundary.

`@article{koumoutsakos1994a, author = {P. Koumoutsakos and A. Leonard and F. P{\'{e}}pin}, doi = {10.1006/jcph.1994.1117}, journal = {Journal of Computational Physics}, month = {jul}, number = {1}, pages = {52--61}, publisher = {Elsevier {BV}}, title = {Boundary Conditions for Viscous Vortex Methods}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos1994a.pdf}, volume = {113}, year = {1994} }`

### 1993

- P. Koumoutsakos and A. Leonard, “Improved boundary integral method for inviscid boundary condition applications," AIAA journal, vol. 31, iss. 2, pp. 401-404, 1993.

[BibTeX] [Abstract] [PDF] [DOI]

THIS Note deals with the computation of the potential part of an unsteady, incompressible, viscous flow around an arbitrary configuration and the enforcement of the no-through flow boundary condition. To solve the full problem, it should be complemented by a solver to account for the convective and viscous part of the flow.

`@article{koumoutsakos1993a, author = {P. Koumoutsakos and A. Leonard}, doi = {10.2514/3.11682}, journal = {{AIAA} Journal}, month = {feb}, number = {2}, pages = {401--404}, publisher = {American Institute of Aeronautics and Astronautics ({AIAA})}, title = {Improved boundary integral method for inviscid boundary condition applications}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos1993a.pdf}, volume = {31}, year = {1993} }`

### 2017

- A. Economides, L. Amoudruz, S. Litvinov, D. Alexeev, S. Nizzero, P. E. Hadjidoukas, D. Rossinelli, and P. Koumoutsakos, “Towards the virtual rheometer," in Proceedings of the platform for advanced scientific computing – PASC ’17, 2017.

[BibTeX] [PDF] [DOI]`@inproceedings{economides2017a, author = {Athena Economides and Lucas Amoudruz and Sergey Litvinov and Dmitry Alexeev and Sara Nizzero and Panagiotis E. Hadjidoukas and Diego Rossinelli and Petros Koumoutsakos}, booktitle = {Proceedings of the Platform for Advanced Scientific Computing - {PASC} {\textquotesingle}17}, doi = {10.1145/3093172.3093226}, publisher = {{ACM} Press}, title = {Towards the Virtual Rheometer}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/economides2017a.pdf}, year = {2017} }`

- P. Koumoutsakos, E. Chatzi, V. V. Krzhizhanovskaya, M. Lees, J. Dongarra, and P. M. A. Sloot, “The art of computational science, bridging gaps — forming alloys. preface for ICCS 2017," Procedia computer science, vol. 108, pp. 1-6, 2017.

[BibTeX] [PDF] [DOI]`@article{koumoutsakos2017a, author = {Petros Koumoutsakos and Eleni Chatzi and Valeria V. Krzhizhanovskaya and Michael Lees and Jack Dongarra and Peter M.A. Sloot}, doi = {10.1016/j.procs.2017.05.281}, journal = {Procedia Computer Science}, pages = {1--6}, publisher = {Elsevier {BV}}, title = {The Art of Computational Science, Bridging Gaps {\textendash} Forming Alloys. Preface for {ICCS} 2017}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos2017a.pdf}, volume = {108}, year = {2017} }`

- U. Rasthofer, F. Wermelinger, P. Hadjidoukas, and P. Koumoutsakos, “Large scale simulation of cloud cavitation collapse," Procedia computer science, vol. 108, pp. 1763-1772, 2017.

[BibTeX] [PDF] [DOI]`@article{rasthofer2017b, author = {U. Rasthofer and F. Wermelinger and P. Hadjidoukas and P. Koumoutsakos}, doi = {10.1016/j.procs.2017.05.158}, journal = {Procedia Computer Science}, pages = {1763--1772}, publisher = {Elsevier {BV}}, title = {Large Scale Simulation of Cloud Cavitation Collapse}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rasthofer2017b.pdf}, volume = {108}, year = {2017} }`

- S. Verma, P. Hadjidoukas, P. Wirth, and P. Koumoutsakos, “Multi-objective optimization of artificial swimmers," in 2017 IEEE congress on evolutionary computation (CEC), 2017.

[BibTeX] [PDF] [DOI]`@inproceedings{verma2017b, author = {Siddhartha Verma and Panagiotis Hadjidoukas and Philipp Wirth and Petros Koumoutsakos}, booktitle = {2017 {IEEE} Congress on Evolutionary Computation ({CEC})}, doi = {10.1109/cec.2017.7969422}, month = {jun}, publisher = {IEEE}, title = {Multi-objective optimization of artificial swimmers}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/verma2017b.pdf}, year = {2017} }`

- S. Verma, P. Hadjidoukas, P. Wirth, D. Rossinelli, and P. Koumoutsakos, “Pareto optimal swimmers," in Proceedings of the platform for advanced scientific computing – PASC ’17, 2017.

[BibTeX] [PDF] [DOI]`@inproceedings{verma2017c, author = {Siddhartha Verma and Panagiotis Hadjidoukas and Philipp Wirth and Diego Rossinelli and Petros Koumoutsakos}, booktitle = {Proceedings of the Platform for Advanced Scientific Computing - {PASC} {\textquotesingle}17}, doi = {10.1145/3093172.3093232}, publisher = {{ACM} Press}, title = {Pareto Optimal Swimmers}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/verma2017c.pdf}, year = {2017} }`

- S. Verma, G. Novati, F. Noca, and P. Koumoutsakos, “Fast motion of heaving airfoils," Procedia computer science, vol. 108, pp. 235-244, 2017.

[BibTeX] [PDF] [DOI]`@article{verma2017d, author = {Siddhartha Verma and Guido Novati and Flavio Noca and Petros Koumoutsakos}, doi = {10.1016/j.procs.2017.05.166}, journal = {Procedia Computer Science}, pages = {235--244}, publisher = {Elsevier {BV}}, title = {Fast Motion of Heaving Airfoils}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/verma2017d.pdf}, volume = {108}, year = {2017} }`

### 2016

- L. Kulakova, P. Angelikopoulos, P. E. Hadjidoukas, C. Papadimitriou, and P. Koumoutsakos, “Approximate Bayesian computation for granular and molecular dynamics simulations," in Proceedings of the platform for advanced scientific computing – PASC ’16, 2016.

[BibTeX] [PDF] [DOI]`@inproceedings{kulakova2016a, author = {Lina Kulakova and Panagiotis Angelikopoulos and Panagiotis E. Hadjidoukas and Costas Papadimitriou and Petros Koumoutsakos}, booktitle = {Proceedings of the Platform for Advanced Scientific Computing - {PASC} {\textquotesingle}16}, doi = {10.1145/2929908.2929918}, publisher = {{ACM} Press}, title = {Approximate {B}ayesian Computation for Granular and Molecular Dynamics Simulations}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/kulakova2016a.pdf}, year = {2016} }`

- F. Wermelinger, B. Hejazialhosseini, P. Hadjidoukas, D. Rossinelli, and P. Koumoutsakos, “An efficient compressible multicomponent flow solver for heterogeneous CPU/GPU architectures," in Proceedings of the platform for advanced scientific computing – PASC ’16, 2016.

[BibTeX] [PDF] [DOI]`@inproceedings{wermelinger2016a, author = {Fabian Wermelinger and Babak Hejazialhosseini and Panagiotis Hadjidoukas and Diego Rossinelli and Petros Koumoutsakos}, booktitle = {Proceedings of the Platform for Advanced Scientific Computing - {PASC} {\textquotesingle}16}, doi = {10.1145/2929908.2929914}, publisher = {{ACM} Press}, title = {An Efficient Compressible Multicomponent Flow Solver for Heterogeneous {CPU}/{GPU} Architectures}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/wermelinger2016a.pdf}, year = {2016} }`

### 2015

- P. E. Hadjidoukas, D. Rossinelli, F. Wermelinger, J. Sukys, U. Rasthofer, C. Conti, B. Hejazialhosseini, and P. Koumoutsakos, “High throughput simulations of two-phase flows on Blue Gene/Q," in Parallel computing: on the road to exascale, proceedings of the international conference on parallel computing, parco 2015, 1-4 september 2015, edinburgh, scotland, UK, 2015, pp. 767-776.

[BibTeX] [PDF] [DOI]`@inproceedings{hadjidoukas2015c, author = {Panagiotis E. Hadjidoukas and Diego Rossinelli and Fabian Wermelinger and Jonas Sukys and Ursula Rasthofer and Christian Conti and Babak Hejazialhosseini and Petros Koumoutsakos}, booktitle = {Parallel Computing: On the Road to Exascale, Proceedings of the International Conference on Parallel Computing, ParCo 2015, 1-4 September 2015, Edinburgh, Scotland, {UK}}, doi = {10.3233/978-1-61499-621-7-767}, pages = {767--776}, title = {High throughput simulations of two-phase flows on {Blue Gene/Q}}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hadjidoukas2015c.pdf}, year = {2015} }`

- P. E. Hadjidoukas, D. Rossinelli, B. Hejazialhosseini, and P. Koumoutsakos, “From 11 to 14.4 PFLOPs: performance optimization for finite volume flow solver," in Proceedings of the 3rd international conference on exascale applications and software, 2015.

[BibTeX] [PDF]`@inproceedings{hadjidoukas2015d, author = {Panagiotis E. Hadjidoukas and Diego Rossinelli and Babak Hejazialhosseini and Petros Koumoutsakos}, booktitle = {Proceedings of the 3rd International Conference on Exascale Applications and Software}, title = {From 11 to 14.4 {PFLOPs}: Performance Optimization for Finite Volume Flow Solver}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hadjidoukas2015d.pdf}, year = {2015} }`

- D. Rossinelli, Y. Tang, K. Lykov, D. Alexeev, M. Bernaschi, P. Hadjidoukas, M. Bisson, W. Joubert, C. Conti, G. Karniadakis, M. Fatica, I. Pivkin, and P. Koumoutsakos, “The In-Silico Lab-on-a-Chip: petascale and high-throughput simulations of microfluidics at cell resolution," in Proceedings of the international conference for high performance computing, networking, storage and analysis on – SC ’15, 2015.

[BibTeX] [PDF] [DOI]`@inproceedings{rossinelli2015b, author = {Diego Rossinelli and Yu-Hang Tang and Kirill Lykov and Dmitry Alexeev and Massimo Bernaschi and Panagiotis Hadjidoukas and Mauro Bisson and Wayne Joubert and Christian Conti and George Karniadakis and Massimiliano Fatica and Igor Pivkin and Petros Koumoutsakos}, booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on - {SC} {\textquotesingle}15}, doi = {10.1145/2807591.2807677}, publisher = {{ACM} Press}, title = {The {In-Silico Lab-on-a-Chip}: Petascale and High-Throughput Simulations of Microfluidics at Cell Resolution}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rossinelli2015b.pdf}, year = {2015} }`

### 2013

- C. Papadimitriou, P. Angelikopoulos, P. Koumoutsakos, and D. Papadioti, “Efficient techniques for Bayesian inverse modeling of large-order computational models," in Icossar 2013: 11th international conference on structural safety & reliability, 2013.

[BibTeX] [PDF]`@inproceedings{papadimitriou2013a, author = {Papadimitriou, C and Angelikopoulos, P and Koumoutsakos, P and Papadioti, DC}, booktitle = {ICOSSAR 2013: 11th International Conference on Structural Safety \& Reliability}, title = {Efficient techniques for {B}ayesian inverse modeling of large-order computational models}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/papadimitriou2013a.pdf}, year = {2013} }`

- D. Rossinelli, P. Koumoutsakos, B. Hejazialhosseini, P. Hadjidoukas, C. Bekas, A. Curioni, A. Bertsch, S. Futral, S. J. Schmidt, and N. A. Adams, “11 PFLOP/s simulations of cloud cavitation collapse," in Proceedings of the international conference for high performance computing, networking, storage and analysis on – SC ’13, 2013.

[BibTeX] [PDF] [DOI]`@inproceedings{rossinelli2013a, author = {Diego Rossinelli and Petros Koumoutsakos and Babak Hejazialhosseini and Panagiotis Hadjidoukas and Costas Bekas and Alessandro Curioni and Adam Bertsch and Scott Futral and Steffen J. Schmidt and Nikolaus A. Adams}, booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on - {SC} {\textquotesingle}13}, doi = {10.1145/2503210.2504565}, publisher = {{ACM} Press}, title = {11 {PFLOP}/s simulations of cloud cavitation collapse}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rossinelli2013a.pdf}, year = {2013} }`

- C. Voglis, P. E. Hadjidoukas, K. E. Parsopoulos, D. G. Papageorgiou, and I. E. Lagaris, “Adaptive memetic particle swarm optimization with variable local search pool size," in Proceeding of the fifteenth annual conference on genetic and evolutionary computation conference (GECCO), 2013.

[BibTeX] [PDF] [DOI]`@inproceedings{voglis2013b, author = {Costas Voglis and Panagiotis E. Hadjidoukas and Konstantinos E. Parsopoulos and Dimitrios G. Papageorgiou and Isaac E. Lagaris}, booktitle = {Proceeding of the fifteenth annual conference on Genetic and evolutionary computation conference {(GECCO)}}, doi = {10.1145/2463372.2463383}, publisher = {{ACM} Press}, title = {Adaptive memetic particle swarm optimization with variable local search pool size}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/voglis2013b.pdf}, year = {2013} }`

### 2012

- B. Hejazialhosseini, D. Rossinelli, C. Conti, and P. Koumoutsakos, “High throughput software for direct numerical simulations of compressible two-phase flows," in 2012 international conference for high performance computing, networking, storage and analysis, 2012.

[BibTeX] [Abstract] [PDF] [DOI]

We present an open source, object-oriented software for high throughput Direct Numerical Simulations of compressible, two-phase flows. The Navier-Stokes equations are discretized on uniform grids using high order finite volume methods. The software exploits recent CPU micro-architectures by explicit vectorization and adopts NUMA-aware techniques as well as data and computation reordering. We report a compressible flow solver with unprecedented fractions of peak performance: 45% of the peak for a single node (nominal performance of 840 GFLOP/s) and 30% for a cluster of 47’000 cores (nominal performance of 0.8 PFLOP/s). We suggest that the present work may serve as a performance upper bound, regarding achievable GFLOP/s, for two-phase flow solvers using adaptive mesh refinement. The software enables 3D simulations of shock-bubble interaction including, for the first time, effects of diffusion and surface tension, by efficiently employing two hundred billion computational elements.

`@inproceedings{hejazialhosseini2012a, author = {Babak Hejazialhosseini and Diego Rossinelli and Christian Conti and Petros Koumoutsakos}, booktitle = {2012 International Conference for High Performance Computing, Networking, Storage and Analysis}, doi = {10.1109/sc.2012.66}, month = {nov}, publisher = {IEEE}, title = {High throughput software for direct numerical simulations of compressible two-phase flows}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hejazialhosseini2012a.pdf}, year = {2012} }`

### 2011

- D. Rossinelli, L. Chatagny, and P. Koumoutsakos, “Evolutionary optimization of scalar transport in cylinder arrays on multiGPU/multicore architectures," in Proc. eurogen, 2011.

[BibTeX] [Abstract] [PDF]

We optimize a scalar transported by the flow field past an array of cylinders as a model of feeding behavior in swimming schools. We use an evolutionary optimization approach to identify cylinder arrangements that maximize the scalar field in the vicinity of twelve cylinders at ReD = 100. The large number of evaluations required by the Evolutionary Algorithms are compensated by GPU/multicore implementation of particle based flow solvers. We use an FTLE analysis of the flow field to quantify optimal transport and discuss the physical mechanisms associated with optimal configurations.

`@inproceedings{rossinelli2011c, author = {Rossinelli, D. and Chatagny, L. and Koumoutsakos, P.}, booktitle = {Proc. EuroGen}, title = {Evolutionary optimization of scalar transport in cylinder arrays on {multiGPU}/multicore architectures}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rossinelli2011c.pdf}, year = {2011} }`

### 2007

- K. Fukagata, S. Kern, P. Chatelain, P. Koumoutsakos, and N. Kasagi, “Optimization of an anisotropic compliant surface for turbulent friction drag reduction," in Proc. 5th int symp. on turbulence and shear flow phenomena, 2007, pp. 727-732.

[BibTeX] [DOI]`@inproceedings{fukagata2007a, author = {Koji Fukagata and Stefan Kern and Philippe Chatelain and Petros Koumoutsakos and Nobuhide Kasagi}, booktitle = {Proc. 5th Int Symp. on Turbulence and Shear Flow Phenomena}, doi = {10.1080/14685240802441126}, journal = {Journal of Turbulence}, pages = {727--732}, publisher = {Informa {UK} Limited}, title = {Optimization of an anisotropic compliant surface for turbulent friction drag reduction}, volume = {9}, year = {2007} }`

- S. Kern, P. Chatelain, and P. Koumoutsakos, “Modeling, simulation and optimization of anguilliform swimmers," in Bio-mechanisms of swimming and flying, Springer Japan, 2007, pp. 167-178.

[BibTeX] [DOI]`@incollection{kern2007b, author = {Stefan Kern and Philippe Chatelain and Petros Koumoutsakos}, booktitle = {Bio-mechanisms of Swimming and Flying}, doi = {10.1007/978-4-431-73380-5_14}, pages = {167--178}, publisher = {Springer Japan}, title = {Modeling, Simulation and Optimization of Anguilliform Swimmers}, year = {2007} }`

- S. Kern, N. Hansen, and P. Koumoutsakos, “Optimization of simulated fish swimming using efficient local quadratic meta-models and evolution strategies," in Eurogen, 2007.

[BibTeX]`@inproceedings{kern2007c, author = {Kern, S. and Hansen, N. and Koumoutsakos, P.}, booktitle = {Eurogen}, title = {Optimization of Simulated Fish Swimming using Efficient Local Quadratic Meta-models and Evolution Strategies}, year = {2007} }`

- G. Morgenthal and J. H. Walther, “An immersed interface method for the vortex-in-cell algorithm," Computers & structures, vol. 85, iss. 11-14, pp. 712-726, 2007.

[BibTeX] [DOI]`@article{morgenthal2007b, author = {G. Morgenthal and J.H. Walther}, doi = {10.1016/j.compstruc.2007.01.020}, journal = {Computers {\&} Structures}, month = {jun}, number = {11-14}, pages = {712--726}, publisher = {Elsevier {BV}}, title = {An immersed interface method for the Vortex-In-Cell algorithm}, volume = {85}, year = {2007} }`

- J. H. Walther, M. Guénot, E. Machefaux, J. T. Rasmussen, P. Chatelain, V. L. Okulov, J. N. Sørensen, M. Bergdorf, and P. Koumoutsakos, “A numerical study of the stabilitiy of helical vortices using vortex methods," Journal of physics: conference series, vol. 75, p. 12034, 2007.

[BibTeX] [DOI]`@article{walther2007a, author = {J H Walther and M Gu{\'{e}}not and E Machefaux and J T Rasmussen and P Chatelain and V L Okulov and J N S{\o}rensen and M Bergdorf and P Koumoutsakos}, doi = {10.1088/1742-6596/75/1/012034}, journal = {Journal of Physics: Conference Series}, month = {jul}, pages = {012034}, publisher = {{IOP} Publishing}, title = {A numerical study of the stabilitiy of helical vortices using vortex methods}, volume = {75}, year = {2007} }`

### 2006

- A. Auger and N. Hansen, “Reconsidering the progress rate theory for evolution strategies in finite dimensions," in Proceedings of the 8th annual conference on genetic and evolutionary computation (GECCO), 2006.

[BibTeX] [DOI]`@inproceedings{auger2006b, author = {Anne Auger and Nikolaus Hansen}, booktitle = {Proceedings of the 8th annual conference on Genetic and evolutionary computation {(GECCO)}}, doi = {10.1145/1143997.1144081}, publisher = {{ACM} Press}, title = {Reconsidering the progress rate theory for evolution strategies in finite dimensions}, year = {2006} }`

- M. Bergdorf and P. Koumoutsakos, “Multiresolution simulations using particles," in Lecture notes in computer science, Springer Berlin Heidelberg, 2006, pp. 391-402.

[BibTeX] [DOI]`@incollection{bergdorf2006b, author = {Michael Bergdorf and Petros Koumoutsakos}, booktitle = {Lecture Notes in Computer Science}, doi = {10.1007/978-3-540-71351-7_30}, pages = {391--402}, publisher = {Springer Berlin Heidelberg}, title = {Multiresolution Simulations Using Particles}, year = {2006} }`

- N. Hansen, F. Gemperle, A. Auger, and P. Koumoutsakos, “When do heavy-tail distributions help?," in Parallel problem solving from nature – PPSN IX, Springer Berlin Heidelberg, 2006, pp. 62-71.

[BibTeX] [DOI]`@incollection{hansen2006c, author = {Nikolaus Hansen and Fabian Gemperle and Anne Auger and Petros Koumoutsakos}, booktitle = {Parallel Problem Solving from Nature - {PPSN} {IX}}, doi = {10.1007/11844297_7}, pages = {62--71}, publisher = {Springer Berlin Heidelberg}, title = {When Do Heavy-Tail Distributions Help?}, year = {2006} }`

- C. Igel, T. Suttorp, and N. Hansen, “A computational efficient covariance matrix update and a (1+1)-CMA for evolution strategies," in Proceedings of the 8th annual conference on genetic and evolutionary computation (GECCO), 2006.

[BibTeX] [DOI]`@inproceedings{igel2006a, author = {Christian Igel and Thorsten Suttorp and Nikolaus Hansen}, booktitle = {Proceedings of the 8th annual conference on Genetic and evolutionary computation {(GECCO)}}, doi = {10.1145/1143997.1144082}, publisher = {{ACM} Press}, title = {A computational efficient covariance matrix update and a (11)-{CMA} for evolution strategies}, year = {2006} }`

- S. Kern, N. Hansen, and P. Koumoutsakos, “Local meta-models for optimization using evolution strategies," in Parallel problem solving from nature – PPSN IX, Springer Berlin Heidelberg, 2006, pp. 939-948.

[BibTeX] [PDF] [DOI]`@incollection{kern2006c, author = {Stefan Kern and Nikolaus Hansen and Petros Koumoutsakos}, booktitle = {Parallel Problem Solving from Nature - {PPSN} {IX}}, doi = {10.1007/11844297_95}, pages = {939--948}, publisher = {Springer Berlin Heidelberg}, title = {Local Meta-models for Optimization Using Evolution Strategies}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/kern2006c.pdf}, year = {2006} }`

### 2005

- A. Auger and N. Hansen, “Performance evaluation of an advanced local search evolutionary algorithm," in 2005 IEEE congress on evolutionary computation, 2005.

[BibTeX] [DOI]`@inproceedings{auger2005a, author = {A. Auger and N. Hansen}, booktitle = {2005 {IEEE} Congress on Evolutionary Computation}, doi = {10.1109/cec.2005.1554903}, publisher = {IEEE}, title = {Performance Evaluation of an Advanced Local Search Evolutionary Algorithm}, year = {2005} }`

- A. Auger and N. Hansen, “A restart CMA evolution strategy with increasing population size," in 2005 IEEE congress on evolutionary computation, 2005.

[BibTeX] [DOI]`@inproceedings{auger2005b, author = {A. Auger and N. Hansen}, booktitle = {2005 {IEEE} Congress on Evolutionary Computation}, doi = {10.1109/cec.2005.1554902}, publisher = {IEEE}, title = {A Restart {CMA} Evolution Strategy With Increasing Population Size}, year = {2005} }`

- M. Bergdorf and P. Koumoutsakos, “Multiresolution particle methods," in Lecture notes in computational science and engineering, Springer Berlin Heidelberg, 2005, pp. 49-61.

[BibTeX] [DOI]`@incollection{bergdorf2005b, author = {Michael Bergdorf and Petros Koumoutsakos}, booktitle = {Lecture Notes in Computational Science and Engineering}, doi = {10.1007/978-3-540-34234-2_4}, pages = {49--61}, publisher = {Springer Berlin Heidelberg}, title = {Multiresolution Particle Methods}, year = {2005} }`

### 2004

- P. Gonnet, U. Zimmerli, J. H. Walther, T. Werder, and P. Koumoutsakos, “Wetting and hydrophobicity of nanoscale systems with impurities," Nanotech, pp. 69-72, 2004.

[BibTeX]`@article{gonnet2004b, author = {Gonnet, P. and Zimmerli, U. and Walther, J.H. and Werder, T. and Koumoutsakos, P.}, journal = {Nanotech}, pages = {69--72}, title = {Wetting and Hydrophobicity of Nanoscale Systems with Impurities}, year = {2004} }`

- N. Hansen and S. Kern, “Evaluating the CMA evolution strategy on multimodal test functions," in Lecture notes in computer science, Springer Berlin Heidelberg, 2004, pp. 282-291.

[BibTeX] [PDF] [DOI]`@incollection{hansen2004a, author = {Nikolaus Hansen and Stefan Kern}, booktitle = {Lecture Notes in Computer Science}, doi = {10.1007/978-3-540-30217-9_29}, pages = {282--291}, publisher = {Springer Berlin Heidelberg}, title = {Evaluating the {CMA} Evolution Strategy on Multimodal Test Functions}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hansen2004a.pdf}, year = {2004} }`

- R. Jaffe, J. H. Walther, U. Zimmerli, and P. Koumoutsakos, “Modeling the interaction between ethylene diamine and water films on the surface of a carbon nanotube," in 206th joint international meeting of the electrochemical society, 2004.

[BibTeX]`@inproceedings{jaffe2004b, author = {Jaffe, R. and Walther, J.H. and Zimmerli, U. and Koumoutsakos, P.}, booktitle = {206th Joint International Meeting of the Electrochemical Society}, title = {Modeling the Interaction Between Ethylene Diamine and Water Films on the Surface of a Carbon Nanotube}, year = {2004} }`

- S. C. Kassinos, J. H. Walther, E. Kotsalis, and P. Koumoutsakos, “Flow of aqueous solutions in carbon nanotubes," in Multiscale modelling and simulation, Springer Berlin Heidelberg, 2004, pp. 215-226.

[BibTeX] [DOI]`@incollection{kassinos2004a, author = {S. C. Kassinos and J. H. Walther and E. Kotsalis and P. Koumoutsakos}, booktitle = {Multiscale Modelling and Simulation}, doi = {10.1007/978-3-642-18756-8_16}, pages = {215--226}, publisher = {Springer Berlin Heidelberg}, title = {Flow of Aqueous Solutions in Carbon Nanotubes}, year = {2004} }`

- P. Koumoutsakos, U. Zimmerli, T. Werder, and J. Walther, “Nanoscale fluid mechanics," in The handbook of nanotechnology. nanometer structures: theory, modeling, and simulation, SPIE, 2004, pp. 319-393.

[BibTeX] [DOI]`@incollection{koumoutsakos2004a, author = {Petros Koumoutsakos and Urs Zimmerli and Thomas Werder and Jens Walther}, booktitle = {The Handbook of Nanotechnology. Nanometer Structures: Theory, Modeling, and Simulation}, doi = {10.1117/3.537698.ch8}, pages = {319--393}, publisher = {SPIE}, title = {Nanoscale Fluid Mechanics}, year = {2004} }`

- J. Ocenasek, S. Kern, N. Hansen, and P. Koumoutsakos, “A mixed Bayesian optimization algorithm with variance adaptation," in Lecture notes in computer science, Springer Berlin Heidelberg, 2004, pp. 352-361.

[BibTeX] [PDF] [DOI]`@incollection{ocenasek2004a, author = {Jiri Ocenasek and Stefan Kern and Nikolaus Hansen and Petros Koumoutsakos}, booktitle = {Lecture Notes in Computer Science}, doi = {10.1007/978-3-540-30217-9_36}, pages = {352--361}, publisher = {Springer Berlin Heidelberg}, title = {A Mixed {B}ayesian Optimization Algorithm with Variance Adaptation}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/ocenasek2004a.pdf}, year = {2004} }`

- P. Poncet and P. Koumoutsakos, “Optimization of vortex shedding in 3d wakes using belt actuators," in Isope, 2004, pp. 65-77.

[BibTeX] [PDF] [DOI]`@inproceedings{poncet2004a, author = {Philippe Poncet and Petros Koumoutsakos}, booktitle = {ISOPE}, doi = {10.1016/j.crme.2004.10.007}, month = {jan}, pages = {65--77}, publisher = {Elsevier {BV}}, title = {Optimization of Vortex Shedding in 3D Wakes using Belt Actuators}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/poncet2004a.pdf}, volume = {333}, year = {2004} }`

- T. Werder, J. H. Walther, J. Asikainen, and P. Koumoutsakos, “Continuum-particle hybrid methods for dense fluids," in Multiscale modelling and simulation, Springer Berlin Heidelberg, 2004, pp. 227-235.

[BibTeX] [DOI]`@incollection{werder2004a, author = {Thomas Werder and Jens H. Walther and Joonas Asikainen and Petros Koumoutsakos}, booktitle = {Multiscale Modelling and Simulation}, doi = {10.1007/978-3-642-18756-8_17}, pages = {227--235}, publisher = {Springer Berlin Heidelberg}, title = {Continuum-particle hybrid methods for dense fluids}, year = {2004} }`

- U. Zimmerli, M. Parrinello, and P. Koumoutsakos, “Dispersion corrected density functionals applied to the water naphthalene cluster," in Multiscale modelling and simulation, Springer Berlin Heidelberg, 2004, pp. 205-214.

[BibTeX] [DOI]`@incollection{zimmerli2004b, author = {Urs Zimmerli and Michele Parrinello and Petros Koumoutsakos}, booktitle = {Multiscale Modelling and Simulation}, doi = {10.1007/978-3-642-18756-8_15}, pages = {205--214}, publisher = {Springer Berlin Heidelberg}, title = {Dispersion corrected density functionals applied to the water naphthalene cluster}, year = {2004} }`

### 2003

- D. Bueche, G. Guidati, and P. Stoll, “Automated design optimization of compressor blades for stationary, large-scale turbomachinery," in Volume 6: turbo expo 2003, parts a and b, 2003.

[BibTeX] [PDF] [DOI]`@inproceedings{bueche2003a, author = {Dirk Bueche and Gianfranco Guidati and Peter Stoll}, booktitle = {Volume 6: Turbo Expo 2003, Parts A and B}, doi = {10.1115/gt2003-38421}, publisher = {ASME}, title = {Automated Design Optimization of Compressor Blades for Stationary, Large-Scale Turbomachinery}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bueche2003a.pdf}, year = {2003} }`

- D. Bueche, N. Schraudolph, and P. Koumoutsakos, “Accelerating evolutionary algorithms using fitness function models," in Genetic and evolutionary computation conference, 2003.

[BibTeX] [PDF]`@inproceedings{bueche2003b, author = {Bueche, D. and Schraudolph, N. and Koumoutsakos, P.}, booktitle = {Genetic and Evolutionary Computation Conference}, title = {Accelerating Evolutionary Algorithms Using Fitness Function Models}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bueche2003b.pdf}, year = {2003} }`

- D. Bueche, S. Mueller, and P. Koumoutsakos, “Self-adaptation for multi-objective evolutionary algorithms," in Lecture notes in computer science, Springer Berlin Heidelberg, 2003, pp. 267-281.

[BibTeX] [PDF] [DOI]`@incollection{bueche2003c, author = {Dirk Bueche and Sibylle Mueller and Petros Koumoutsakos}, booktitle = {Lecture Notes in Computer Science}, doi = {10.1007/3-540-36970-8_19}, pages = {267--281}, publisher = {Springer Berlin Heidelberg}, title = {Self-Adaptation for Multi-objective Evolutionary Algorithms}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bueche2003c.pdf}, year = {2003} }`

- D. Bueche, P. Stoll, and P. Koumoutsakos, “Multi-objective evolutionary algorithm for optimization of combustion processes," in Manipulation and control of jets in crossflow, Springer Vienna, 2003, pp. 157-169.

[BibTeX] [DOI]`@incollection{bueche2003d, author = {Dirk Bueche and Peter Stoll and Petros Koumoutsakos}, booktitle = {Manipulation and Control of Jets in Crossflow}, doi = {10.1007/978-3-7091-2792-6_12}, pages = {157--169}, publisher = {Springer Vienna}, title = {Multi-Objective Evolutionary Algorithm for Optimization of Combustion Processes}, year = {2003} }`

- S. Hieber, J. Walther, and P. Koumoutsakos, “Fluid-structure interaction using SPH," in Proceedings of the CoLab summer school on multiscale modeling and simulation, 2003.

[BibTeX]`@inproceedings{hieber2003a, author = {Hieber, S. and Walther, J. and Koumoutsakos, P.}, booktitle = {Proceedings of the {CoLab} summer school on Multiscale Modeling and Simulation}, title = {Fluid-Structure Interaction using {SPH}}, year = {2003} }`

- S. Hieber, J. Walther, and P. Koumoutsakos, “Particle flow simulations for surgical planning," in Proceedings of the international symposium on computer aided surgery around the head, 2003.

[BibTeX]`@inproceedings{hieber2003b, author = {Hieber, S. and Walther, J. and Koumoutsakos, P.}, booktitle = {Proceedings of the International Symposium on Computer Aided Surgery around the Head}, title = {Particle flow simulations for surgical planning}, year = {2003} }`

- S. Kern, S. D. Mueller, D. Bueche, N. Hansen, and P. Koumoutsakos, “Learning probability distributions in continuous evolutionary algorithms," in Workshop on fundamentals in evolutionary algorithms, thirtieth international colloquium on automata, 2003.

[BibTeX]`@inproceedings{kern2003a, author = {Kern, S. and Mueller, S. D. and Bueche, D. and Hansen, N. and Koumoutsakos, P.}, booktitle = {Workshop on Fundamentals in Evolutionary Algorithms, Thirtieth International Colloquium on Automata}, title = {Learning Probability Distributions in Continuous Evolutionary Algorithms}, year = {2003} }`

- P. Koumoutsakos, S. D. Mueller, D. Bueche, and M. Milano, “Stochastic optimization for fluid dynamic applications," in Evolutionary methods for design, optimization and control: applications to industrial and societal problems, 2003.

[BibTeX]`@inproceedings{koumoutsakos2003a, author = {Koumoutsakos, P. and Mueller, S. D. and Bueche, D. and Milano, M.}, booktitle = {Evolutionary Methods for Design, Optimization and Control: Applications to Industrial and Societal Problems}, title = {Stochastic optimization for fluid dynamic applications}, year = {2003} }`

- P. Koumoutsakos, R. Jaffe, T. Werder, and J. H. Walther, “On the validity of the no-slip condition in nanofluidics," in Nanotechnology conference and trade show, 2003.

[BibTeX] [PDF]`@inproceedings{koumoutsakos2003b, author = {Koumoutsakos, P. and Jaffe, R. and Werder, T. and Walther, J. H.}, booktitle = {Nanotechnology Conference and Trade Show}, title = {On the Validity of the No-Slip Condition in Nanofluidics}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos2003b.pdf}, year = {2003} }`

- P. Koumoutsakos, U. Zimmerli, and J. H. Walther, “Simulations of carbon nanotubes in aqueous environments," in ASME international mechanical engineering congress, 2003.

[BibTeX]`@inproceedings{koumoutsakos2003c, author = {Koumoutsakos, P. and Zimmerli, U. and Walther, J. H.}, booktitle = {{ASME} International Mechanical Engineering Congress}, title = {Simulations of carbon nanotubes in aqueous environments}, year = {2003} }`

- A. Larsen and J. H. Walther, “Discrete vortex simulation of vortex excitation and mitigation in bridge engineering," in Computational fluid and solid mechanics, Elsevier, 2003, pp. 1397-1400.

[BibTeX] [PDF] [DOI]`@incollection{larsen2003a, author = {Allan Larsen and Jens H. Walther}, booktitle = {Computational Fluid and Solid Mechanics}, doi = {10.1016/b978-008044046-0.50342-0}, pages = {1397--1400}, publisher = {Elsevier}, title = {Discrete vortex simulation of vortex excitation and mitigation in bridge engineering}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/larsen2003a.pdf}, year = {2003} }`

- S. D. Mueller, M. Fehr, and P. Koumoutsakos, “Solving constrained optimization problems using the cma-evolution strategy combined with the augmented lagrangian method," in Workshop on fundamentals in evolutionary algorithms, thirtieth international colloquium on automata, 2003.

[BibTeX]`@inproceedings{mueller2003a, author = {Mueller, S. D. and Fehr, M. and Koumoutsakos, P.}, booktitle = {Workshop on Fundamentals in Evolutionary Algorithms, Thirtieth International Colloquium on Automata}, title = {Solving Constrained Optimization Problems using the CMA-Evolution Strategy combined with the Augmented Lagrangian Method}, year = {2003} }`

- S. D. Mueller, N. Schraudolph, and P. Koumoutsakos, “Evolutionary and gradient-based algorithms for Lennard-Jones cluster optimization," in Workshop proceedings of the genetic and evolutionary computation conference, 2003.

[BibTeX]`@inproceedings{mueller2003b, author = {Mueller, S. D. and Schraudolph, N. and Koumoutsakos, P.}, booktitle = {Workshop proceedings of the Genetic and Evolutionary Computation Conference}, title = {Evolutionary and Gradient-Based Algorithms for {L}ennard-{J}ones Cluster Optimization}, year = {2003} }`

- C. O. Paschereit, B. Schuermans, and D. Bueche, “Combustion process optimization using evolutionary algorithm," in Volume 2: turbo expo, 2003.

[BibTeX] [PDF] [DOI]`@inproceedings{paschereit2003a, author = {Christian Oliver Paschereit and Bruno Schuermans and Dirk Bueche}, booktitle = {Volume 2: Turbo Expo}, doi = {10.1115/gt2003-38393}, publisher = {ASME}, title = {Combustion Process Optimization Using Evolutionary Algorithm}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/paschereit2003a.pdf}, year = {2003} }`

- I. Sbalzarini, P. Koumoutsakos, A. Mezzacasa, and A. Helenius, “Computing diffusion in intracellular compartments: the influence of organelle geometry," in New horizons in molecular sciences and systems: an integrated approach, 2003.

[BibTeX]`@inproceedings{sbalzarini2003a, author = {Sbalzarini, I. and Koumoutsakos, P. and Mezzacasa, A. and Helenius, A.}, booktitle = {New Horizons in Molecular Sciences and Systems: An Integrated Approach}, title = {Computing diffusion in intracellular compartments: The influence of organelle geometry}, year = {2003} }`

- J. H. Walther, R. L. Jaffe, T. Werder, and P. Koumoutsakos, “Slip boundary conditions for water flows in hydrophobic nanoscale geometries," in Nanotech, 2003.

[BibTeX]`@inproceedings{walther2003b, author = {Walther, J. H. and Jaffe, R. L. and Werder, T. and Koumoutsakos, P.}, booktitle = {Nanotech}, title = {Slip boundary conditions for water flows in hydrophobic nanoscale geometries}, year = {2003} }`

- J. H. Walther, T. Werder, U. Zimmerli, and P. Koumoutsakos, “Molecular fluid mechanics of carbon nanotubes," in New horizons in molecular sciences and systems: an integrated approach, 2003.

[BibTeX]`@inproceedings{walther2003c, author = {Walther, J. H. and Werder, T. and Zimmerli, U. and Koumoutsakos, P.}, booktitle = {New Horizons in Molecular Sciences and Systems: An Integrated Approach}, title = {Molecular fluid mechanics of carbon nanotubes}, year = {2003} }`

- J. H. Walther, “Molecular dynamics simulations of aqueous potassium chloride droplets on graphite," in 81st international bunsen discussion meeting “interfacial water in chemistry and biology", 2003.

[BibTeX]`@inproceedings{walther2003d, author = {Walther, J. H.}, booktitle = {81st International Bunsen Discussion Meeting "Interfacial Water in Chemistry and Biology"}, title = {Molecular dynamics simulations of aqueous potassium chloride droplets on graphite}, year = {2003} }`

- J. H. Walther, R. L. Jaffe, T. Werder, and P. Koumoutsakos, “Carbon nanotubes as biosensors – a molecular dynamics study," in E-mrs spring meeting, 2003.

[BibTeX]`@inproceedings{walther2003e, author = {Walther, J. H. and Jaffe, R. L. and Werder, T. and Koumoutsakos, P.}, booktitle = {E-MRS Spring Meeting}, note = {Symposium B. Advanced Multifunctional Nanocarbon materials and nanosystems}, title = {Carbon Nanotubes as Biosensors - A Molecular Dynamics Study}, year = {2003} }`

- T. Werder, J. H. Walther, R. L. Jaffe, and P. Koumoutsakos, “Water-carbon interactions: potential energy calibration using experimental data," in Nanotechnology conference and trade show, 2003.

[BibTeX] [PDF]`@inproceedings{werder2003b, author = {Werder, T. and Walther, J. H. and Jaffe, R. L. and Koumoutsakos, P.}, booktitle = {Nanotechnology Conference and Trade Show}, title = {Water-Carbon Interactions: Potential Energy Calibration Using Experimental Data}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/werder2003b.pdf}, year = {2003} }`

- T. Werder, J. H. Walther, and P. Koumoutsakos, “Nano fluid mechanics of carbon nanotubes – atomistic and multiscale simulations," in Asme international mechanical engineering congress, 2003.

[BibTeX]`@inproceedings{werder2003c, author = {Werder, T. and Walther, J. H. and Koumoutsakos, P.}, booktitle = {ASME International Mechanical Engineering Congress}, title = {Nano fluid mechanics of carbon nanotubes - atomistic and multiscale simulations}, year = {2003} }`

- U. Zimmerli, P. Koumoutsakos, and M. Parrinello, “Bounds for water graphite interaction from DFT," in Program of the cpmd, 2003.

[BibTeX]`@inproceedings{zimmerli2003a, author = {Zimmerli, U. and Koumoutsakos, P. and Parrinello, M.}, booktitle = {Program of the CPMD}, title = {Bounds for water graphite interaction from {DFT}}, year = {2003} }`

### 2002

- D. Bueche, M. Milano, and P. Koumoutsakos, “Self-organizing maps for multi-objective optimization," in Genetic and evolutionary computation conference, 2002.

[BibTeX] [PDF]`@inproceedings{bueche2002a, author = {Bueche, D. and Milano, M. and Koumoutsakos, P.}, booktitle = {Genetic and Evolutionary Computation Conference}, title = {Self-Organizing Maps for Multi-Objective Optimization}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bueche2002a.pdf}, year = {2002} }`

- D. Bueche, G. Guidati, P. Stoll, and P. Koumoutsakos, “Self-organizing maps for pareto optimization of airfoils," in Parallel problem solving from nature — PPSN VII, Springer Berlin Heidelberg, 2002, pp. 122-131.

[BibTeX] [PDF] [DOI]`@incollection{bueche2002b, author = {Dirk Bueche and Gianfranco Guidati and Peter Stoll and Petros Koumoutsakos}, booktitle = {Parallel Problem Solving from Nature {\textemdash} {PPSN} {VII}}, doi = {10.1007/3-540-45712-7_12}, pages = {122--131}, publisher = {Springer Berlin Heidelberg}, title = {Self-organizing Maps for Pareto Optimization of Airfoils}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bueche2002b.pdf}, year = {2002} }`

- P. Catalano, M. Wang, G. Iaccarino, I. F. Sbalzarini, and P. Koumoutsakos, “Optimization of cylinder flow control via zero net mass flux actuators," in Proceedings of the CTR summer program, 2002.

[BibTeX] [PDF]`@inproceedings{catalano2002a, author = {Catalano, P. and Wang, M. and Iaccarino, G. and Sbalzarini, I. F. and Koumoutsakos, P.}, booktitle = {Proceedings of the {CTR} summer program}, title = {Optimization of cylinder flow control via zero net mass flux actuators}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/catalano2002a.pdf}, year = {2002} }`

- G. -H. Cottet, A. Ghoniem, and P. Koumoutsakos, “No title given!," in 4th international workshop on vortex flows and related numerical methods, 2002.

[BibTeX]`@inproceedings{cottet2002a, author = {Cottet, G.-H and Ghoniem, A. and Koumoutsakos, P.}, booktitle = {4th International Workshop on Vortex Flows and Related Numerical Methods}, title = {NO TITLE GIVEN!}, year = {2002} }`

- R. Gaemperle, S. D. Mueller, and P. Koumoutsakos, “A parameter study for differential evolution," in Advances in intelligent systems, fuzzy systems, evolutionary computation, 2002, pp. 293-298.

[BibTeX] [PDF]`@inproceedings{gaemperle2002a, author = {Gaemperle, R. and Mueller, S. D. and Koumoutsakos, P.}, booktitle = {Advances in Intelligent Systems, Fuzzy Systems, Evolutionary Computation}, pages = {293--298}, publisher = {WSEAS Press}, title = {A Parameter Study for Differential Evolution}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/gaemperle2002a.pdf}, year = {2002} }`

- T. Graepel and N. N. Schraudolph, “Stable adaptive momentum for rapid online learning in nonlinear systems," in Artificial neural networks — ICANN 2002, Springer Berlin Heidelberg, 2002, pp. 450-455.

[BibTeX] [PDF] [DOI]`@incollection{graepel2002a, author = {Thore Graepel and Nicol N. Schraudolph}, booktitle = {Artificial Neural Networks {\textemdash} {ICANN} 2002}, doi = {10.1007/3-540-46084-5_73}, pages = {450--455}, publisher = {Springer Berlin Heidelberg}, title = {Stable Adaptive Momentum for Rapid Online Learning in Nonlinear Systems}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/graepel2002a.pdf}, year = {2002} }`

- T. Graepel, “Kernel matrix completion by semidefinite programming," in Artificial neural networks — ICANN 2002, Springer Berlin Heidelberg, 2002, pp. 694-699.

[BibTeX] [PDF] [DOI]`@incollection{graepel2002b, author = {Thore Graepel}, booktitle = {Artificial Neural Networks {\textemdash} {ICANN} 2002}, doi = {10.1007/3-540-46084-5_113}, pages = {694--699}, publisher = {Springer Berlin Heidelberg}, title = {Kernel Matrix Completion by Semidefinite Programming}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/graepel2002b.pdf}, year = {2002} }`

- K. Hermanson, S. Kern, G. Picker, and S. Parneix, “Predictions of external heat transfer for turbine vanes and blades with secondary flowfields," in Proceedings of asme turbo expo, 2002, p. 107.

[BibTeX] [DOI]`@inproceedings{hermanson2002a, author = {K. Hermanson and S. Kern and G. Picker and S. Parneix}, booktitle = {Proceedings of ASME Turbo Expo}, doi = {10.1115/1.1529201}, journal = {Proceedings of ASME Turbo Expo}, pages = {107}, publisher = {{ASME} International}, title = {Predictions of External Heat Transfer for Turbine Vanes and Blades With Secondary Flowfields}, volume = {125}, year = {2002} }`

- R. L. Jaffe, J. H. Walther, E. M. Kotsalis, T. Werder, P. Koumoutsakos, and T. Halicioglu, “Molecular dynamics simulations of fullerenes and carbon nanotubes in water," in In 201st meeting of the electrochemical society, 2002.

[BibTeX]`@inproceedings{jaffe2002a, author = {Jaffe, R. L. and Walther, J. H. and Kotsalis, E. M. and Werder, T. and Koumoutsakos, P. and Halicioglu, T.}, booktitle = {In 201st Meeting of the Electrochemical Society}, title = {Molecular dynamics simulations of fullerenes and carbon nanotubes in water}, year = {2002} }`

- P. Koumoutsakos, “Nanofluidics of carbon nanotubes: towards the development of nanoscale biosensors," in Proceedings of the fifth world congress on computational mechanics (WCCM V), 2002.

[BibTeX]`@inproceedings{koumoutsakos2002a, author = {Koumoutsakos, P.}, booktitle = {Proceedings of the Fifth World Congress on Computational Mechanics {(WCCM V)}}, title = {Nanofluidics of Carbon Nanotubes: Towards the Development of Nanoscale Biosensors}, year = {2002} }`

- G. Morgenthal and J. H. Walther, “An immersed interface method for the vortex-in-cell method," in Fourth international workshop on vortex flow and related numerical methods, 2002, pp. 712-726.

[BibTeX] [DOI]`@inproceedings{morgenthal2002a, author = {G. Morgenthal and J.H. Walther}, booktitle = {Fourth International Workshop on Vortex Flow and Related Numerical Methods}, doi = {10.1016/j.compstruc.2007.01.020}, journal = {Computers {\&} Structures}, month = {jun}, pages = {712--726}, publisher = {Elsevier {BV}}, title = {An immersed interface method for the Vortex-In-Cell method}, volume = {85}, year = {2002} }`

- S. D. Mueller, N. N. Schraudolph, P. Koumoutsakos, and N. Hansen, “Step size adaptation in evolution strategies – two approaches," in Workshop on learning and adaptation in evolutionary computation (GECCO), 2002.

[BibTeX] [PDF]`@inproceedings{mueller2002a, author = {Mueller, S. D. and Schraudolph, N. N. and Koumoutsakos, P. and Hansen, N.}, booktitle = {Workshop on Learning and Adaptation in Evolutionary Computation {(GECCO)}}, title = {Step Size Adaptation in Evolution Strategies - Two Approaches}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/mueller2002a.pdf}, year = {2002} }`

- S. D. Mueller, N. Hansen, and P. Koumoutsakos, “Increasing the serial and the parallel performance of the CMA-evolution strategy with large populations," in Parallel problem solving from nature — PPSN VII, Springer Berlin Heidelberg, 2002, pp. 422-431.

[BibTeX] [PDF] [DOI]`@incollection{mueller2002b, author = {Sibylle D. Mueller and Nikolaus Hansen and Petros Koumoutsakos}, booktitle = {Parallel Problem Solving from Nature {\textemdash} {PPSN} {VII}}, doi = {10.1007/3-540-45712-7_41}, pages = {422--431}, publisher = {Springer Berlin Heidelberg}, title = {Increasing the Serial and the Parallel Performance of the {CMA}-Evolution Strategy with Large Populations}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/mueller2002b.pdf}, year = {2002} }`

- S. D. Mueller and P. Koumoutsakos, “Control of micromixers, jets, and turbine cooling using evolution strategies," in Manipulation and control of transverse jets (CISM), 2002.

[BibTeX] [PDF]`@inproceedings{mueller2002c, author = {Mueller, S. D. and Koumoutsakos, P.}, booktitle = {Manipulation and Control of Transverse Jets ({CISM})}, title = {Control of Micromixers, Jets, and Turbine Cooling Using Evolution Strategies}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/mueller2002c.pdf}, year = {2002} }`

- S. D. Mueller, N. N. Schraudolph, and P. Koumoutsakos, “Step size adaptation in evolution strategies using reinforcement learning," in Proceedings of the ieee world congress on computational intelligence (WCCI), 2002, pp. 151-156.

[BibTeX] [PDF]`@inproceedings{mueller2002d, author = {Mueller, S. D. and Schraudolph, N. N. and Koumoutsakos, P.}, booktitle = {Proceedings of the IEEE World Congress on Computational Intelligence {(WCCI)}}, pages = {151--156}, title = {Step Size Adaptation in Evolution Strategies using Reinforcement Learning}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/mueller2002d.pdf}, year = {2002} }`

- I. F. Sbalzarini, A. Mezzacasa, A. Helenius, and P. Koumoutsakos, “Organelle shape has an influencer on fluorescence recovery results," in Mol. biol. of the cell, 2002.

[BibTeX]`@inproceedings{sbalzarini2002a, author = {Sbalzarini, I. F. and Mezzacasa, A. and Helenius, A. and Koumoutsakos, P.}, booktitle = {Mol. Biol. of the Cell}, title = {Organelle shape has an influencer on fluorescence recovery results}, volume = {13}, year = {2002} }`

- I. F. Sbalzarini, J. Theriot, and P. Koumoutsakos, “Machine learning for biological trajectory classification applications," in Proceedings of the CTR summer program, 2002.

[BibTeX] [PDF]`@inproceedings{sbalzarini2002b, author = {Sbalzarini, I. F. and Theriot, J. and Koumoutsakos, P.}, booktitle = {Proceedings of the {CTR} summer program}, organization = {Center for Turbulence Research}, title = {Machine Learning for Biological Trajectory Classification Applications}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/sbalzarini2002b.pdf}, year = {2002} }`

- N. N. Schraudolph and T. Graepel, “Conjugate directions for stochastic gradient descent," in Artificial neural networks — ICANN 2002, Springer Berlin Heidelberg, 2002, pp. 1351-1356.

[BibTeX] [PDF] [DOI]`@incollection{schraudolph2002b, author = {Nicol N. Schraudolph and Thore Graepel}, booktitle = {Artificial Neural Networks {\textemdash} {ICANN} 2002}, doi = {10.1007/3-540-46084-5_218}, pages = {1351--1356}, publisher = {Springer Berlin Heidelberg}, title = {Conjugate Directions for Stochastic Gradient Descent}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/schraudolph2002b.pdf}, year = {2002} }`

- N. N. Schraudolph and T. Graepel, “Towards stochastic conjugate gradient methods," in Proceedings of the 9th international conference on neural information processing, 2002. ICONIP ’02., 2002.

[BibTeX] [DOI]`@inproceedings{schraudolph2002c, author = {N.N. Schraudolph and T. Graepel}, booktitle = {Proceedings of the 9th International Conference on Neural Information Processing, 2002. {ICONIP} {\textquotesingle}02.}, doi = {10.1109/iconip.2002.1198180}, publisher = {Nanyang Technol. Univ}, title = {Towards stochastic conjugate gradient methods}, year = {2002} }`

- J. H. Walther, R. L. Jaffe, T. Werder, T. Halicioglu, and P. Koumoutsakos, “On the boundary condition for water at a hydrophobic surface," in In proceedings of the summer program, 2002, pp. 317-329.

[BibTeX] [PDF]`@inproceedings{walther2002b, author = {Walther, J. H. and Jaffe, R. L. and Werder, T. and Halicioglu, T. and Koumoutsakos, P.}, booktitle = {In Proceedings of the Summer Program}, organization = {Center for Turbulence Research}, pages = {317--329}, title = {On the boundary condition for water at a hydrophobic surface}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther2002b.pdf}, year = {2002} }`

- J. H. Walther, S. Kern, and P. Koumoutsakos, “Simulation of particulate flow using particle methods a P3M algorithm for charged particulates," in Sedimentation and sediment transport, Springer Netherlands, 2002, pp. 165-168.

[BibTeX] [PDF] [DOI]`@incollection{walther2002c, author = {J. H. Walther and S. Kern and P. Koumoutsakos}, booktitle = {Sedimentation and Sediment Transport}, doi = {10.1007/978-94-017-0347-5_26}, pages = {165--168}, publisher = {Springer Netherlands}, title = {Simulation of Particulate Flow Using Particle Methods a {P3M} Algorithm for Charged Particulates}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther2002c.pdf}, year = {2002} }`

- T. Werder, J. H. Walther, and P. Koumoutsakos, “Hydrodynamics of carbon nanotubes – contact angle and hydrophobic hydration," in Technical proceedings of the second international conference on computational nanoscience and nanotechnology (ICCN), 2002.

[BibTeX] [PDF]`@inproceedings{werder2002a, author = {Werder, T. and Walther, J. H. and Koumoutsakos, P.}, booktitle = {Technical Proceedings of the Second International Conference on Computational Nanoscience and Nanotechnology {(ICCN)}}, title = {Hydrodynamics of Carbon Nanotubes - Contact Angle and Hydrophobic Hydration}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/werder2002a.pdf}, year = {2002} }`

### 2001

- D. Bueche, P. Stoll, and P. Koumoutsakos, “An evolutionary algorithm for multi-objective optimization of combustion processes," in CTR annual research briefs, 2001.

[BibTeX]`@inproceedings{bueche2001a, author = {Bueche, D. and Stoll, P. and Koumoutsakos, P.}, booktitle = {{CTR} Annual Research Briefs}, title = {An evolutionary algorithm for multi-objective optimization of combustion processes}, year = {2001} }`

- D. Bueche, P. Stoll, and P. Koumoutsakos, “Multi-objective optimization of combustion processes," in Cism, 2001.

[BibTeX]`@inproceedings{bueche2001b, author = {Bueche, D. and Stoll, P. and Koumoutsakos, P.}, booktitle = {CISM}, title = {Multi-Objective Optimization of Combustion Processes}, year = {2001} }`

- D. Bueche and R. Dornberger, “New evolutionary algorithm for multi-objective optimization and the application to engineering design problems," in Proceedings of the fourth world congress of structural and multidisciplinary optimization, 2001.

[BibTeX] [PDF]`@inproceedings{bueche2001c, author = {Bueche, D. and Dornberger, R.}, booktitle = {Proceedings of the Fourth World Congress of Structural and Multidisciplinary Optimization}, title = {New Evolutionary Algorithm for Multi-Objective Optimization and the Application to Engineering Design Problems}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bueche2001c.pdf}, year = {2001} }`

- M. Klapper-Rybicka, N. N. Schraudolph, and J. Schmidhuber, “Unsupervised learning in LSTM recurrent neural networks," in Artificial neural networks — ICANN 2001, Springer Berlin Heidelberg, 2001, pp. 684-691.

[BibTeX] [PDF] [DOI]`@incollection{klapperrybicka2001b, author = {Magdalena Klapper-Rybicka and Nicol N. Schraudolph and J{\"u}rgen Schmidhuber}, booktitle = {Artificial Neural Networks {\textemdash} {ICANN} 2001}, doi = {10.1007/3-540-44668-0_95}, pages = {684--691}, publisher = {Springer Berlin Heidelberg}, title = {Unsupervised Learning in {LSTM} Recurrent Neural Networks}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/klapperrybicka2001b.pdf}, year = {2001} }`

- E. M. Kotsalis, R. L. Jaffe, J. H. Walther, T. Werder, and P. Koumoutsakos, “Buckyballs in water: structural characteristics and energetics," in CTR annual research briefs, 2001, pp. 283-291.

[BibTeX] [PDF]`@inproceedings{kotsalis2001a, author = {Kotsalis, E. M. and Jaffe, R. L. and Walther, J. H. and Werder, T. and Koumoutsakos, P.}, booktitle = {{CTR} Annual Research Briefs}, pages = {283--291}, title = {Buckyballs in Water: Structural Characteristics and Energetics}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/kotsalis2001a.pdf}, year = {2001} }`

- P. Koumoutsakos, T. Werder, J. H. Walther, R. L. Jaffe, and T. Halicioglu, “Carbon nanotubes in water: MD simulations of internal & external flow," in Ninth foresight conference on molecular nanotechnology, 2001.

[BibTeX] [PDF]`@inproceedings{koumoutsakos2001b, author = {Koumoutsakos, P. and Werder, T. and Walther, J. H. and Jaffe, R. L. and Halicioglu, T.}, booktitle = {Ninth Foresight Conference on Molecular Nanotechnology}, title = {Carbon Nanotubes in Water: {MD} Simulations of Internal \& External Flow}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos2001b.pdf}, year = {2001} }`

- M. Milano, J. Schmidhuber, and P. Koumoutsakos, “An evolution strategy using self-organizing maps," in International conference on artificial neural networks (ICANN), 2001.

[BibTeX]`@inproceedings{milano2001a, author = {Milano, M. and Schmidhuber, J. and Koumoutsakos, P.}, booktitle = {International Conference on Artificial Neural Networks {(ICANN)}}, title = {An Evolution Strategy using Self-Organizing Maps}, year = {2001} }`

- M. Milano, J. Schmidhuber, and P. Koumoutsakos, “Active learning with adaptive grids," in Artificial neural networks — ICANN 2001, Springer Berlin Heidelberg, 2001, pp. 436-442.

[BibTeX] [PDF] [DOI]`@incollection{milano2001b, author = {Michele Milano and J{\"u}rgen Schmidhuber and Petros Koumoutsakos}, booktitle = {Artificial Neural Networks {\textemdash} {ICANN} 2001}, doi = {10.1007/3-540-44668-0_61}, pages = {436--442}, publisher = {Springer Berlin Heidelberg}, title = {Active Learning with Adaptive Grids}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/milano2001b.pdf}, year = {2001} }`

- S. D. Mueller and P. Koumoutsakos, “Mixing optimization with evolution strategies," in Eurogen, 2001.

[BibTeX] [PDF]`@inproceedings{mueller2001b, author = {Mueller, S. D. and Koumoutsakos, P.}, booktitle = {EUROGEN}, title = {Mixing Optimization with Evolution Strategies}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/mueller2001b.pdf}, year = {2001} }`

- S. D. Mueller, I. F. Sbalzarini, J. H. Walther, and P. Koumoutsakos, “Evolution strategies for the optimization of microdevices," in Proceedings of the congress on evolutionary computation (CEC), 2001, pp. 302-309.

[BibTeX] [PDF]`@inproceedings{mueller2001c, author = {Mueller, S. D. and Sbalzarini, I. F. and Walther, J. H. and Koumoutsakos, P.}, booktitle = {Proceedings of the Congress on Evolutionary Computation {(CEC)}}, pages = {302--309}, title = {Evolution Strategies for the Optimization of Microdevices}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/mueller2001c.pdf}, year = {2001} }`

- M. Papanikolaou, “Respace – a virtual environment for rethinking about space," in Caadria, 2001.

[BibTeX]`@inproceedings{papanikolaou2001a, author = {Papanikolaou, M.}, booktitle = {CAADRIA}, title = {ReSpace - a virtual environment for rethinking about space}, year = {2001} }`

- I. F. Sbalzarini, S. D. Mueller, P. Koumoutsakos, and G. -H. Cottet, “Evolution strategies for computational and experimental fluid dynamics applications," in Proceedings of the genetic and evolutionary computation conference (GECCO), 2001.

[BibTeX] [PDF]`@inproceedings{sbalzarini2001a, author = {Sbalzarini, I. F. and Mueller, S. D. and Koumoutsakos, P. and Cottet, G.-H.}, booktitle = {Proceedings of the Genetic and Evolutionary Computation Conference {(GECCO)}}, publisher = {Morgan Kaufmann}, title = {Evolution Strategies for Computational and Experimental Fluid Dynamics Applications}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/sbalzarini2001a.pdf}, year = {2001} }`

- I. F. Sbalzarini, S. Müller, and P. Koumoutsakos, “Microchannel optimization using multiobjective evolution strategies," in Lecture notes in computer science, Springer Berlin Heidelberg, 2001, pp. 516-530.

[BibTeX] [PDF] [DOI]`@incollection{sbalzarini2001b, author = {Ivo F. Sbalzarini and Sibylle M{\"u}ller and Petros Koumoutsakos}, booktitle = {Lecture Notes in Computer Science}, doi = {10.1007/3-540-44719-9_36}, pages = {516--530}, publisher = {Springer Berlin Heidelberg}, title = {Microchannel Optimization Using Multiobjective Evolution Strategies}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/sbalzarini2001b.pdf}, year = {2001} }`

- N. N. Schraudolph, “Fast curvature matrix-vector products," in Artificial neural networks — ICANN 2001, Springer Berlin Heidelberg, 2001, pp. 19-26.

[BibTeX] [PDF] [DOI]`@incollection{schraudolph2001a, author = {Nicol N. Schraudolph}, booktitle = {Artificial Neural Networks {\textemdash} {ICANN} 2001}, doi = {10.1007/3-540-44668-0_4}, pages = {19--26}, publisher = {Springer Berlin Heidelberg}, title = {Fast Curvature Matrix-Vector Products}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/schraudolph2001a.pdf}, year = {2001} }`

### 2000

- G. -H. Cottet, I. F. Sbalzarini, S. D. Mueller, and P. Koumoutsakos, “Optimization of trailing vortex destruction by evolution strategies," in CTR proceedings of the 2000 summer program, 2000.

[BibTeX] [PDF]`@inproceedings{cottet2000c, author = {Cottet, G.-H. and Sbalzarini, I. F. and Mueller, S. D. and Koumoutsakos, P.}, booktitle = {{CTR} Proceedings of the 2000 Summer Program}, title = {Optimization of trailing vortex destruction by evolution strategies}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/cottet2000c.pdf}, year = {2000} }`

- R. Dornberger, P. Stoll, D. Bueche, and A. Neu, “Multidisciplinary turbomachinery blade design optimization," in 38th aerospace sciences meeting and exhibit, 2000.

[BibTeX] [PDF] [DOI]`@inproceedings{dornberger2000a, author = {Rolf Dornberger and Peter Stoll and Dirk Bueche and Alexander Neu}, booktitle = {38th Aerospace Sciences Meeting and Exhibit}, doi = {10.2514/6.2000-838}, month = {jan}, publisher = {American Institute of Aeronautics and Astronautics}, title = {Multidisciplinary turbomachinery blade design optimization}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/dornberger2000a.pdf}, year = {2000} }`

- R. Dornberger, D. Bueche, and P. Stoll, “Multidisciplinary optimization in turbomachinery design," in Eccomas CMNM, 2000.

[BibTeX] [PDF]`@inproceedings{dornberger2000b, author = {Dornberger, R. and Bueche, D. and Stoll, P.}, booktitle = {Eccomas {CMNM}}, title = {Multidisciplinary Optimization in Turbomachinery Design}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/dornberger2000b.pdf}, volume = {102}, year = {2000} }`

- L. Glielmo, S. Santini, and M. Milano, “Three-way catalytic converter modelling: neural networks and genetic algorithms for the reaction kinetics submodel," in SAE technical paper series, 2000.

[BibTeX] [DOI]`@inproceedings{glielmo2000b, author = {Luigi Glielmo and Stefania Santini and Michele Milano}, booktitle = {{SAE} Technical Paper Series}, doi = {10.4271/2000-01-0212}, month = {mar}, publisher = {{SAE} International}, title = {Three-way Catalytic Converter Modelling: Neural Networks and Genetic Algorithms for the Reaction Kinetics Submodel}, year = {2000} }`

- P. Koumoutsakos, K. Shariff, A. Wray, and A. Pohorille, “Particle methods : from vortex dynamics to biology," in Computational aerosciences, 2000.

[BibTeX]`@inproceedings{koumoutsakos2000a, author = {Koumoutsakos, P. and Shariff, K. and Wray, A. and Pohorille, A.}, booktitle = {Computational Aerosciences}, title = {Particle Methods : From Vortex Dynamics to Biology}, year = {2000} }`

- M. Milano, P. Koumoutsakos, X. Giannakopoulos, and J. Schmidhuber, “Evolutionary computation," in Proceedings of the 2000 congress, 2000, pp. 212-218.

[BibTeX] [PDF]`@inproceedings{milano2000a, author = {Milano, M. and Koumoutsakos, P. and Giannakopoulos, X. and Schmidhuber, J.}, booktitle = {Proceedings of the 2000 Congress}, pages = {212--218}, title = {Evolutionary Computation}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/milano2000a.pdf}, volume = {1}, year = {2000} }`

- M. Milano and P. Koumoutsakos, “A clustering genetic algorithm for actuator optimization in flow control," in Proceedings of 2nd NASA/DoD workshop on evovable hardware, 2000, pp. 263-269.

[BibTeX] [PDF]`@inproceedings{milano2000b, author = {Milano, M. and Koumoutsakos, P.}, booktitle = {Proceedings of 2nd {NASA/DoD} Workshop on Evovable Hardware}, pages = {263--269}, title = {A clustering genetic algorithm for actuator optimization in flow control}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/milano2000b.pdf}, year = {2000} }`

- M. Milano, P. Koumoutsakos, X. Giannakopoulos, and J. Schmidhuber, “Evolving strategies for active flow control," in Proceedings of the 2000 congress on evolutionary computation. CEC00 (cat. no.00th8512), 2000.

[BibTeX] [DOI]`@inproceedings{milano2000c, author = {M. Milano and P. Koumoutsakos and X. Giannakopoulos and J. Schmidhuber}, booktitle = {Proceedings of the 2000 Congress on Evolutionary Computation. {CEC}00 (Cat. No.00TH8512)}, doi = {10.1109/cec.2000.870297}, publisher = {IEEE}, title = {Evolving strategies for active flow control}, year = {2000} }`

- S. D. Mueller, I. F. Sbalzarini, I. Mezic, J. H. Walther, and P. Koumoutsakos, “Evolutionary optimization of mixing microdevices," in Nanotech, 2000.

[BibTeX] [PDF]`@inproceedings{mueller2000a, author = {Mueller, S. D. and Sbalzarini, I. F. and Mezic, I. and Walther, J. H. and Koumoutsakos, P.}, booktitle = {NanoTech}, title = {Evolutionary Optimization of Mixing Microdevices}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/mueller2000a.pdf}, year = {2000} }`

- S. D. Mueller, S. Airaghi, J. Marchetto, and P. Koumoutsakos, “Optimization algorithms based on a model of bacterial chemotaxis," in Sixth international conference on simulation of adaptive behavior: from animals to animats (SAB), 2000.

[BibTeX] [PDF]`@inproceedings{mueller2000b, author = {Mueller, S. D. and Airaghi, S. and Marchetto, J. and Koumoutsakos, P.}, booktitle = {Sixth International Conference on Simulation of Adaptive Behavior: From Animals to Animats {(SAB)}}, note = {Proceedings Supplement}, publisher = {International Society for Adaptive Behavior}, title = {Optimization Algorithms based on a Model of Bacterial Chemotaxis}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/mueller2000b.pdf}, year = {2000} }`

- F. Noca, M. Hoenk, B. Hunt, P. Koumoutsakos, J. Walther, and T. Werder, “Bio-inspired acoustic sensors based on artificial stereocilia," The journal of the acoustical society of america, vol. 108, iss. 5, pp. 2494-2494, 2000.

[BibTeX] [DOI]`@article{noca2000b, author = {Flavio Noca and Michael Hoenk and Brian Hunt and Petros Koumoutsakos and Jens Walther and Thomas Werder}, doi = {10.1121/1.4743209}, journal = {The Journal of the Acoustical Society of America}, month = {nov}, number = {5}, pages = {2494--2494}, publisher = {Acoustical Society of America ({ASA})}, title = {Bio-inspired acoustic sensors based on artificial stereocilia}, volume = {108}, year = {2000} }`

- J. T. Sagredo, J. H. Walther, and P. Koumoutsakos, “Simulation of particulate flows using vortex methods," in Ercoftac conference on dynamics of particle-laden flows, 2000.

[BibTeX]`@inproceedings{sagredo2000a, author = {Sagredo, J. T. and Walther, J. H. and Koumoutsakos, P.}, booktitle = {Ercoftac Conference on Dynamics of Particle-Laden Flows}, title = {Simulation of particulate flows using vortex methods}, year = {2000} }`

- I. F. Sbalzarini, L. K. Su, and P. Koumoutsakos, “Evolutionary optimization for flow experiments," in CTR annual research briefs, 2000.

[BibTeX] [PDF]`@inproceedings{sbalzarini2000a, author = {Sbalzarini, I. F. and Su, L. K. and Koumoutsakos, P.}, booktitle = {{CTR} Annual Research Briefs}, title = {Evolutionary Optimization for Flow Experiments}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/sbalzarini2000a.pdf}, year = {2000} }`

- I. F. Sbalzarini, S. D. Mueller, and P. Koumoutsakos, “Multiobjective optimization using evolutionary algorithms," in Proceedings of the CTR summer program, 2000.

[BibTeX] [PDF]`@inproceedings{sbalzarini2000b, author = {Sbalzarini, I. F. and Mueller, S. D. and Koumoutsakos, P.}, booktitle = {Proceedings of the {CTR} summer program}, title = {Multiobjective Optimization using Evolutionary Algorithms}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/sbalzarini2000b.pdf}, year = {2000} }`

- J. H. Walther, R. L. Jaffe, T. Halicioglu, and P. Koumoutsakos, “Molecular dynamics simulations of carbon nanotubes in water," in CTR proceedings of the 2000 summer program, 2000.

[BibTeX] [PDF]`@inproceedings{walther2000b, author = {Walther, J. H. and Jaffe, R. L. and Halicioglu, T. and Koumoutsakos, P.}, booktitle = {{CTR} Proceedings of the 2000 Summer Program}, title = {Molecular dynamics simulations of carbon nanotubes in water}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther2000b.pdf}, year = {2000} }`

- J. H. Walther, R. L. Jaffe, T. Halicioglu, and P. Koumoutsakos, “Computational studies of carbon nanotubes in water," in Annual meeting of the division of fluid dynamics (APS), 2000.

[BibTeX]`@inproceedings{walther2000c, author = {Walther, J. H. and Jaffe, R. L. and Halicioglu, T. and Koumoutsakos, P.}, booktitle = {Annual Meeting of the Division of Fluid Dynamics {(APS)}}, title = {Computational studies of carbon nanotubes in water}, year = {2000} }`

- J. H. Walther and P. Koumoutsakos, “A computational study of flows in carbon nanotubes," in Nanotech, 2000.

[BibTeX]`@inproceedings{walther2000d, author = {Walther, J. H. and Koumoutsakos, P.}, booktitle = {NanoTech}, title = {A Computational study of flows in carbon nanotubes}, year = {2000} }`

### 1999

- L. Glielmo, S. Santini, M. Milano, and G. Serra, “Three-way catalytic converter modelling: a machine learning approach for the reaction kinetics," in 1999 IEEE/ASME international conference on advanced intelligent mechatronics (cat. no.99th8399), 1999.

[BibTeX] [DOI]`@inproceedings{glielmo1999a, author = {L. Glielmo and S. Santini and M. Milano and G. Serra}, booktitle = {1999 {IEEE}/{ASME} International Conference on Advanced Intelligent Mechatronics (Cat. No.99TH8399)}, doi = {10.1109/aim.1999.803173}, publisher = {IEEE}, title = {Three-way catalytic converter modelling: a machine learning approach for the reaction kinetics}, year = {1999} }`

- P. Koumoutsakos and P. Moin, “Algorithms for shear flow control and optimization," in Proceedings of the 38th IEEE conference on decision and control (cat. no.99ch36304), 1999.

[BibTeX] [PDF] [DOI]`@inproceedings{koumoutsakos1999b, author = {P. Koumoutsakos and P. Moin}, booktitle = {Proceedings of the 38th {IEEE} Conference on Decision and Control (Cat. No.99CH36304)}, doi = {10.1109/cdc.1999.831364}, publisher = {IEEE}, title = {Algorithms for shear flow control and optimization}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos1999b.pdf}, year = {1999} }`

- P. Koumoutsakos and P. Moin, “Machine learning algorithms for flow optimization," in IEEE conf. on decision and control, 1999.

[BibTeX]`@inproceedings{koumoutsakos1999c, author = {Koumoutsakos, P. and Moin, P.}, booktitle = {{IEEE} Conf. on Decision and Control}, title = {Machine Learning Algorithms for Flow Optimization}, year = {1999} }`

- S. D. Mueller, M. Milano, and P. Koumoutsakos, “Application of machine learning algorithms to flow modeling and optimization," in CTR annual research briefs, 1999.

[BibTeX] [PDF]`@inproceedings{mueller1999a, author = {Mueller, S. D. and Milano, M. and Koumoutsakos, P.}, booktitle = {{CTR} Annual Research Briefs}, title = {Application of machine learning algorithms to flow modeling and optimization}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/mueller1999a.pdf}, year = {1999} }`

- M. Papanikolaou and B. Tuncer, “The fake space experience – exploring new spaces," in Ecaade, 1999, pp. 395-402.

[BibTeX]`@inproceedings{papanikolaou1999a, author = {Papanikolaou, M. and Tuncer, B.}, booktitle = {ECAADE}, pages = {395--402}, title = {The Fake Space Experience - Exploring New Spaces}, year = {1999} }`

- J. H. Walther, J. T. Sagredo, and P. Koumoutsakos, “Simulation of particulate flow using vortex methods," in The first international conference on vortex methods, 1999.

[BibTeX]`@inproceedings{walther1999c, author = {Walther, J. H. and Sagredo, J. T. and Koumoutsakos, P.}, booktitle = {The First International Conference on Vortex Methods}, title = {Simulation of Particulate Flow Using Vortex Methods}, year = {1999} }`

### 1998

- P. Koumoutsakos, “Feedback control algorithms for flow control," in IUTAM conf. flow control, 1998.

[BibTeX]`@inproceedings{koumoutsakos1998a, author = {Koumoutsakos, P.}, booktitle = {{IUTAM} Conf. Flow Control}, title = {Feedback Control Algorithms for Flow Control}, year = {1998} }`

- P. Koumoutsakos, “Particle methods for the simulation of multiscale phenomena," in CTR annual research briefs, 1998.

[BibTeX] [PDF]`@inproceedings{koumoutsakos1998b, author = {Koumoutsakos, P.}, booktitle = {{CTR} Annual Research Briefs}, title = {Particle methods for the simulation of multiscale phenomena}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos1998b.pdf}, year = {1998} }`

- P. Koumoutsakos, J. Freund, and D. Parekh, “Evolution strategies for the optimization of jet flow parameters," in CTR summer research briefs, 1998.

[BibTeX] [PDF]`@inproceedings{koumoutsakos1998c, author = {Koumoutsakos, P. and Freund, J. and Parekh, D.}, booktitle = {{CTR} Summer Research Briefs}, title = {Evolution strategies for the optimization of jet flow parameters}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos1998c.pdf}, year = {1998} }`

- A. Larsen and J. H. Walther, “A two dimensional discrete vortex method for bridge aerodynamics applications," in Eccomas, 1998.

[BibTeX] [PDF]`@inproceedings{larsen1998b, author = {Larsen, A. and Walther, J. H.}, booktitle = {ECCOMAS}, title = {A two dimensional discrete vortex method for bridge aerodynamics applications}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/larsen1998b.pdf}, year = {1998} }`

- J. H. Walther, “Discrete vortex methods in bridge aerodynamics and prospects for parallel computing techniques," in International symposium on advances in bridge aerodynamics, 1998.

[BibTeX] [PDF]`@inproceedings{walther1998a, author = {Walther, J. H.}, booktitle = {International Symposium on Advances in Bridge Aerodynamics}, title = {Discrete vortex methods in bridge aerodynamics and prospects for parallel computing techniques}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther1998a.pdf}, year = {1998} }`

### 1997

- G. Abate, L. Glielmo, P. Rinaldi, S. Santini, M. Milano, and G. Serra, “Numerical simulation and analysis of the dynamic behavior of three way catalytic converters," in International conference on combustion, 1997.

[BibTeX]`@inproceedings{abate1997a, author = {Abate, G. and Glielmo, L. and Rinaldi, P. and Santini, S. and Milano, M. and Serra, G.}, booktitle = {International Conference on Combustion}, title = {Numerical Simulation and Analysis of the Dynamic Behavior of Three Way Catalytic Converters}, year = {1997} }`

- P. Koumoutsakos, T. Bewley, E. Hammond, P. Moin, P. Koumoutsakos, T. Bewley, E. Hammond, and P. Moin, “Feedback algorithms for turbulence control – some recent developments," in 28th fluid dynamics conference, 1997.

[BibTeX] [DOI]`@inproceedings{koumoutsakos1997c, author = {Petros Koumoutsakos and Thomas Bewley and Edward Hammond and Parviz Moin and Petros Koumoutsakos and Thomas Bewley and Edward Hammond and Parviz Moin}, booktitle = {28th Fluid Dynamics Conference}, doi = {10.2514/6.1997-2008}, month = {jun}, publisher = {American Institute of Aeronautics and Astronautics}, title = {Feedback algorithms for turbulence control - Some recent developments}, year = {1997} }`

- M. Milano, P. Marino, and F. Vasca, “Robust neural network observer for induction motor control," in IEEE power electronics specialists conference (PESC), 1997.

[BibTeX]`@inproceedings{milano1997c, author = {Milano, M. and Marino, P. and Vasca, F.}, booktitle = {{IEEE} Power Electronics Specialists Conference {(PESC)}}, title = {Robust Neural Network Observer for Induction Motor Control}, year = {1997} }`

- J. H. Walther and A. Larsen, “Analytical and discrete vortex models for an oscillating flat plate with trailing edge flap," in Eighth u.s. national conference on wind engineering, 1997.

[BibTeX] [PDF]`@inproceedings{walther1997b, author = {Walther, J. H. and Larsen, A.}, booktitle = {Eighth U.S. National Conference on Wind Engineering}, title = {Analytical and discrete vortex models for an oscillating flat plate with trailing edge flap}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther1997b.pdf}, year = {1997} }`

### Books

- Control of fluid flow, P. Koumoutsakos and I. Mezic, Eds., Springer-Verlag, 2006.

[BibTeX] [PDF] [DOI]`@book{koumoutsakos2006b, doi = {10.1007/978-3-540-36085-8}, editor = {Koumoutsakos, P. and Mezic, I.}, publisher = {Springer-Verlag}, series = {Lecture Notes in Control and Information}, title = {Control of Fluid Flow}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/koumoutsakos2006b.pdf}, year = {2006} }`

- Multiscale modelling and simulation, S. Attinger and P. D. Koumoutsakos, Eds., Springer, 2004.

[BibTeX] [PDF]`@book{attinger2004a, editor = {Attinger, Sabine and Koumoutsakos, Petros D}, publisher = {Springer}, title = {Multiscale modelling and simulation}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/attinger2004a.pdf}, year = {2004} }`

- G. Cottet and P. D. Koumoutsakos, Vortex methods, Cambridge University Press, 2000.

[BibTeX] [Abstract] [PDF] [DOI]

Vortex methods have matured in recent years, offering an interesting alternative to finite difference and spectral methods for high resolution numerical solutions of the Navier Stokes equations. In the past three decades, research into the numerical analysis aspects of vortex methods has provided a solid mathematical background for understanding the accuracy and stability of the method. At the same time vortex methods retain their appealing physical character, which was the motivation for their introduction. This book presents and analyzes vortex methods as a tool for the direct numerical simulation of impressible viscous flows. It will interest graduate students and researchers in numerical analysis and fluid mechanics and also serve as an ideal textbook for courses in fluid dynamics.

`@book{cottet2000b, author = {Georges-Henri Cottet and Petros D. Koumoutsakos}, doi = {10.1017/cbo9780511526442}, publisher = {Cambridge University Press}, title = {Vortex Methods}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/cottet2000b.pdf}, year = {2000} }`

- A. Gyr, P. Koumoutsakos, and U. Burr, Science and art symposium 2000: 3rd international conference on flow interaction of science and art with exhibition/lectures on interaction of science & art, 28.2—3.3 2000 at the eth zurich, Springer Science & Business Media, 2000.

[BibTeX] [Abstract] [PDF]

Some words about SCART 2000. SCART stands for science and art. SCART meetings are organized in a loose time sequence by an international group of scientists, most of them fluid-dynamicists. The first meeting was held in Hong-Kong, the second one in Berlin, and the third, and latest, one in Zurich. SCART meetings include a scientific conference and a number of art events. The intention is to restart a dialogue between scientists and artists which was so productive in the past. To achieve this goal several lectures given by scientists at the conference are intended for a broader public. In the proceedings they are denoted as SCART lectures. The artists in tum address the main theme of the conference with their contributions. The lectures at SCART 2000 covered the entire field of fluiddynamics, from laminar flows in biological systems to astrophysical events, such as the explosion of a neutron star. The main exhibition by Dutch and Swiss artists showed video and related art under the title ‘Walking on Air’. Experimental music was performed in two concerts. Video and related art was chosen because this medium of expression is very technical and closely related to science and technology. In addition, a common aspect of this kind of art and science is the dimension of time. New ways of possible creative processes were shown with music. The ear decomposes sound by a Fourier analysis, the brain therefore interprets sound in a phase space, whereas images are seen in an analogous form in a physical space. These two impressions are analyzed in two different processing centers in the brain, and it is more than a philosophical question whether we need both types of information to get a reliable grasp of reality. Such ideas were also discussed in two seminars organized by the Collegium Helveticum during the conference. In the proceedings all those interactions cannot be shown, but we hope to transmit a flavor of the interdisciplinary effort, which could stimulate the creativity of the reader as well. Some words about these proceedings. These proceedings contain the scientific contributions, ordered by themes, as they were presented at the conference. To show the close relation between science and art, the proceedings also contain the art part which is reproduced as a catalogue of the exhibition. This part is edited by Nadia Gyr, the curator of the exhibition. Due to this concept and due to the esthetic aspects of many scientific contributions, this book contains a rather extensive representation in colors, 32 pages. It is the hope of the editors, that this book helps in stimulating the dialog between science and art, and that it may also contribute to the continuation of such common efforts.

`@book{gyr2000a, author = {Gyr, Albert and Koumoutsakos, Petros and Burr, Ulrich}, publisher = {Springer Science \& Business Media}, title = {Science and Art Symposium 2000: 3rd International Conference on Flow Interaction of Science and Art with Exhibition/Lectures on Interaction of Science \& Art, 28.2{\textemdash}3.3 2000 at the ETH Zurich}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/gyr2000a.pdf}, year = {2000} }`

### In Collections

- G. Cottet and P. Koumoutsakos, “High order semi-Lagrangian particle methods," in Spectral and high order methods for partial differential equations icosahom 2016, M. Bittencourt, N. Dumont, and J. S. Hesthaven, Eds., Springer International Publishing, 2017, pp. 103-117.

[BibTeX] [Abstract] [PDF] [DOI]

Semi-Lagrangian (or remeshed) particle methods are conservative particle methods where the particles are remeshed at each time-step. The numerical analysis of these methods show that their accuracy is governed by the regularity and moment properties of the remeshing kernel and that their stability is guaranteed by a lagrangian condition which does not rely on the grid size. Turbulent transport and more generally advection dominated flows are applications where these features make them appealing tools. The adaptivity of the method and its ability to capture fine scales at minimal cost can be further reinforced by remeshing particles on adapted grids, in particular through wavelet-based multi-resolution analysis

`@incollection{cottet2017a, author = {Cottet, Georges-Henri and Koumoutsakos, Petros}, booktitle = {Spectral and High Order Methods for Partial Differential Equations ICOSAHOM 2016}, chapter = {6}, doi = {10.1007/978-3-319-65870-4_6}, editor = {Bittencourt, Marco and Dumont, Ney and Hesthaven, Jan S.}, pages = {103-117}, publisher = {Springer International Publishing}, title = {High Order Semi-{L}agrangian Particle Methods}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/cottet2017a.pdf}, year = {2017} }`

- M. Bergdorf, F. Milde, and P. Koumoutsakos, “Particle simulations of growth: application to tumorigenesis," in Modeling tumor vasculature, Springer New York, 2011, pp. 261-303.

[BibTeX] [Abstract] [PDF] [DOI]

We present a particle-based framework for simulations of growth as described by continuum laws. We outline methodological developments such as the use of implicit representations of surfaces and the solution of reaction {—} diffusion equations on volumes and surfaces. We validate the framework on benchmark problems and apply it to simulations of tumor growth and study the effects of boundary conditions on tumor morphology.

`@incollection{bergdorf2011a, author = {Michael Bergdorf and Florian Milde and Petros Koumoutsakos}, booktitle = {Modeling Tumor Vasculature}, doi = {10.1007/978-1-4614-0052-3_11}, month = {nov}, pages = {261--303}, publisher = {Springer New York}, title = {Particle Simulations of Growth: Application to Tumorigenesis}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bergdorf2011a.pdf}, year = {2011} }`

- F. Milde, M. Bergdorf, and P. Koumoutsakos, “Particle simulations of growth: application to angiogenesis," in Modeling tumor vasculature, Springer New York, 2011, pp. 305-334.

[BibTeX] [Abstract] [PDF] [DOI]

We apply the particle-based framework developed in the previous chapter to develop continuum and discrete-continuum models of sprouting angiogenesis under consideration of a detailed tumor microenvironment. We present results on the vessel development as a function of the extracellular matrix and different VEGF isoforms.

`@incollection{milde2011a, author = {Florian Milde and Michael Bergdorf and Petros Koumoutsakos}, booktitle = {Modeling Tumor Vasculature}, doi = {10.1007/978-1-4614-0052-3_12}, month = {nov}, pages = {305--334}, publisher = {Springer New York}, title = {Particle Simulations of Growth: Application to Angiogenesis}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/milde2011a.pdf}, year = {2011} }`

- M. Bergdorf, F. Milde, and P. Koumoutsakos, “Continuum models of mesenchymal cell migration and sprouting angiogenesis," in Multiscale cancer modeling, {CRC} Press, 2010, pp. 213-235.

[BibTeX] [PDF] [DOI]`@incollection{bergdorf2010a, author = {Michael Bergdorf and Florian Milde and Petros Koumoutsakos}, booktitle = {Multiscale Cancer Modeling}, doi = {10.1201/b10407-12}, month = {dec}, pages = {213--235}, publisher = {{CRC} Press}, title = {Continuum Models of Mesenchymal Cell Migration and Sprouting Angiogenesis}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bergdorf2010a.pdf}, year = {2010} }`

- A. Leonard and P. Koumoutsakos, “High resolution vortex simulation of bluff body flows," in Computational wind engineering 1, Elsevier, 1993, pp. 315-325.

[BibTeX] [Abstract] [PDF] [DOI]

New advances in vortex methods for the simulation of unsteady incompressible flows, the fast-vortex algorithm for convection and the method of particle-strength exchange for viscous diffusion, are discussed. The application to bluff body flows is demonstrated for transient flows past a circular cylinder for Re = 40 to 9500.

`@incollection{leonard1993a, author = {A. Leonard and P. Koumoutsakos}, booktitle = {Computational Wind Engineering 1}, doi = {10.1016/b978-0-444-81688-7.50035-8}, pages = {315--325}, publisher = {Elsevier}, title = {High Resolution Vortex Simulation of Bluff Body Flows}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/leonard1993a.pdf}, year = {1993} }`

### 2018

- N. Karvounis, K. M. Pang, S. Mayer, and J. H. Walther, “Numerical simulation of condensation of sulfuric acid and water in a large two-stroke marine diesel engine," Applied energy, vol. 211, pp. 1009-1020, 2018.

[BibTeX] [PDF] [DOI]`@article{karvounis2018a, author = {Nikolas Karvounis and Kar Mun Pang and Stefan Mayer and Jens Honor{\'{e}} Walther}, doi = {10.1016/j.apenergy.2017.11.085}, journal = {Applied Energy}, month = {feb}, pages = {1009--1020}, publisher = {Elsevier {BV}}, title = {Numerical simulation of condensation of sulfuric acid and water in a large two-stroke marine diesel engine}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/karvounis2018a.pdf}, volume = {211}, year = {2018} }`

- J. C. Ong, K. M. Pang, J. H. Walther, J. Ho, and H. K. Ng, “Evaluation of a lagrangian soot tracking method for the prediction of primary soot particle size under engine-like conditions," Journal of aerosol science, vol. 115, pp. 70-95, 2018.

[BibTeX] [PDF] [DOI]`@article{ong2018a, author = {Jiun Cai Ong and Kar Mun Pang and Jens Honore Walther and Jee-Hou Ho and Hoon Kiat Ng}, doi = {10.1016/j.jaerosci.2017.10.013}, journal = {Journal of Aerosol Science}, month = {jan}, pages = {70--95}, publisher = {Elsevier {BV}}, title = {Evaluation of a Lagrangian Soot Tracking Method for the prediction of primary soot particle size under engine-like conditions}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/ong2018a.pdf}, volume = {115}, year = {2018} }`

- E. Oyarzua, J. H. Walther, and H. A. Zambrano, “Water thermophoresis in carbon nanotubes: the interplay between thermophoretic and friction forces," Physical chemistry chemical physics, vol. 20, iss. 5, pp. 3672-3677, 2018.

[BibTeX] [PDF] [DOI]`@article{oyarzua2018a, author = {Elton Oyarzua and Jens H. Walther and Harvey A. Zambrano}, doi = {10.1039/c7cp05749k}, journal = {Physical Chemistry Chemical Physics}, number = {5}, pages = {3672--3677}, publisher = {Royal Society of Chemistry ({RSC})}, title = {Water thermophoresis in carbon nanotubes: the interplay between thermophoretic and friction forces}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/oyarzua2018a.pdf}, volume = {20}, year = {2018} }`

- K. M. Pang, M. Jangi, X. Bai, J. Schramm, and J. H. Walther, “Modelling of diesel spray flames under engine-like conditions using an accelerated eulerian stochastic field method," Combustion and flame, vol. 193, pp. 363-383, 2018.

[BibTeX] [PDF] [DOI]`@article{pang2018a, author = {Kar Mun Pang and Mehdi Jangi and Xue-Song Bai and Jesper Schramm and Jens Honore Walther}, doi = {10.1016/j.combustflame.2018.03.030}, journal = {Combustion and Flame}, month = {jul}, pages = {363--383}, publisher = {Elsevier {BV}}, title = {Modelling of diesel spray flames under engine-like conditions using an accelerated Eulerian Stochastic Field method}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/pang2018a.pdf}, volume = {193}, year = {2018} }`

- R. Podgornik, J. Zavadlav, and M. Praprotnik, “Molecular dynamics simulation of high density DNA arrays," Computation, vol. 6, iss. 1, p. 3, 2018.

[BibTeX] [DOI]`@article{podgornik2018a, author = {Rudolf Podgornik and Julija Zavadlav and Matej Praprotnik}, doi = {10.3390/computation6010003}, journal = {Computation}, month = {jan}, number = {1}, pages = {3}, publisher = {{MDPI} {AG}}, title = {Molecular Dynamics Simulation of High Density {DNA} Arrays}, volume = {6}, year = {2018} }`

- H. J. Spietz, M. M. Hejlesen, and J. H. Walther, “A regularization method for solving the Poisson equation for mixed unbounded-periodic domains," Journal of computational physics, vol. 356, pp. 439-447, 2018.

[BibTeX] [PDF] [DOI]`@article{spietz2018a, author = {Henrik Juul Spietz and Mads M{\o}lholm Hejlesen and Jens Honor{\'{e}} Walther}, doi = {10.1016/j.jcp.2017.12.018}, journal = {Journal of Computational Physics}, month = {mar}, pages = {439--447}, publisher = {Elsevier {BV}}, title = {A regularization method for solving the {P}oisson equation for mixed unbounded-periodic domains}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/spietz2018a.pdf}, volume = {356}, year = {2018} }`

- M. L. Szanyi, C. S. Hemmingsen, W. Yan, J. H. Walther, and S. L. Glimberg, “Near-wellbore modeling of a horizontal well with computational fluid dynamics," Journal of petroleum science and engineering, vol. 160, pp. 119-128, 2018.

[BibTeX] [PDF] [DOI]`@article{szanyi2018a, author = {M{\'{a}}rton L. Szanyi and Casper S. Hemmingsen and Wei Yan and Jens H. Walther and Stefan L. Glimberg}, doi = {10.1016/j.petrol.2017.10.011}, journal = {Journal of Petroleum Science and Engineering}, month = {jan}, pages = {119--128}, publisher = {Elsevier {BV}}, title = {Near-wellbore modeling of a horizontal well with Computational Fluid Dynamics}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/szanyi2018a.pdf}, volume = {160}, year = {2018} }`

- J. Zavadlav, J. Sablić, R. Podgornik, and M. Praprotnik, “Open-boundary molecular dynamics of a DNA molecule in a hybrid explicit/implicit salt solution," Biophysical journal, vol. 114, iss. 10, pp. 2352-2362, 2018.

[BibTeX] [DOI]`@article{zavadlav2018a, author = {Julija Zavadlav and Jurij Sabli{\'{c}} and Rudolf Podgornik and Matej Praprotnik}, doi = {10.1016/j.bpj.2018.02.042}, journal = {Biophysical Journal}, month = {may}, number = {10}, pages = {2352--2362}, publisher = {Elsevier {BV}}, title = {Open-Boundary Molecular Dynamics of a {DNA} Molecule in a Hybrid Explicit/Implicit Salt Solution}, volume = {114}, year = {2018} }`

- J. Zavadlav, S. J. Marrink, and M. Praprotnik, “Multiscale simulation of protein hydration using the SWINGER dynamical clustering algorithm," Journal of chemical theory and computation, vol. 14, iss. 3, pp. 1754-1761, 2018.

[BibTeX] [DOI]`@article{zavadlav2018b, author = {Julija Zavadlav and Siewert J. Marrink and Matej Praprotnik}, doi = {10.1021/acs.jctc.7b01129}, journal = {Journal of Chemical Theory and Computation}, month = {feb}, number = {3}, pages = {1754--1761}, publisher = {American Chemical Society ({ACS})}, title = {Multiscale Simulation of Protein Hydration Using the {SWINGER} Dynamical Clustering Algorithm}, volume = {14}, year = {2018} }`

### 2017

- A. Andersen, T. Bohr, T. Schnipper, and J. H. Walther, “Wake structure and thrust generation of a flapping foil in two-dimensional flow," Journal of fluid mechanics, vol. 812, 2017.

[BibTeX] [PDF] [DOI]`@article{andersen2017a, author = {A. Andersen and T. Bohr and T. Schnipper and J. H. Walther}, doi = {10.1017/jfm.2016.808}, journal = {Journal of Fluid Mechanics}, month = {dec}, publisher = {Cambridge University Press ({CUP})}, title = {Wake structure and thrust generation of a flapping foil in two-dimensional flow}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/andersen2017a.pdf}, volume = {812}, year = {2017} }`

- C. K. Christiansen, J. H. Walther, P. Klit, and A. Vølund, “Investigation of journal orbit and flow pattern in a dynamically loaded journal bearing," Tribology international, vol. 114, pp. 450-457, 2017.

[BibTeX] [PDF] [DOI]`@article{christiansen2017a, author = {Christian Kim Christiansen and Jens Honore Walther and Peder Klit and Anders V{\o}lund}, doi = {10.1016/j.triboint.2017.04.013}, journal = {Tribology International}, month = {oct}, pages = {450--457}, publisher = {Elsevier {BV}}, title = {Investigation of journal orbit and flow pattern in a dynamically loaded journal bearing}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/christiansen2017a.pdf}, volume = {114}, year = {2017} }`

- L. Fu, S. Litvinov, X. Y. Hu, and N. A. Adams, “A novel partitioning method for block-structured adaptive meshes," Journal of computational physics, vol. 341, pp. 447-473, 2017.

[BibTeX] [PDF] [DOI]`@article{fu2017a, author = {Lin Fu and Sergej Litvinov and Xiangyu Y. Hu and Nikolaus A. Adams}, doi = {10.1016/j.jcp.2016.11.016}, journal = {Journal of Computational Physics}, month = {jul}, pages = {447--473}, publisher = {Elsevier {BV}}, title = {A novel partitioning method for block-structured adaptive meshes}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/fu2017a.pdf}, volume = {341}, year = {2017} }`

- I. Hanasaki and J. H. Walther, “Suspended particle transport through constriction channel with Brownian motion," Physical review e, vol. 96, iss. 2, 2017.

[BibTeX] [PDF] [DOI]`@article{hanasaki2017a, author = {Itsuo Hanasaki and Jens H. Walther}, doi = {10.1103/physreve.96.023109}, journal = {Physical Review E}, month = {aug}, number = {2}, publisher = {American Physical Society ({APS})}, title = {Suspended particle transport through constriction channel with {B}rownian motion}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hanasaki2017a.pdf}, volume = {96}, year = {2017} }`

- E. Hovad, P. Larsen, J. Spangenberg, J. H. Walther, J. Thorborg, and J. H. Hattel, “Cavity prediction in sand mould production applying the DISAMATIC process," Powder technology, vol. 321, pp. 204-217, 2017.

[BibTeX] [PDF] [DOI]`@article{hovad2017a, author = {Emil Hovad and Per Larsen and Jon Spangenberg and Jens H. Walther and Jesper Thorborg and Jesper H. Hattel}, doi = {10.1016/j.powtec.2017.08.037}, journal = {Powder Technology}, month = {nov}, pages = {204--217}, publisher = {Elsevier {BV}}, title = {Cavity prediction in sand mould production applying the {DISAMATIC} process}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hovad2017a.pdf}, volume = {321}, year = {2017} }`

- D. Kim, C. Bowman, J. D. T. Bonis-O’Donnell, A. Matzavinos, and D. Stein, “Giant acceleration of DNA diffusion in an array of entropic barriers," Physical review letters, vol. 118, iss. 4, 2017.

[BibTeX] [PDF] [DOI]`@article{kim2017a, author = {Daniel Kim and Clark Bowman and Jackson T. Del Bonis-O'Donnell and Anastasios Matzavinos and Derek Stein}, doi = {10.1103/physrevlett.118.048002}, journal = {Physical Review Letters}, month = {jan}, number = {4}, publisher = {American Physical Society ({APS})}, title = {Giant Acceleration of {DNA} Diffusion in an Array of Entropic Barriers}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/kim2017a.pdf}, volume = {118}, year = {2017} }`

- L. T. Nielsen, S. S. Asadzadeh, J. Dölger, J. H. Walther, T. Kiørboe, and A. Andersen, “Hydrodynamics of microbial filter feeding," Proceedings of the national academy of sciences, vol. 114, iss. 35, pp. 9373-9378, 2017.

[BibTeX] [PDF] [DOI]`@article{nielsen2017a, author = {Nielsen, Lasse Tor and Asadzadeh, Seyed Saeed and D{\"o}lger, Julia and Walther, Jens H. and Ki{\o}rboe, Thomas and Andersen, Anders}, doi = {10.1073/pnas.1708873114}, journal = {Proceedings of the National Academy of Sciences}, month = {aug}, number = {35}, pages = {9373--9378}, publisher = {Proceedings of the National Academy of Sciences}, title = {Hydrodynamics of microbial filter feeding}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/nielsen2017a.pdf}, volume = {114}, year = {2017} }`

- J. J. Olsen, C. S. Hemmingsen, L. Bergmann, K. K. Nielsen, S. L. Glimberg, and J. H. Walther, “Characterization and erosion modeling of a nozzle-based inflow-control device," SPE drilling & completion, 2017.

[BibTeX] [PDF] [DOI]`@article{olsen2017a, author = {J{\'{o}}gvan J. Olsen and Casper S. Hemmingsen and Line Bergmann and Kenny K. Nielsen and Stefan L. Glimberg and Jens H. Walther}, doi = {10.2118/186090-pa}, journal = {{SPE} Drilling {\&} Completion}, month = {may}, publisher = {Society of Petroleum Engineers ({SPE})}, title = {Characterization and Erosion Modeling of a Nozzle-Based Inflow-Control Device}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/olsen2017a.pdf}, year = {2017} }`

- K. M. Pang, N. Karvounis, J. H. Walther, J. Schramm, P. Glarborg, and S. Mayer, “Modelling of temporal and spatial evolution of sulphur oxides and sulphuric acid under large, two-stroke marine engine-like conditions using integrated CFD-chemical kinetics," Applied energy, vol. 193, pp. 60-73, 2017.

[BibTeX] [PDF] [DOI]`@article{pang2017a, author = {Kar Mun Pang and Nikolas Karvounis and Jens Honore Walther and Jesper Schramm and Peter Glarborg and Stefan Mayer}, doi = {10.1016/j.apenergy.2017.02.020}, journal = {Applied Energy}, month = {may}, pages = {60--73}, publisher = {Elsevier {BV}}, title = {Modelling of temporal and spatial evolution of sulphur oxides and sulphuric acid under large, two-stroke marine engine-like conditions using integrated {CFD}-chemical kinetics}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/pang2017a.pdf}, volume = {193}, year = {2017} }`

- N. Ramos-García, M. M. Hejlesen, J. N. Sørensen, and J. H. Walther, “Hybrid vortex simulations of wind turbines using a three-dimensional viscous-inviscid panel method," Wind energy, vol. 20, iss. 11, pp. 1871-1889, 2017.

[BibTeX] [PDF] [DOI]`@article{ramosgarcia2017a, author = {N{\'{e}}stor Ramos-Garc{\'{\i}}a and Mads M{\o}lholm Hejlesen and Jens N{\o}rkaer S{\o}rensen and Jens Honor{\'{e}} Walther}, doi = {10.1002/we.2126}, journal = {Wind Energy}, month = {jun}, number = {11}, pages = {1871--1889}, publisher = {Wiley-Blackwell}, title = {Hybrid vortex simulations of wind turbines using a three-dimensional viscous-inviscid panel method}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/ramosgarcia2017a.pdf}, volume = {20}, year = {2017} }`

- U. Rasthofer and V. Gravemeier, “Recent developments in variational multiscale methods for large-eddy simulation of turbulent flow," Archives of computational methods in engineering, 2017.

[BibTeX] [PDF] [DOI]`@article{rasthofer2017a, author = {Ursula Rasthofer and Volker Gravemeier}, doi = {10.1007/s11831-017-9209-4}, journal = {Archives of Computational Methods in Engineering}, month = {feb}, publisher = {Springer Nature}, title = {Recent Developments in Variational Multiscale Methods for Large-Eddy Simulation of Turbulent Flow}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rasthofer2017a.pdf}, year = {2017} }`

- H. J. Spietz, M. M. Hejlesen, and J. H. Walther, “Iterative Brinkman penalization for simulation of impulsively started flow past a sphere and a circular disc," Journal of computational physics, vol. 336, pp. 261-274, 2017.

[BibTeX] [PDF] [DOI]`@article{spietz2017a, author = {Spietz, Henrik Juul and Hejlesen, Mads M{\o}lholm and Walther, Jens Honor{\'{e}}}, doi = {10.1016/j.jcp.2017.01.064}, journal = {Journal of Computational Physics}, month = {may}, pages = {261--274}, publisher = {Elsevier {BV}}, title = {Iterative {B}rinkman penalization for simulation of impulsively started flow past a sphere and a circular disc}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/spietz2017a.pdf}, volume = {336}, year = {2017} }`

- E. Wagemann, E. Oyarzua, J. H. Walther, and H. A. Zambrano, “Slip divergence of water flow in graphene nanochannels: the role of chirality," Phys. chem. chem. phys., vol. 19, iss. 13, pp. 8646-8652, 2017.

[BibTeX] [PDF] [DOI]`@article{wagemann2017a, author = {Enrique Wagemann and Elton Oyarzua and Jens H. Walther and Harvey A. Zambrano}, doi = {10.1039/c6cp07755b}, journal = {Phys. Chem. Chem. Phys.}, number = {13}, pages = {8646--8652}, publisher = {Royal Society of Chemistry ({RSC})}, title = {Slip divergence of water flow in graphene nanochannels: the role of chirality}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/wagemann2017a.pdf}, volume = {19}, year = {2017} }`

- Y. Yang, J. H. Walther, Y. Yan, and C. Wen, “CFD modeling of condensation process of water vapor in supersonic flows," Applied thermal engineering, vol. 115, pp. 1357-1362, 2017.

[BibTeX] [PDF] [DOI]`@article{yang2017a, author = {Yan Yang and Jens Honore Walther and Yuying Yan and Chuang Wen}, doi = {10.1016/j.applthermaleng.2017.01.047}, journal = {Applied Thermal Engineering}, month = {mar}, pages = {1357--1362}, publisher = {Elsevier {BV}}, title = {{CFD} modeling of condensation process of water vapor in supersonic flows}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/yang2017a.pdf}, volume = {115}, year = {2017} }`

- J. Zavadlav and M. Praprotnik, “Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics," The journal of chemical physics, vol. 147, iss. 11, p. 114110, 2017.

[BibTeX] [Abstract] [PDF] [DOI]

Multiscale methods are the most efficient way to address the interlinked spatiotemporal scales encoun- tered in soft matter and molecular liquids. In the literature reported hybrid approaches span from quantum to atomistic, coarse-grained, and continuum length scales. In this article, we present the hybrid coupling of the molecular dynamics (MD) and dissipative particle dynamics (DPD) methods, bridging the micro- and mesoscopic descriptions. The interfacing is performed within the adap- tive resolution scheme (AdResS), which is a linear momentum conserving coupling technique. Our methodology is hence suitable to simulate fluids on the micro/mesoscopic scale, where hydrodynam- ics plays an important role. The presented approach is showcased for water at ambient conditions. The supramolecular coupling is enabled by a recently developed clustering algorithm SWINGER that assembles, disassembles, and reassembles clusters as needed during the course of the simulation. This allows for a seamless coupling between standard atomistic MD and DPD models. The developed framework can be readily applied to various applications in the fields of materials and life sciences, e.g., simulations of phospholipids and polymer melts, or to study the red blood cells behavior in normal and disease states.

`@article{zavadlav2017a, author = {Julija Zavadlav and Matej Praprotnik}, doi = {10.1063/1.4986916}, journal = {The Journal of Chemical Physics}, month = {sep}, number = {11}, pages = {114110}, publisher = {{AIP} Publishing}, title = {Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/zavadlav2017a.pdf}, volume = {147}, year = {2017} }`

### 2016

- B. O. Andersen, N. F. Nielsen, and J. H. Walther, “Numerical and experimental study of pulse-jet cleaning in fabric filters," Powder technology, vol. 291, pp. 284-298, 2016.

[BibTeX] [PDF] [DOI]`@article{andersen2016a, author = {B.O. Andersen and N.F. Nielsen and J.H. Walther}, doi = {10.1016/j.powtec.2015.12.028}, journal = {Powder Technology}, month = {apr}, pages = {284--298}, publisher = {Elsevier {BV}}, title = {Numerical and experimental study of pulse-jet cleaning in fabric filters}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/andersen2016a.pdf}, volume = {291}, year = {2016} }`

- D. Azarnykh, S. Litvinov, X. Bian, and N. A. Adams, “Determination of macroscopic transport coefficients of a dissipative particle dynamics solvent," Physical review e, vol. 93, iss. 1, 2016.

[BibTeX] [PDF] [DOI]`@article{azarnykh2016a, author = {Dmitrii Azarnykh and Sergey Litvinov and Xin Bian and Nikolaus A. Adams}, doi = {10.1103/physreve.93.013302}, journal = {Physical Review E}, month = {jan}, number = {1}, publisher = {American Physical Society ({APS})}, title = {Determination of macroscopic transport coefficients of a dissipative particle dynamics solvent}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/azarnykh2016a.pdf}, volume = {93}, year = {2016} }`

- M. M. Hejlesen and J. H. Walther, “A multiresolution method for solving the poisson equation using high order regularization," Journal of computational physics, vol. 326, pp. 188-196, 2016.

[BibTeX] [PDF] [DOI]`@article{hejlesen2016a, author = {Hejlesen, Mads M{\o}lholm and Walther, Jens Honor{\'{e}}}, doi = {10.1016/j.jcp.2016.08.053}, journal = {Journal of Computational Physics}, month = {dec}, pages = {188--196}, publisher = {Elsevier {BV}}, title = {A multiresolution method for solving the Poisson equation using high order regularization}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hejlesen2016a.pdf}, volume = {326}, year = {2016} }`

- C. S. Hemmingsen, K. M. Ingvorsen, S. Mayer, and J. H. Walther, “LES and URANS simulations of the swirling flow in a dynamic model of a uniflow-scavenged cylinder," International journal of heat and fluid flow, vol. 62, pp. 213-223, 2016.

[BibTeX] [PDF] [DOI]`@article{hemmingsen2016a, author = {Casper S. Hemmingsen and Kristian M. Ingvorsen and Stefan Mayer and Jens H. Walther}, doi = {10.1016/j.ijheatfluidflow.2016.10.008}, journal = {International Journal of Heat and Fluid Flow}, month = {dec}, pages = {213--223}, publisher = {Elsevier {BV}}, title = {{LES} And {URANS} simulations of the swirling flow in a dynamic model of a uniflow-scavenged cylinder}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hemmingsen2016a.pdf}, volume = {62}, year = {2016} }`

- E. Hovad, J. Spangenberg, P. Larsen, J. H. Walther, J. Thorborg, and J. H. Hattel, “Simulating the DISAMATIC process using the discrete element method — a dynamical study of granular flow," Powder technology, vol. 303, pp. 228-240, 2016.

[BibTeX] [PDF] [DOI]`@article{hovad2016a, author = {E. Hovad and J. Spangenberg and P. Larsen and J.H. Walther and J. Thorborg and J.H. Hattel}, doi = {10.1016/j.powtec.2016.09.039}, journal = {Powder Technology}, month = {dec}, pages = {228--240}, publisher = {Elsevier {BV}}, title = {Simulating the {DISAMATIC} process using the discrete element method {\textemdash} a dynamical study of granular flow}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hovad2016a.pdf}, volume = {303}, year = {2016} }`

- N. Karathanasopoulos and P. Angelikopoulos, “Optimal structural arrangements of multilayer helical assemblies," International journal of solids and structures, vol. 78-79, pp. 1-8, 2016.

[BibTeX] [PDF] [DOI]`@article{karathanasopoulos2016a, author = {Nikolaos Karathanasopoulos and Panagiotis Angelikopoulos}, doi = {10.1016/j.ijsolstr.2015.09.023}, journal = {International Journal of Solids and Structures}, month = {jan}, pages = {1--8}, publisher = {Elsevier {BV}}, title = {Optimal structural arrangements of multilayer helical assemblies}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/karathanasopoulos2016a.pdf}, volume = {78-79}, year = {2016} }`

- N. K. Karna, E. Oyarzua, J. H. Walther, and H. A. Zambrano, “Effect of the meniscus contact angle during early regimes of spontaneous imbibition in nanochannels," Phys. chem. chem. phys., vol. 18, iss. 47, pp. 31997-32001, 2016.

[BibTeX] [PDF] [DOI]`@article{karna2016a, author = {Nabin Kumar Karna and Elton Oyarzua and Jens H. Walther and Harvey A. Zambrano}, doi = {10.1039/c6cp06155a}, journal = {Phys. Chem. Chem. Phys.}, number = {47}, pages = {31997--32001}, publisher = {Royal Society of Chemistry ({RSC})}, title = {Effect of the meniscus contact angle during early regimes of spontaneous imbibition in nanochannels}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/karna2016a.pdf}, volume = {18}, year = {2016} }`

- S. Litvinov, Q. Xie, X. Hu, N. Adams, and M. Ellero, “Simulation of individual polymer chains and polymer solutions with smoothed dissipative particle dynamics," Fluids, vol. 1, iss. 1, p. 7, 2016.

[BibTeX] [DOI]`@article{litvinov2016a, author = {Sergey Litvinov and Qingguang Xie and Xiangyu Hu and Nikolaus Adams and Marco Ellero}, doi = {10.3390/fluids1010007}, journal = {Fluids}, month = {feb}, number = {1}, pages = {7}, publisher = {{MDPI} {AG}}, title = {Simulation of Individual Polymer Chains and Polymer Solutions with Smoothed Dissipative Particle Dynamics}, volume = {1}, year = {2016} }`

- S. Mishra, C. Schwab, and J. Šukys, “Multi-level Monte Carlo finite volume methods for uncertainty quantification of acoustic wave propagation in random heterogeneous layered medium," Journal of computational physics, vol. 312, pp. 192-217, 2016.

[BibTeX] [PDF] [DOI]`@article{mishra2016a, author = {S. Mishra and Ch. Schwab and J. {\v{S}}ukys}, doi = {10.1016/j.jcp.2016.02.014}, journal = {Journal of Computational Physics}, month = {may}, pages = {192--217}, publisher = {Elsevier {BV}}, title = {Multi-level {M}onte {C}arlo finite volume methods for uncertainty quantification of acoustic wave propagation in random heterogeneous layered medium}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/mishra2016a.pdf}, volume = {312}, year = {2016} }`

- K. M. Pang, N. Karvounis, J. H. Walther, and J. Schramm, “Numerical investigation of soot formation and oxidation processes under large two-stroke marine diesel engine-like conditions using integrated CFD-chemical kinetics," Applied energy, vol. 169, pp. 874-887, 2016.

[BibTeX] [PDF] [DOI]`@article{pang2016a, author = {Kar Mun Pang and Nikolas Karvounis and Jens Honore Walther and Jesper Schramm}, doi = {10.1016/j.apenergy.2016.02.081}, journal = {Applied Energy}, month = {may}, pages = {874--887}, publisher = {Elsevier {BV}}, title = {Numerical investigation of soot formation and oxidation processes under large two-stroke marine diesel engine-like conditions using integrated {CFD}-chemical kinetics}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/pang2016a.pdf}, volume = {169}, year = {2016} }`

- C. Wen, A. Li, J. H. Walther, and Y. Yang, “Effect of swirling device on flow behavior in a supersonic separator for natural gas dehydration," Separation and purification technology, vol. 168, pp. 68-73, 2016.

[BibTeX] [PDF] [DOI]`@article{wen2016a, author = {Chuang Wen and Anqi Li and Jens Honore Walther and Yan Yang}, doi = {10.1016/j.seppur.2016.05.019}, journal = {Separation and Purification Technology}, month = {aug}, pages = {68--73}, publisher = {Elsevier {BV}}, title = {Effect of swirling device on flow behavior in a supersonic separator for natural gas dehydration}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/wen2016a.pdf}, volume = {168}, year = {2016} }`

- C. Wen, Y. Yang, J. H. Walther, K. M. Pang, and Y. Feng, “Effect of delta wing on the particle flow in a novel gas supersonic separator," Powder technology, vol. 304, pp. 261-267, 2016.

[BibTeX] [PDF] [DOI]`@article{wen2016b, author = {Chuang Wen and Yan Yang and Jens Honore Walther and Kar Mun Pang and Yuqing Feng}, doi = {10.1016/j.powtec.2016.07.061}, journal = {Powder Technology}, month = {dec}, pages = {261--267}, publisher = {Elsevier {BV}}, title = {Effect of delta wing on the particle flow in a novel gas supersonic separator}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/wen2016b.pdf}, volume = {304}, year = {2016} }`

- M. Zayernouri and A. Matzavinos, “Fractional adams—bashforth/moulton methods: an application to the fractional keller—segel chemotaxis system," Journal of computational physics, vol. 317, pp. 1-14, 2016.

[BibTeX] [PDF] [DOI]`@article{zayernouri2016a, author = {Mohsen Zayernouri and Anastasios Matzavinos}, doi = {10.1016/j.jcp.2016.04.041}, journal = {Journal of Computational Physics}, month = {jul}, pages = {1--14}, publisher = {Elsevier {BV}}, title = {Fractional Adams{\textendash}Bashforth/Moulton methods: An application to the fractional Keller{\textendash}Segel chemotaxis system}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/zayernouri2016a.pdf}, volume = {317}, year = {2016} }`

### 2015

- M. M. Hejlesen, J. T. Rasmussen, A. Larsen, and J. H. Walther, “On estimating the aerodynamic admittance of bridge sections by a mesh-free vortex method," Journal of wind engineering and industrial aerodynamics, vol. 146, pp. 117-127, 2015.

[BibTeX] [PDF] [DOI]`@article{hejlesen2015a, author = {Hejlesen, Mads M{\o}lholm and Rasmussen, Johannes Toph{\o}j and Larsen, Allan and Walther, Jens Honor{\'{e}}}, doi = {10.1016/j.jweia.2015.08.003}, journal = {Journal of Wind Engineering and Industrial Aerodynamics}, month = {nov}, pages = {117--127}, publisher = {Elsevier {BV}}, title = {On estimating the aerodynamic admittance of bridge sections by a mesh-free vortex method}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hejlesen2015a.pdf}, volume = {146}, year = {2015} }`

- M. M. Hejlesen, J. T. Rasmussen, P. Chatelain, and J. H. Walther, “High order poisson solver for unbounded flows," Procedia IUTAM, vol. 18, pp. 56-65, 2015.

[BibTeX] [PDF] [DOI]`@article{hejlesen2015b, author = {Hejlesen, Mads M{\o}lholm and Rasmussen, Johannes Toph{\o}j and Chatelain, Philippe and Walther, Jens Honor{\'{e}}}, doi = {10.1016/j.piutam.2015.11.006}, journal = {Procedia {IUTAM}}, pages = {56--65}, publisher = {Elsevier {BV}}, title = {High Order Poisson Solver for Unbounded Flows}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hejlesen2015b.pdf}, volume = {18}, year = {2015} }`

- E. Oyarzua, J. H. Walther, A. Mejía, and H. A. Zambrano, “Early regimes of water capillary flow in slit silica nanochannels," Phys. chem. chem. phys., vol. 17, iss. 22, pp. 14731-14739, 2015.

[BibTeX] [PDF] [DOI]`@article{oyarzua2015a, author = {Elton Oyarzua and Jens H. Walther and Andr{\'{e}}s Mej{\'{\i}}a and Harvey A. Zambrano}, doi = {10.1039/c5cp01862e}, journal = {Phys. Chem. Chem. Phys.}, number = {22}, pages = {14731--14739}, publisher = {Royal Society of Chemistry ({RSC})}, title = {Early regimes of water capillary flow in slit silica nanochannels}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/oyarzua2015a.pdf}, volume = {17}, year = {2015} }`

- C. Voglis, P. E. Hadjidoukas, K. E. Parsopoulos, D. G. Papageorgiou, I. E. Lagaris, and M. N. Vrahatis, “P-MEMPSODE: parallel and irregular memetic global optimization," Computer physics communications, vol. 197, pp. 190-211, 2015.

[BibTeX] [PDF] [DOI]`@article{voglis2015a, author = {C. Voglis and P.E. Hadjidoukas and K.E. Parsopoulos and D.G. Papageorgiou and I.E. Lagaris and M.N. Vrahatis}, doi = {10.1016/j.cpc.2015.07.011}, journal = {Computer Physics Communications}, month = {dec}, pages = {190--211}, publisher = {Elsevier {BV}}, title = {p-{MEMPSODE}: Parallel and irregular memetic global optimization}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/voglis2015a.pdf}, volume = {197}, year = {2015} }`

### 2014

- M. Fasil, D. Plesner, J. H. Walther, N. Mijatovic, J. Holbøll, and B. B. Jensen, “Numerical and experimental investigation of heat flow in permanent magnet brushless DC hub motor," SAE international journal of alternative powertrains, vol. 4, iss. 1, 2014.

[BibTeX] [PDF] [DOI]`@article{fasil2014a, author = {Muhammed Fasil and Daniel Plesner and Jens Honore Walther and Nenad Mijatovic and Joachim Holb{\o}ll and Bogi Bech Jensen}, doi = {10.4271/2014-01-2900}, journal = {{SAE} International Journal of Alternative Powertrains}, month = {oct}, number = {1}, publisher = {{SAE} International}, title = {Numerical and Experimental Investigation of Heat Flow in Permanent Magnet Brushless {DC} Hub Motor}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/fasil2014a.pdf}, volume = {4}, year = {2014} }`

- C. L. Felter, J. H. Walther, and C. Henriksen, “Moving least squares simulation of free surface flows," Computers & fluids, vol. 91, pp. 47-56, 2014.

[BibTeX] [PDF] [DOI]`@article{felter2014a, author = {C.L. Felter and J.H. Walther and C. Henriksen}, doi = {10.1016/j.compfluid.2013.12.006}, journal = {Computers {\&} Fluids}, month = {mar}, pages = {47--56}, publisher = {Elsevier {BV}}, title = {Moving least squares simulation of free surface flows}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/felter2014a.pdf}, volume = {91}, year = {2014} }`

- P. E. Hadjidoukas, P. Angelikopoulos, C. Voglis, D. G. Papageorgiou, and I. E. Lagaris, “NDL-v2.0: a new version of the numerical differentiation library for parallel architectures," Computer physics communications, vol. 185, iss. 7, pp. 2217-2219, 2014.

[BibTeX] [PDF] [DOI]`@article{hadjidoukas2014a, author = {P.E. Hadjidoukas and P. Angelikopoulos and C. Voglis and D.G. Papageorgiou and I.E. Lagaris}, doi = {10.1016/j.cpc.2014.04.002}, journal = {Computer Physics Communications}, month = {jul}, number = {7}, pages = {2217--2219}, publisher = {Elsevier {BV}}, title = {{NDL}-v2.0: A new version of the numerical differentiation library for parallel architectures}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hadjidoukas2014a.pdf}, volume = {185}, year = {2014} }`

- P. E. Hadjidoukas, C. Voglis, V. V. Dimakopoulos, I. E. Lagaris, and D. G. Papageorgiou, “Supporting adaptive and irregular parallelism for non-linear numerical optimization," Applied mathematics and computation, vol. 231, pp. 544-559, 2014.

[BibTeX] [PDF] [DOI]`@article{hadjidoukas2014b, author = {P.E. Hadjidoukas and C. Voglis and V.V. Dimakopoulos and I.E. Lagaris and D.G. Papageorgiou}, doi = {10.1016/j.amc.2013.12.092}, journal = {Applied Mathematics and Computation}, month = {mar}, pages = {544--559}, publisher = {Elsevier {BV}}, title = {Supporting adaptive and irregular parallelism for non-linear numerical optimization}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hadjidoukas2014b.pdf}, volume = {231}, year = {2014} }`

- K. M. Ingvorsen, K. E. Meyer, J. H. Walther, and S. Mayer, “Turbulent swirling flow in a dynamic model of a uniflow-scavenged two-stroke engine," Experiments in fluids, vol. 55, iss. 6, 2014.

[BibTeX] [Abstract] [PDF] [DOI]

The turbulent and swirling flow of a uniflow- scavenged two-stroke engine cylinder is investigated using a scale model with a static geometry and a transparent cylinder. The swirl is generated by 30 equally spaced ports with angles of 0{\textdegree}, 10{\textdegree}, 20{\textdegree}, and 30{\textdegree}. A detailed charac- terization of the flow field is performed using stereoscopic particle image velocimetry. Mean fields are calculated using both a fixed coordinate system and a coordinate system based on the instantaneous flow topology. Time- resolved measurements of axial velocity are performed with laser Doppler anemometry, and power spectra are calculated in order to determine vortex core precession frequencies. The results show a very different flow dynamics for cases with weak and strong swirl. In the strongly swirling cases, a vortex breakdown is observed. Downstream of the breakdown, the vortex becomes highly concentrated and the vortex core precesses around the exhaust valve, resulting in an axial suction effect at the vortex center. Mean fields based on the instantaneous flow topology are shown to be more representative than mean fields based on a fixed coordinate system in cases with significant variations in the swirl center location.

`@article{ingvorsen2014a, author = {K. M. Ingvorsen and K. E. Meyer and J. H. Walther and S. Mayer}, doi = {10.1007/s00348-014-1748-y}, journal = {Experiments in Fluids}, month = {may}, number = {6}, publisher = {Springer Nature}, title = {Turbulent swirling flow in a dynamic model of a uniflow-scavenged two-stroke engine}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/ingvorsen2014a.pdf}, volume = {55}, year = {2014} }`

- A. Obeidat, T. Schnipper, K. M. Ingvorsen, S. Haider, K. E. Meyer, S. Mayer, and J. H. Walther, “Large eddy simulations of the influence of piston position on the swirling flow in a model two-stroke diesel engine," International journal of numerical methods for heat & fluid flow, vol. 24, iss. 2, pp. 325-341, 2014.

[BibTeX] [PDF] [DOI]`@article{obeidat2014a, author = {Anas Obeidat and Teis Schnipper and Kristian M. Ingvorsen and Sajjad Haider and Knud Erik Meyer and Stefan Mayer and Jens H. Walther}, doi = {10.1108/hff-09-2011-0189}, journal = {International Journal of Numerical Methods for Heat {\&} Fluid Flow}, month = {feb}, number = {2}, pages = {325--341}, publisher = {Emerald}, title = {Large eddy simulations of the influence of piston position on the swirling flow in a model two-stroke diesel engine}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/obeidat2014a.pdf}, volume = {24}, year = {2014} }`

- E. Sigurdsson, K. M. Ingvorsen, M. V. Jensen, S. Mayer, S. Matlok, and J. H. Walther, “Numerical analysis of the scavenge flow and convective heat transfer in large two-stroke marine diesel engines," Applied energy, vol. 123, pp. 37-46, 2014.

[BibTeX] [PDF] [DOI]`@article{sigurdsson2014a, author = {E. Sigurdsson and K.M. Ingvorsen and M.V. Jensen and S. Mayer and S. Matlok and J.H. Walther}, doi = {10.1016/j.apenergy.2014.02.036}, journal = {Applied Energy}, month = {jun}, pages = {37--46}, publisher = {Elsevier {BV}}, title = {Numerical analysis of the scavenge flow and convective heat transfer in large two-stroke marine diesel engines}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/sigurdsson2014a.pdf}, volume = {123}, year = {2014} }`

- H. A. Zambrano, J. H. Walther, and R. L. Jaffe, “Molecular dynamics simulations of water on a hydrophilic silica surface at high air pressures," Journal of molecular liquids, vol. 198, pp. 107-113, 2014.

[BibTeX] [PDF] [DOI]`@article{zambrano2014a, author = {H.A. Zambrano and J.H. Walther and R.L. Jaffe}, doi = {10.1016/j.molliq.2014.06.003}, journal = {Journal of Molecular Liquids}, month = {oct}, pages = {107--113}, publisher = {Elsevier {BV}}, title = {Molecular dynamics simulations of water on a hydrophilic silica surface at high air pressures}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/zambrano2014a.pdf}, volume = {198}, year = {2014} }`

### 2013

- M. M. Hejlesen, J. T. Rasmussen, P. Chatelain, and J. H. Walther, “A high order solver for the unbounded poisson equation," Journal of computational physics, vol. 252, pp. 458-467, 2013.

[BibTeX] [Abstract] [PDF] [DOI]

A high order converging Poisson solver is presented, based on the Green{‘}s function solution to Poisson{‘}s equation subject to free-space boundary conditions. The high order convergence is achieved by formulating regularised integration kernels, analogous to a smoothing of the solution field. The method is extended to directly solve the derivatives of the solution to Poisson{‘}s equation. In this way differential operators such as the divergence or curl of the solution field can be solved to the same high order convergence without additional computational effort. The method, is applied and validated, however not restricted, to the equations of fluid mechanics, and can be used in many applications to solve Poisson{‘}s equation on a rectangular unbounded domain.

`@article{hejlesen2013a, author = {Hejlesen, Mads M{\o}lholm and Rasmussen, Johannes Toph{\o}j and Chatelain, Philippe and Walther, Jens Honor{\'{e}}}, doi = {10.1016/j.jcp.2013.05.050}, journal = {Journal of Computational Physics}, month = {nov}, pages = {458--467}, publisher = {Elsevier {BV}}, title = {A high order solver for the unbounded Poisson equation}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hejlesen2013a.pdf}, volume = {252}, year = {2013} }`

- M. V. Jensen and J. H. Walther, “Numerical analysis of jet impingement heat transfer at high jet Reynolds number and large temperature difference," Heat transfer engineering, vol. 34, iss. 10, pp. 801-809, 2013.

[BibTeX] [Abstract] [PDF] [DOI]

Jet impingement heat transfer from a round gas jet to a flat wall was investigated numerically for a ratio of 2 between the jet inlet to wall distance and the jet inlet diameter. The influence of turbulence intensity at the jet inlet and choice of turbulence model on the wall heat transfer was investigated at a jet Reynolds number of 1.66 {\texttimes} 105 and a temperature difference between jet inlet and wall of 1600 K. The focus was on the convective heat transfer contribution as thermal radiation was not included in the investigation. A considerable influence of the turbulence intensity at the jet inlet was observed in the stagnation region, where the wall heat flux increased by a factor of almost 3 when increasing the turbulence intensity from 1.5% to 10%. The choice of turbulence model also influenced the heat transfer predictions significantly, especially in the stagnation region, where differences of up to about 100% were observed. Furthermore, the variation in stagnation point heat transfer was examined for jet Reynolds numbers in the range from 1.10 {\texttimes} 105 to 6.64 {\texttimes} 105. Based on the investigations, a correlation is suggested between the stagnation point Nusselt number, the jet Reynolds number, and the turbulence intensity at the jet inlet for impinging jet flows at high jet Reynolds numbers.

`@article{jensen2013a, author = {Michael V. Jensen and Jens H. Walther}, doi = {10.1080/01457632.2012.746153}, journal = {Heat Transfer Engineering}, month = {aug}, number = {10}, pages = {801--809}, publisher = {Informa {UK} Limited}, title = {Numerical Analysis of Jet Impingement Heat Transfer at High Jet {R}eynolds Number and Large Temperature Difference}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/jensen2013a.pdf}, volume = {34}, year = {2013} }`

- C. Voglis, P. E. Hadjidoukas, D. G. Papageorgiou, and I. E. Lagaris, “A parallel hybrid optimization algorithm for fitting interatomic potentials," Applied soft computing, vol. 13, iss. 12, pp. 4481-4492, 2013.

[BibTeX] [Abstract] [PDF] [DOI]

In this work we present the parallel implementation of a hybrid global optimization algorithm assembled specifically to tackle a class of time consuming interatomic potential fitting problems. The resulting objec- tive function is characterized by large and varying execution times, discontinuity and lack of derivative information. The presented global optimization algorithm corresponds to an irregular, two-level execu- tion task graph where tasks are spawned dynamically. We use the OpenMP tasking model to express the inherent parallelism of the algorithm on shared-memory systems and a runtime library which imple- ments the execution environment for adaptive task-based parallelism on multicore clusters. We describe in detail the hybrid global optimization algorithm and various parallel implementation issues. The pro- posed methodology is then applied to a specific instance of the interatomic potential fitting problem for the metal titanium. Extensive numerical experiments indicate that the proposed algorithm achieves the best parallel performance. In addition, its serial implementation performs well and therefore can also be used as a general purpose optimization algorithm.

`@article{voglis2013a, author = {C. Voglis and P.E. Hadjidoukas and D.G. Papageorgiou and I.E. Lagaris}, doi = {10.1016/j.asoc.2013.08.007}, journal = {Applied Soft Computing}, month = {dec}, number = {12}, pages = {4481--4492}, publisher = {Elsevier {BV}}, title = {A parallel hybrid optimization algorithm for fitting interatomic potentials}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/voglis2013a.pdf}, volume = {13}, year = {2013} }`

### 2012

- S. Haider, T. Schnipper, A. Obeidat, K. E. Meyer, V. L. Okulov, S. Mayer, and J. H. Walther, “PIV study of the effect of piston position on the in-cylinder swirling flow during the scavenging process in large two-stroke marine diesel engines," Journal of marine science and technology, vol. 18, iss. 1, pp. 133-143, 2012.

[BibTeX] [Abstract] [PDF] [DOI]

A simplified model of a low speed large two- stroke marine diesel engine cylinder is developed. The effect of piston position on the in-cylinder swirling flow during the scavenging process is studied using the stereo- scopic particle image velocimetry technique. The mea- surements are conducted at different cross-sectional planes along the cylinder length and at piston positions covering the air intake port by 0, 25, 50 and 75 %. When the intake port is fully open, the tangential velocity profile is similar to a Burgers vortex, whereas the axial velocity has a wake- like profile. Due to internal wall friction, the swirl decays downstream, and the size of the vortex core increases. For increasing port closures, the tangential velocity profile changes from a Burgers vortex to a forced vortex, and the axial velocity changes correspondingly from a wake-like profile to a jet-like profile. For piston position with 75 % intake port closure, the jet-like axial velocity profile at a cross-sectional plane close to the intake port changes back to a wake-like profile at the adjacent downstream cross-sectional plane. This is characteristic of a vortex breakdown. The non-dimensional velocity profiles show no significant variation with the variation in Reynolds number.

`@article{haider2012a, author = {S. Haider and T. Schnipper and A. Obeidat and K. E. Meyer and V. L. Okulov and S. Mayer and J. H. Walther}, doi = {10.1007/s00773-012-0192-z}, journal = {Journal of Marine Science and Technology}, month = {sep}, number = {1}, pages = {133--143}, publisher = {Springer Nature}, title = {{PIV} study of the effect of piston position on the in-cylinder swirling flow during the scavenging process in large two-stroke marine diesel engines}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/haider2012a.pdf}, volume = {18}, year = {2012} }`

### 2011

- J. T. Rasmussen, G. Cottet, and J. H. Walther, “A multiresolution remeshed vortex-in-cell algorithm using patches," Journal of computational physics, vol. 230, iss. 17, pp. 6742-6755, 2011.

[BibTeX] [Abstract] [PDF] [DOI]

We present a novel multiresolution Vortex-In-Cell algorithm using patches of varying resolution. The Poisson equation relating the fluid vorticity and velocity is solved using Fast Fourier Transforms subject to free space boundary conditions. Solid boundaries are implemented using the semi-implicit formulation of Brinkman penalization and we show that the penalization can be carried out as a simple interpolation. We validate the implementation against the analytic solution to the Perlman test case and by free-space simulations of the onset flow around fixed and rotating circular cylinders and bluff body flows around bridge sections.

`@article{rasmussen2011a, author = {Johannes Toph{\o}j Rasmussen and Georges-Henri Cottet and Jens Honor{\'{e}} Walther}, doi = {10.1016/j.jcp.2011.05.006}, journal = {Journal of Computational Physics}, month = {jul}, number = {17}, pages = {6742--6755}, publisher = {Elsevier {BV}}, title = {A multiresolution remeshed Vortex-In-Cell algorithm using patches}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rasmussen2011a.pdf}, volume = {230}, year = {2011} }`

- H. Riisgård, H. B. Jørgensen, K. Lundgreen, F. Storti, J. Walther, K. Meyer, and P. Larsen, “The exhalant jet of mussels mytilus edulis," Marine ecology progress series, vol. 437, pp. 147-164, 2011.

[BibTeX] [Abstract] [PDF] [DOI]

Literature values of the exhalant jet velocity of mussels vary considerably, and the detailed fluid mechanics of the mussel-near flow generated by the exhalant jet has hitherto been uncertain although this flow in conjunction with currents and/or other mussels may strongly influence their grazing impact. Computational modelling of this phenomenon depends on knowledge of the velocity distribution near the exhalant siphon aperture of mussels to provide appropriate boundary conditions for numerical flow models, and to be useful such information should be available for a range of mussel shell lengths. Here, we present results of a detailed study of fully open mussels (Mytilus edulis) in terms of filtration rate, exhalant siphon-aperture area and jet velocity, gill area, dry body weight, all as function of shell length over the range L = 16.0 +/- 0.4 to 82.6 +/- 2.9 mm. Scaling laws for these parameters in terms of size by shell length are presented. The exhalant jet velocity was determined by three methods: 1) measured clearance rate divided by exhalant aperture area, 2) manual particle tracking velocimetry (PTV) using video-microscope recordings, and 3) particle image velocimetry (PIV). The latter provides detailed two-component velocity distributions near the exhalant siphon in 5 planes parallel to the axis of the jet and the major axis of the oval aperture, hence estimates of momentum and kinetic energy flows in addition to mean velocity. Here, data obtained on particles inside the exhalant jet of filtered water was ensured by the use of TiO2 seeding particles which were de-agglomerated by ultrasound to size-range 0.7 to 2 {\mathrm{μ}}m prior to addition to avoid retention by the gill-filter of the mussels. Notably it was found that the exhalant jet velocity is essentially constant, about 8 cm s-1, and independent of shell length. Based on geometric similarity and scaling of pump-system characteristics of the mussel it was found that these characteristics coincide approximately for all sizes when expressed as pressure head versus volume flow divided by shell length squared.

`@article{riisgard2011a, author = {HU Riisg{\aa}rd and B Hoffmann J{\o}rgensen and K Lundgreen and F Storti and JH Walther and KE Meyer and PS Larsen}, doi = {10.3354/meps09268}, journal = {Marine Ecology Progress Series}, month = {sep}, pages = {147--164}, publisher = {Inter-Research Science Center}, title = {The exhalant jet of mussels Mytilus edulis}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/riisgard2011a.pdf}, volume = {437}, year = {2011} }`

### 2010

- J. T. Rasmussen, M. M. Hejlesen, A. Larsen, and J. H. Walther, “Discrete vortex method simulations of the aerodynamic admittance in bridge aerodynamics," Journal of wind engineering and industrial aerodynamics, vol. 98, iss. 12, pp. 754-766, 2010.

[BibTeX] [Abstract] [PDF] [DOI]

We present a novel method for the simulation of the aerodynamic admittance in bluff body aerodynamics. The method introduces a model for describing oncoming turbulence in two-dimensional discrete vortex method simulations by seeding the upstream flow with vortex particle.s The turbulence is generated prior to the simulations and is based on analytic spectral densities of the atmospheric turbulence and a coherence function defining the spatial correlation of the flow. The method is validated by simulating the turbulent flow past a flat plate and past the Great Belt East bridge. The results are generally found in good agreement with the potential flow solution due to Liepmann.

`@article{rasmussen2010a, author = {Rasmussen, Johannes Toph{\o}j and Hejlesen, Mads M{\o}lholm and Larsen, Allan and Walther, Jens Honor{\'{e}}}, doi = {10.1016/j.jweia.2010.06.011}, journal = {Journal of Wind Engineering and Industrial Aerodynamics}, month = {dec}, number = {12}, pages = {754--766}, publisher = {Elsevier {BV}}, title = {Discrete vortex method simulations of the aerodynamic admittance in bridge aerodynamics}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/rasmussen2010a.pdf}, volume = {98}, year = {2010} }`

### 2009

- J. H. Walther and I. F. Sbalzarini, “Large-scale parallel discrete element simulations of granular flow," Engineering computations, vol. 26, iss. 6, pp. 688-697, 2009.

[BibTeX] [Abstract] [PDF] [DOI]

The purpose of this paper is to present large-scale parallel direct numerical simulations of granular flow, using a novel, portable software program for discrete element method (DEM) simulations. Since particle methods provide a unifying framework for both discrete and continuous systems, the program is based on the parallel particle mesh (PPM) library, which has already been demonstrated to provide transparent parallelization and state-of-the-art parallel efficiency using particle methods for continuous systems. By adapting PPM to discrete systems, results are reported from three-dimensional simulations of a sand avalanche down an inclined plane. The paper demonstrates the parallel performance and scalability of the new simulation program using up to 122 million particles on 192 processors, employing adaptive domain decomposition and load balancing techniques.

`@article{walther2009a, author = {Jens H. Walther and Ivo F. Sbalzarini}, doi = {10.1108/02644400910975478}, editor = {Antonio Munjiza}, journal = {Engineering Computations}, month = {aug}, number = {6}, pages = {688--697}, publisher = {Emerald}, title = {Large-scale parallel discrete element simulations of granular flow}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther2009a.pdf}, volume = {26}, year = {2009} }`

- H. A. Zambrano, J. H. Walther, and R. L. Jaffe, “Thermally driven molecular linear motors: a molecular dynamics study," The journal of chemical physics, vol. 131, iss. 24, p. 241104, 2009.

[BibTeX] [Abstract] [PDF] [DOI]

We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsulelike nanotube. The simulations indicate that the motion of the capsule can be controlled by thermophoretic forces induced by thermal gradients. The simulations find large terminal velocities of 100{—}400 nm/ns for imposed thermal gradients in the range of 1{—}3 K/nm. Moreover, the results indicate that the thermophoretic force is velocity dependent and its magnitude decreases for increasing velocity.

`@article{zambrano2009a, author = {H. A. Zambrano and J. H. Walther and R. L. Jaffe}, doi = {10.1063/1.3281642}, journal = {The Journal of Chemical Physics}, month = {dec}, number = {24}, pages = {241104}, publisher = {{AIP} Publishing}, title = {Thermally driven molecular linear motors: A molecular dynamics study}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/zambrano2009a.pdf}, volume = {131}, year = {2009} }`

### 2007

- G. Morgenthal and J. H. Walther, “An immersed interface method for the vortex-in-cell algorithm," Computers & structures, vol. 85, iss. 11-14, pp. 712-726, 2007.

[BibTeX] [Abstract] [PDF] [DOI]

The paper presents a two-dimensional immersed interface technique for the Vortex-In-Cell (VIC) method for simulation of flows past bodies of complex geometry. The particle-mesh VIC algorithm is augmented by a local particle-particle correction term in a Particle-Particle Particle-Mesh ((PM)-M-3) context to resolve sub-grid scales incurred by the presence of the immersed interface. The particle-particle correction furthermore allows to disjoin mesh and particle resolution by explicitly resolving sub-grid scales on the particles. This (PM)-M-3 algorithm uses an influence matrix technique to annihilate the anisotropic sub-grid scales and adds an exact particle-particle correction term. Free-space boundary conditions are satisfied through the use of modified Green’s functions in the solution of the Poisson equation for the streamfunction. The concept is extended such as to provide exact velocity predictions on the mesh with free-space boundary conditions. The random walk technique is employed for the diffusion in order to relax the need for a remeshing of the computational elements close to solid boundaries. A novel partial remeshing technique is introduced which only performs remeshing of the vortex elements which are located sufficiently distant from the immersed interfaces, thus maintaining a sufficient spatial representation of the vorticity field. Convergence of the present (PM)-M-3 algorithm is demonstrated for a circular patch of vorticity. The immersed interface technique is applied to the flow past a circular cylinder at a Reynolds number of 3000 and the convergence of the method is demonstrated by a systematic refinement of the spatial parameters. Finally, the flow past a cactus-like geometry is considered to demonstrate the efficient handling of complex bluff body geometries. The simulations offer an insight into physically interesting flow behavior involving a temporarily negative total drag force on the section. (C) 2007 Elsevier Ltd. All rights reserved.

`@article{morgenthal2007a, author = {G. Morgenthal and J.H. Walther}, doi = {10.1016/j.compstruc.2007.01.020}, journal = {Computers {\&} Structures}, month = {jun}, number = {11-14}, pages = {712--726}, publisher = {Elsevier {BV}}, title = {An immersed interface method for the Vortex-In-Cell algorithm}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/morgenthal2007a.pdf}, volume = {85}, year = {2007} }`

### 2006

- N. Hansen, “An analysis of mutative Σ-self-adaptation on linear fitness functions," Evolutionary computation, vol. 14, iss. 3, pp. 255-275, 2006.

[BibTeX] [Abstract] [PDF] [DOI]

This paper investigates sigma-self-adaptation for real valued evolutionary algorithms on linear fitness functions. We identify the step-size logarithm log sigma as a key quantity to understand strategy behavior. Knowing the bias of mutation, recombination, and selection on log sigma is sufficient to explain sigma-dynamics and strategy behavior in many cases, even from previously reported results on non-linear and/or noisy fitness functions. On a linear fitness function, if intermediate multi-recombination is applied on the object parameters, the i-th best and the i-th worst individual have the same sigma-distribution. Consequently, the correlation between fitness and step-size sigma is zero. Assuming additionally that sigma-changes due to mutation and recombination are unbiased, then sigma-self-adaptation enlarges sigma if and only if mu < lambda/2, given (mu, lambda)-truncation selection. Experiments show the relevance of the given assumptions.

`@article{hansen2006a, author = {Nikolaus Hansen}, doi = {10.1162/evco.2006.14.3.255}, journal = {Evolutionary Computation}, month = {sep}, number = {3}, pages = {255--275}, publisher = {{MIT} Press - Journals}, title = {An Analysis of Mutative -Self-Adaptation on Linear Fitness Functions}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hansen2006a.pdf}, volume = {14}, year = {2006} }`

- S. Zimmermann, P. Bauer, R. Held, W. Kinzelbach, and J. H. Walther, “Salt transport on islands in the okavango delta: numerical investigations," Advances in water resources, vol. 29, iss. 1, pp. 11-29, 2006.

[BibTeX] [Abstract] [PDF] [DOI]

This study uses a numerical model to investigate the groundwater flow and salt transport mechanisms below islands in the Okavango Delta. Continuous evapotranspiration on the islands results in accumulation of solutes and the formation of a saline boundary layer, which may eventually become unstable. A novel Lagrangian method is employed in this study and compared to other numerical methods. The numerical results support the geophysical observations of density fingering on Thata Island. However, the process is slow and it takes some hundreds of years until density fingering is triggered. The results are sensitive to changes of the hydraulic gradient and the evapotranspiration rate. Small changes may lead to different plume developments. Results further demonstrate that density effects may be entirely overridden by lateral flow on islands embedded in a sufficiently high regional hydraulic gradient. (c) 2005 Elsevier Ltd. All rights reserved.

`@article{zimmermann2006a, author = {S. Zimmermann and P. Bauer and R. Held and W. Kinzelbach and J.H. Walther}, doi = {10.1016/j.advwatres.2005.04.013}, journal = {Advances in Water Resources}, month = {jan}, number = {1}, pages = {11--29}, publisher = {Elsevier {BV}}, title = {Salt transport on islands in the Okavango Delta: Numerical investigations}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/zimmermann2006a.pdf}, volume = {29}, year = {2006} }`

### 2005

- C. Luedeke, S. B. Frei, I. Sbalzarini, H. Schwarz, A. Spang, and Y. Barral, “Septin-dependent compartmentalization of the endoplasmic reticulum during yeast polarized growth," The journal of cell biology, vol. 169, iss. 6, pp. 897-908, 2005.

[BibTeX] [Abstract] [PDF] [DOI]

Polarized cells frequently use diffusion barriers to separate plasma membrane domains. It is unknown whether diffusion barriers also compartmentalize intracellular organelles. We used photobleaching techniques to characterize protein diffusion in the yeast endoplasmic reticulum (ER). Although a soluble protein diffused rapidly throughout the ER lumen, diffusion of ER membrane proteins was restricted at the bud neck. Ultrastructural studies and fluorescence microscopy revealed the presence of a ring of smooth ER at the bud neck. This ER domain and the restriction of diffusion for ER membrane proteins through the bud neck depended on septin function. The membrane-associated protein Bud6 localized to the bud neck in a septin-dependent manner and was required to restrict the diffusion of ER membrane proteins. Our results indicate that Bud6 acts downstream of septins to assemble a fence in the ER membrane at the bud neck. Thus, in polarized yeast cells, diffusion barriers compartmentalize the ER and the plasma membrane along parallel lines.

`@article{luedeke2005a, author = {Cosima Luedeke and St{\'{e}}phanie Buvelot Frei and Ivo Sbalzarini and Heinz Schwarz and Anne Spang and Yves Barral}, doi = {10.1083/jcb.200412143}, journal = {The Journal of Cell Biology}, month = {jun}, number = {6}, pages = {897--908}, publisher = {Rockefeller University Press}, title = {Septin-dependent compartmentalization of the endoplasmic reticulum during yeast polarized growth}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/luedeke2005a.pdf}, volume = {169}, year = {2005} }`

### 2004

- P. Gonnet, K. E. Rudd, and F. Lisacek, “Fine-tuning the prediction of sequences cleaved by signal peptidase II: a curated set of proven and predicted lipoproteins ofEscherichia coli k-12," Proteomics, vol. 4, iss. 6, pp. 1597-1613, 2004.

[BibTeX] [Abstract] [PDF] [DOI]

A curated set of 81 proven and 44 predicted lipoproteins of Escherichia coli K-12 was defined with the combined use of a literature survey, a variety of predictive tools and human expertise. The well-documented Gram-negative proteome of E. coli K-12 was chosen to assess how the different approaches complement each other and to ensure a stable definition of a consistent set of lipoproteins. The results of detailed analysis of such proteins at the level of a single proteome are presented, corroborated and rationalized.

`@article{gonnet2004a, author = {Pedro Gonnet and Kenneth E. Rudd and Fr{\'{e}}d{\'{e}}rique Lisacek}, doi = {10.1002/pmic.200300749}, journal = {PROTEOMICS}, month = {jun}, number = {6}, pages = {1597--1613}, publisher = {Wiley-Blackwell}, title = {Fine-tuning the prediction of sequences cleaved by signal peptidase {II}: A curated set of proven and predicted lipoproteins {ofEscherichia} coli K-12}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/gonnet2004a.pdf}, volume = {4}, year = {2004} }`

- F. Lisacek, C. Chichester, P. Gonnet, O. Jaillet, S. Kappus, F. Nikitin, P. Roland, G. Rossier, L. Truong, and R. Appel, “Shaping biological knowledge: applications in proteomics," Comparative and functional genomics, vol. 5, iss. 2, pp. 190-195, 2004.

[BibTeX] [Abstract] [PDF] [DOI]

The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small-scale studies. We analyse proteomics data while following both a data-driven (focus on proteins smaller than 10 kDa) and a hypothesis-driven (focus on whole bacterial proteomes) approach. These applications are potentially the source of specialized complements to classical biological ontologies. Copyright (C) 2004 John Wiley Sons, Ltd.

`@article{lisacek2004a, author = {F. Lisacek and C. Chichester and P. Gonnet and O. Jaillet and S. Kappus and F. Nikitin and P. Roland and G. Rossier and L. Truong and R. Appel}, doi = {10.1002/cfg.379}, journal = {Comparative and Functional Genomics}, number = {2}, pages = {190--195}, publisher = {Hindawi Limited}, title = {Shaping Biological Knowledge: Applications in Proteomics}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/lisacek2004a.pdf}, volume = {5}, year = {2004} }`

### 2003

- M. Bergdorf, C. Peter, and P. H. Hünenberger, “Influence of cut-off truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions: a continuum electrostatics study," The journal of chemical physics, vol. 119, iss. 17, pp. 9129-9144, 2003.

[BibTeX] [Abstract] [PDF] [DOI]

A new algorithm relying on finite integration is presented that solves the equations of continuum electrostatics for truncated (and possibly reaction-field corrected) solute-solvent and solvent-solvent interactions under either nonperiodic or periodic boundary conditions. After testing and validation by comparison with existing methods, the algorithm is applied to investigate the effect of cut-off truncation and artificial periodicity in explicit-solvent simulations of ionic solvation and ion-ion interactions. Both cut-off truncation and artificial periodicity significantly alter the polarization around a spherical ion and thus, its solvation free energy. The nature and magnitude of the two perturbations are analyzed in details, and correction terms are proposed for both effects. Cut-off truncation is also shown to induce strong alterations in the potential of mean force for ion-ion interaction. These observations help to rationalize artifacts previously observed in explicit-solvent simulations, namely spurious features in the radial distribution functions close to the cut-off distance and alterations in the relative stabilities of contact, solvent-separated and free ion pairs. (C) 2003 American Institute of Physics.

`@article{bergdorf2003a, author = {Michael Bergdorf and Christine Peter and Philippe H. H{\"u}nenberger}, doi = {10.1063/1.1614202}, journal = {The Journal of Chemical Physics}, month = {nov}, number = {17}, pages = {9129--9144}, publisher = {{AIP} Publishing}, title = {Influence of cut-off truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions: A continuum electrostatics study}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bergdorf2003a.pdf}, volume = {119}, year = {2003} }`

- F. A. Gers, N. N. Schraudolph, and J. Schmidhuber, “Learning precise timing with lstm recurrent networks," J. mach. learn. res., vol. 3, pp. 115-143, 2003.

[BibTeX] [Abstract] [PDF] [DOI]

The temporal distance between events conveys information essential for numerous sequential tasks such as motor control and rhythm detection. While Hidden Markov Models tend to ignore this information, recurrent neural networks (RNNs) can in principle learn to make use of it. We focus on Long Short-Term Memory (LSTM) because it has been shown to outperform other RNNs on tasks involving long time lags. We find that LSTM augmented by “peephole connections" from its internal cells to its multiplicative gates can learn the fine distinction between sequences of spikes spaced either 50 or 49 time steps apart without the help of any short training exemplars. Without external resets or teacher forcing, our LSTM variant also learns to generate stable streams of precisely timed spikes and other highly nonlinear periodic patterns. This makes LSTM a promising approach for tasks that require the accurate measurement or generation of time intervals.

`@article{gers2003a, acmid = {944925}, author = {Gers, Felix A. and Schraudolph, Nicol N. and Schmidhuber, J\"{u}rgen}, doi = {10.1162/153244303768966139}, issn = {1532-4435}, issue_date = {3/1/2003}, journal = {J. Mach. Learn. Res.}, keywords = {long short-term memory, recurrent neural networks, timing}, month = {mar}, numpages = {29}, pages = {115--143}, publisher = {JMLR.org}, title = {Learning Precise Timing with Lstm Recurrent Networks}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/gers2003a.pdf}, volume = {3}, year = {2003} }`

- J. H. Walther, “An influence matrix particle—particle particle-mesh algorithm with exact particle—particle correction," Journal of computational physics, vol. 184, iss. 2, pp. 670-678, 2003.

[BibTeX] [PDF] [DOI]`@article{walther2003a, author = {J.H. Walther}, doi = {10.1016/s0021-9991(02)00035-9}, journal = {Journal of Computational Physics}, month = {jan}, number = {2}, pages = {670--678}, publisher = {Elsevier {BV}}, title = {An influence matrix particle{\textendash}particle particle-mesh algorithm with exact particle{\textendash}particle correction}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther2003a.pdf}, volume = {184}, year = {2003} }`

### 2002

- S. Attinger, “Parameterizing macro-dispersivity: first pick a length scale," Hydrological processes, vol. 16, iss. 8, pp. 1685-1687, 2002.

[BibTeX] [PDF] [DOI]`@article{attinger2002a, author = {Sabine Attinger}, doi = {10.1002/hyp.5009}, journal = {Hydrological Processes}, number = {8}, pages = {1685--1687}, publisher = {Wiley-Blackwell}, title = {Parameterizing macro-dispersivity: first pick a length scale}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/attinger2002a.pdf}, volume = {16}, year = {2002} }`

- S. Attinger, J. Eberhard, and N. Neuss, “Filtering procedures for flow in heterogeneous porous media: numerical results," Computing and visualization in science, vol. 5, iss. 2, pp. 67-72, 2002.

[BibTeX] [Abstract] [PDF] [DOI]

This paper focuses on heterogeneous soil permeabilities and on the impact their resolution has on the solution of the piezometric head equation. The method of coarse graining is proposed in order to filter the piezometric head equation on arbitrary support scales: Large scale fluctuations of the permeabilities are resolved, whereas small scale fluctuations are smoothed by a spatial filtering procedure. The filtering procedure is performed in Fourier space with the aid of a low-frequency cut-off function. In the filtered equations, the impact of the small scale variability is modeled by scale dependent effective permeabilities which are determined by additional differential equations. The additional differential equations are equivalent to the piezometric head equation on cells which are solved numerically by using the software toolbox UG. The numerical results are compared with the theoretical results derived in Attinger 2001

`@article{attinger2002b, author = {Sabine Attinger and Jens Eberhard and Nicolas Neuss}, doi = {10.1007/s00791-002-0088-2}, journal = {Computing and Visualization in Science}, month = {oct}, number = {2}, pages = {67--72}, publisher = {Springer Nature}, title = {Filtering procedures for flow in heterogeneous porous media: numerical results}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/attinger2002b.pdf}, volume = {5}, year = {2002} }`

- M. Dentz, H. Kinzelbach, S. Attinger, and W. Kinzelbach, “Temporal behavior of a solute cloud in a heterogeneous porous medium 3. numerical simulations," Water resources research, vol. 38, iss. 7, p. 23–1–23–13, 2002.

[BibTeX] [Abstract] [PDF] [DOI]

The article presents systematic numerical simulations of the temporal behavior of a passive solute in a saturated three-dimensional heterogeneous medium. The groundwater flow is derived from the linearized solution of the Darcy equation with Gauss-distributed log hydraulic conductivity. The transport of a passive solute is studied by a random-walk method, which allows for a systematic study of the temporal behavior of the effective and ensemble dispersion coefficients. The numerical results are compared to the second-order perturbation theory expressions given in two companion papers [Dentz et al., 2000a, 2000b] and to nonperturbative results which follow from Corrsin{‘}s conjecture. The low-order perturbation theory is intrinsically based on the assumption of small heterogeneity, while Corrsin{‘}s conjecture does not take into account certain contributions due to higher-order terms of the perturbation series. The simulations yield, for the first time, systematic quantitative information on the validity and the limitations of these analytic approximations. For increasing heterogeneities, considerable deviations from the theoretically predicted transport behavior are observed.

`@article{dentz2002a, author = {Marco Dentz and Harald Kinzelbach and Sabine Attinger and Wolfgang Kinzelbach}, doi = {10.1029/2001wr000436}, journal = {Water Resources Research}, month = {jul}, number = {7}, pages = {23--1--23--13}, publisher = {Wiley-Blackwell}, title = {Temporal behavior of a solute cloud in a heterogeneous porous medium 3. Numerical simulations}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/dentz2002a.pdf}, volume = {38}, year = {2002} }`

- P. Gonnet and F. Lisacek, “Probabilistic alignment of motifs with sequences," Bioinformatics, vol. 18, iss. 8, pp. 1091-1101, 2002.

[BibTeX] [Abstract] [PDF] [DOI]

Motivation: Motif detection is an important component of the classification and annotation of protein sequences. A method for aligning motifs with an amino acid sequence is introduced. The motifs can be described by the secondary (i.e. functional, biophysical, etc…) characteristics of a signal or pattern to be detected. The results produced are based on the statistical relevance of the alignment. The method was targeted to avoid the problems (i.e. over-fitting, biological interpretation and mathematical soundness) encountered in other methods currently available.

`@article{gonnet2002a, author = {P. Gonnet and F. Lisacek}, doi = {10.1093/bioinformatics/18.8.1091}, journal = {Bioinformatics}, month = {aug}, number = {8}, pages = {1091--1101}, publisher = {Oxford University Press ({OUP})}, title = {Probabilistic alignment of motifs with sequences}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/gonnet2002a.pdf}, volume = {18}, year = {2002} }`

- R. Herbrich and T. Graepel, “A PAC-Bayesian margin bound for linear classifiers," IEEE transactions on information theory, vol. 48, iss. 12, pp. 3140-3150, 2002.

[BibTeX] [Abstract] [PDF] [DOI]

We present a bound on the generalization error of linear classifiers in terms of a refined margin quantity on the training sample. The result is obtained in a probably approximately correct (PAC)-Bayesian framework and is based on geometrical arguments in the space of linear classifiers. The new bound constitutes an exponential improvement of the so far tightest margin bound, which was developed in the luckiness framework, and scales logarithmically in the inverse margin. Even in the case of less training examples than input dimensions sufficiently large margins lead to nontrivial bound values and-for maximum margins-to a vanishing complexity term. In contrast to previous results, however, the new bound does depend on the dimensionality of feature space. The analysis shows that the classical margin is too coarse a measure for the essential quantity that controls the generalization error: the fraction of hypothesis space consistent with the training sample. The practical relevance of the result lies in the fact that the well-known support vector machine is optimal with respect to the new bound only if the feature vectors in the training sample are all of the same length. As a consequence, we recommend to use support vector machines (SVMs) on normalized feature vectors only. Numerical simulations support this recommendation and demonstrate that the new error bound can be used for the purpose of model selection.

`@article{herbrich2002a, author = {R. Herbrich and T. Graepel}, doi = {10.1109/tit.2002.805090}, journal = {{IEEE} Transactions on Information Theory}, month = {dec}, number = {12}, pages = {3140--3150}, publisher = {Institute of Electrical and Electronics Engineers ({IEEE})}, title = {A {PAC}-{B}ayesian margin bound for linear classifiers}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/herbrich2002a.pdf}, volume = {48}, year = {2002} }`

- I. Lunati, S. Attinger, and W. Kinzelbach, “Macrodispersivity for transport in arbitrary nonuniform flow fields: asymptotic and preasymptotic results," Water resources research, vol. 38, iss. 10, p. 5–1–5–11, 2002.

[BibTeX] [Abstract] [PDF] [DOI]

We use homogenization theory to investigate the asymptotic macrodispersion in arbitrary nonuniform velocity fields, which show small-scale fluctuations. In the first part of the paper, a multiple-scale expansion analysis is performed to study transport phenomena in the asymptotic limit epsilon << 1, where epsilon represents the ratio between typical lengths of the small and large scale. In this limit the effects of small-scale velocity fluctuations on the transport behavior are described by a macrodispersive term, and our analysis provides an additional local equation that allows calculating the macrodispersive tensor. For Darcian flow fields we show that the macrodispersivity is a fourth-rank tensor. If dispersion/diffusion can be neglected, it depends only on the direction of the mean flow with respect to the principal axes of anisotropy of the medium. Hence the macrodispersivity represents a medium property. In the second part of the paper, we heuristically extend the theory to finite epsilon effects. Our results differ from those obtained in the common probabilistic approach employing ensemble averages. This demonstrates that standard ensemble averaging does not consistently account for finite scale effects: it tends to overestimate the dispersion coefficient in the single realization.

`@article{lunati2002a, author = {Ivan Lunati and Sabine Attinger and Wolfgang Kinzelbach}, doi = {10.1029/2001wr001203}, journal = {Water Resources Research}, month = {oct}, number = {10}, pages = {5--1--5--11}, publisher = {Wiley-Blackwell}, title = {Macrodispersivity for transport in arbitrary nonuniform flow fields: Asymptotic and preasymptotic results}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/lunati2002a.pdf}, volume = {38}, year = {2002} }`

- N. N. Schraudolph, “Fast curvature matrix-vector products for second-order gradient descent," Neural computation, vol. 14, iss. 7, pp. 1723-1738, 2002.

[BibTeX] [PDF] [DOI]`@article{schraudolph2002a, author = {Nicol N. Schraudolph}, doi = {10.1162/08997660260028683}, journal = {Neural Computation}, month = {jul}, number = {7}, pages = {1723--1738}, publisher = {{MIT} Press - Journals}, title = {Fast Curvature Matrix-Vector Products for Second-Order Gradient Descent}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/schraudolph2002a.pdf}, volume = {14}, year = {2002} }`

- F. Stauffer, S. Attinger, S. Zimmermann, and W. Kinzelbach, “Uncertainty estimation of well catchments in heterogeneous aquifers," Water resources research, vol. 38, iss. 11, p. 20–1–20–8, 2002.

[BibTeX] [Abstract] [PDF] [DOI]

The uncertainty in the boundary of two-dimensional, steady state well catchments due to the uncertainty of the spatially variable hydraulic conductivity field is investigated. The well discharge rate and the areal recharge rate are assumed constant. The catchment boundary is traced by backward particle tracking in the velocity field. The uncertainty bandwidth of the catchment boundary is approximated in first order by formulating the time-dependent longitudinal and transversal second moments of the particle displacements along and normal to the mean particle trajectory. Applications of the approach are presented for a set of simple configurations. The results are compared with the results from unconditional numerical Monte Carlo simulations. The comparison allows an assessment of the accuracy, the applicability, and the limits of the method. The approximation corresponds quite well with the Monte Carlo simulations provided that the distance to the domain boundary is sufficiently large.

`@article{stauffer2002a, author = {Fritz Stauffer and Sabine Attinger and Stephanie Zimmermann and Wolfgang Kinzelbach}, doi = {10.1029/2001wr000819}, journal = {Water Resources Research}, month = {nov}, number = {11}, pages = {20--1--20--8}, publisher = {Wiley-Blackwell}, title = {Uncertainty estimation of well catchments in heterogeneous aquifers}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/stauffer2002a.pdf}, volume = {38}, year = {2002} }`

- J. H. Walther and G. Morgenthal, “An immersed interface method for the vortex-in-cell algorithm," Journal of turbulence, vol. 3, p. N39, 2002.

[BibTeX] [Abstract] [PDF] [DOI]

The paper presents a two-dimensional immersed interface technique for the vortex-in-cell (VIC) method for the simulation of flows past complex geometries. The particle mesh VIC algorithm is augmented by a local particle-particle (PP) correction term in a particle-particle particle-mesh (PPPM) context to resolve sub-grid scales incurred by the presence of the immersed interface. The PP correction furthermore allows mesh and particle resolution to be disjoined by explicitly resolving sub-grid scales on the particles. This PPPM algorithm uses an influence matrix technique to annihilate the anisotropic subgrid scales and an exact PP correction term. Free-space boundary conditions are satisfied through the use of modified Green’s functions in the solution of the Poisson equation for the stream function. The random walk technique is employed for the diffusion in order to relax the need for a remeshing of the computational elements close to solid boundaries. The immersed interface technique is applied to the flow past a circular cylinder at a Reynolds number of 3000 and the convergence of the method is demonstrated by a systematic refinement of the spatial and temporal parameters. Finally, the flow past a cactus-like geometry is considered, demonstrating the efficient handling of complex bluff body flows.

`@article{walther2002a, author = {J H Walther and G Morgenthal}, doi = {10.1088/1468-5248/3/1/039}, eprint = {http://dx.doi.org/10.1088/1468-5248/3/1/039}, journal = {Journal of Turbulence}, pages = {N39}, title = {An immersed interface method for the vortex-in-cell algorithm}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther2002a.pdf}, volume = {3}, year = {2002} }`

- P. Yi, D. Poulikakos, J. Walther, and G. Yadigaroglu, “Molecular dynamics simulation of vaporization of an ultra-thin liquid argon layer on a surface," International journal of heat and mass transfer, vol. 45, iss. 10, pp. 2087-2100, 2002.

[BibTeX] [Abstract] [PDF] [DOI]

We performed molecular dynamics simulations of the vaporization phenomenon of an ultra-thin layer (2 nm) of liquid argon on a platinum surface. The simulation started from a molecular system of three phases (liquid argon, solid platinum and argon vapor) in equilibrium at 110 K. The platinum wall was then suddenly heated to a higher temperature (a moderately higher temperature of 150 K and a much higher temperature of 300 K were investigated). Features of our simulation model include a fast algorithm based on a tree data structure and a constant temperature solid wall model based on a 3-D Langevin equation. The entire vaporization process was successfully simulated. The results reveal trends that agree with our knowledge of vaporization of a similar macroscopic system. For example, for the high surface temperature the vaporization process is reminiscent of the Leidenfrost phenomenon and after the formation of a vapor region between the surface and the liquid mass, the latter deforms and tends to approximately acquire a spherical “droplet" shape, as one would have expected from macroscopic considerations. Contrary to this, a gradual evaporation process occurs at moderate wall temperatures. After complete evaporation and upon reduction of the wall temperature, condensation takes place leading to reconstruction of the initial liquid layer. (C) 2002 Elsevier Science Ltd. All rights reserved.

`@article{yi2002a, author = {Pan Yi and D. Poulikakos and J. Walther and G. Yadigaroglu}, doi = {10.1016/s0017-9310(01)00310-6}, journal = {International Journal of Heat and Mass Transfer}, month = {may}, number = {10}, pages = {2087--2100}, publisher = {Elsevier {BV}}, title = {Molecular dynamics simulation of vaporization of an ultra-thin liquid argon layer on a surface}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/yi2002a.pdf}, volume = {45}, year = {2002} }`

### 2001

- N. Hansen and A. Ostermeier, “Completely derandomized self-adaptation in evolution strategies," Evolutionary computation, vol. 9, iss. 2, pp. 159-195, 2001.

[BibTeX] [Abstract] [PDF] [DOI]

This paper puts forward two useful methods for self-adaptation of the mutation distribution – the concepts of derandomization and cumulation. Principle shortcomings of the concept of mutative strategy parameter control and two levels of derandomization are reviewed. Basic demands on the self-adaptation of arbitrary (normal) mutation distributions are developed. Applying arbitrary, normal Mutation distributions is equivalent to applying a general, linear problem encoding. The underlying objective of mutative strategy parameter control is roughly to favor previously selected mutation steps in the future. If this objective is pursued rigorously, a completely derandomized self-adaptation scheme results, which adapts arbitrary normal mutation distributions. This scheme, called covariance matrix adaptation (CMA), meets the previously stated demands. It can still be considerably improved by cumulation – utilizing an evolution path rather than single search steps. Simulations on various test functions reveal local and global search properties of the evolution strategy with and without covariance matrix adaptation. Their performances are comparable only on perfectly scaled functions. On badly scaled, nonseparable functions usually a speed up factor of several orders of magnitude is observed. On moderately mis-scaled functions a speed up factor of three to ten can be expected.

`@article{hansen2001a, author = {Nikolaus Hansen and Andreas Ostermeier}, doi = {10.1162/106365601750190398}, journal = {Evolutionary Computation}, month = {jun}, number = {2}, pages = {159--195}, publisher = {{MIT} Press - Journals}, title = {Completely Derandomized Self-Adaptation in Evolution Strategies}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/hansen2001a.pdf}, volume = {9}, year = {2001} }`

- M. Klapper-Rybicka, N. N. Schraudolph, and J. Schmidhuber, “Unsupervised learning in LSTM recurrent neural networks," in Artificial neural networks — ICANN 2001, Springer Berlin Heidelberg, 2001, pp. 684-691.

[BibTeX] [DOI]`@incollection{klapperrybicka2001a, author = {Magdalena Klapper-Rybicka and Nicol N. Schraudolph and J{\"u}rgen Schmidhuber}, booktitle = {Artificial Neural Networks {\textemdash} {ICANN} 2001}, doi = {10.1007/3-540-44668-0_95}, pages = {684--691}, publisher = {Springer Berlin Heidelberg}, title = {Unsupervised Learning in {LSTM} Recurrent Neural Networks}, year = {2001} }`

- T. Werder, K. Gerdes, D. Schötzau, and C. Schwab, “Hp-discontinuous galerkin time stepping for parabolic problems," Computer methods in applied mechanics and engineering, vol. 190, iss. 49-50, pp. 6685-6708, 2001.

[BibTeX] [Abstract] [PDF] [DOI]

The algorithmic pattern of the lip-discontinuous Galerkin finite element method (DGFEM) for the time semidiscretization of parabolic evolution equations is presented. In combination with a continuous hp-discretization in space we obtain a fully discrete hp-scheme for the numerical solution of parabolic problems. Numerical examples for the heat equation in a two-dimensional domain confirm the exponential convergence rates which are predicted by theoretical results, under realistic assumptions on the init.

`@article{werder2001a, author = {T. Werder and K. Gerdes and D. Sch{\"o}tzau and C. Schwab}, doi = {10.1016/s0045-7825(01)00258-4}, journal = {Computer Methods in Applied Mechanics and Engineering}, month = {oct}, number = {49-50}, pages = {6685--6708}, publisher = {Elsevier {BV}}, title = {hp-Discontinuous Galerkin time stepping for parabolic problems}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/werder2001a.pdf}, volume = {190}, year = {2001} }`

### 2000

- D. Bueche, N. Sukumar, and B. Moran, “Dispersive properties of the natural element method," Computational mechanics, vol. 25, iss. 2-3, pp. 207-219, 2000.

[BibTeX] [Abstract] [PDF] [DOI]

The Natural Element Method (NEM) is a meshfree numerical method for the solution of partial differential equations. In the natural element method, natural neighbor coordinates, which are based on the Voronoi tesselation of a set of nodes, are used to construct the interpolant. The performance of NEM in two-dimensional linear elastodynamics is investigated. A standard Galerkin formulation is used to obtain the weak form and a central-difference time integration scheme is chosen for time history analyses. Two different applications are considered: vibration of a cantilever beam and dispersion analysis of the wave equations. The NEM results are compared to finite element and analytical solutions. Excellent dispersive properties of NEM are observed and good agreement with analytical solutions is obtained.

`@article{bueche2000a, author = {D. Bueche and N. Sukumar and B. Moran}, doi = {10.1007/s004660050470}, journal = {Computational Mechanics}, month = {mar}, number = {2-3}, pages = {207--219}, publisher = {Springer Nature}, title = {Dispersive properties of the natural element method}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/bueche2000a.pdf}, volume = {25}, year = {2000} }`

- L. Glielmo, M. Milano, and S. Santini, “A machine learning approach to modeling and identification of automotive three-way catalytic converters," IEEE/ASME transactions on mechatronics, vol. 5, iss. 2, pp. 132-141, 2000.

[BibTeX] [Abstract] [PDF] [DOI]

The working of three-way catalytic converters (TWC’s) is based on chemical reactions whose rates are nonlinear functions of temperature and reactant concentrations all along the device. Unfortunately, the choice of suitable expressions and the tuning of their parameters is particularly difficult in dynamic conditions. In this paper we introduce a hybrid modeling technique which allows us to preserve the most important features of an accurate distributed parameter TWC model, while it circumvents both the structural and the parameter uncertainties of “classical" reaction kinetics models, and saves computational time. In particular, we compute the rates within the TWC dynamic model by a neural network which, thus, becomes a static nonlinear component of a larger dynamic system. A purposely designed genetic algorithm, in conjunction with a fast ad hoc partial differential equation integration procedure, allows us to train the neural network, embedded in the whole model structure, using currently available measurement data and without computing gradient information.

`@article{glielmo2000a, author = {L. Glielmo and M. Milano and S. Santini}, doi = {10.1109/3516.847086}, journal = {{IEEE}/{ASME} Transactions on Mechatronics}, month = {jun}, number = {2}, pages = {132--141}, publisher = {Institute of Electrical and Electronics Engineers ({IEEE})}, title = {A machine learning approach to modeling and identification of automotive three-way catalytic converters}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/glielmo2000a.pdf}, volume = {5}, year = {2000} }`

### 1999

- P. Marino, M. Milano, and F. Vasca, “Linear quadratic state feedback and robust neural network estimator for field-oriented-controlled induction motors," IEEE transactions on industrial electronics, vol. 46, iss. 1, pp. 150-161, 1999.

[BibTeX] [Abstract] [PDF] [DOI]

A field oriented control scheme for induction motor with a Linear Quadratic optimal regulator and a robust neural network estimator is proposed. The state feedback is designed by using the synchronous frame motor model. The number of the states is increased in order to take into account the presence of two integrators on the flux and torque errors. The resulting model is suitably simplified and the corresponding approximations are discussed. The procedure proposed is shown to be suitable also for the design of the state feedback via pole placement technique. A comparison with standard PI regulators is provided. The rotor flux is estimated by using a robust neural network observer. The network training set is suitably designed in order to preserve the drive effectiveness also in the presence of large parameter uncertainties. The robust neural observer is compared with an Extended Kalman filter and a standard neural network observer. Using a 250 kW induction motor as case study, the simulation results show the effectiveness of the proposed solution both during transient and steady state operating conditions.

`@article{marino1999a, author = {P. Marino and M. Milano and F. Vasca}, doi = {10.1109/41.744406}, journal = {{IEEE} Transactions on Industrial Electronics}, number = {1}, pages = {150--161}, publisher = {Institute of Electrical and Electronics Engineers ({IEEE})}, title = {Linear quadratic state feedback and robust neural network estimator for field-oriented-controlled induction motors}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/marino1999a.pdf}, volume = {46}, year = {1999} }`

### 1998

- A. Larsen and J. H. Walther, “Discrete vortex simulation of flow around five generic bridge deck sections," Journal of wind engineering and industrial aerodynamics, vol. 77-78, pp. 591-602, 1998.

[BibTeX] [Abstract] [PDF] [DOI]

We present a bound on the generalization error of linear classifiers in terms of a refined margin quantity on the training sample. The result is obtained in a probably approximately correct (PAC)-Bayesian framework and is based on geometrical arguments in the space of linear classifiers. The new bound constitutes an exponential improvement of the so far tightest margin bound, which was developed in the luckiness framework, and scales logarithmically in the inverse margin. Even in the case of less training examples than input dimensions sufficiently large margins lead to nontrivial bound values and-for maximum margins-to a vanishing complexity term. In contrast to previous results, however, the new bound does depend on the dimensionality of feature space. The analysis shows that the classical margin is too coarse a measure for the essential quantity that controls the generalization error: the fraction of hypothesis space consistent with the training sample. The practical relevance of the result lies in the fact that the well-known support vector machine is optimal with respect to the new bound only if the feature vectors in the training sample are all of the same length. As a consequence, we recommend to use support vector machines (SVMs) on normalized feature vectors only. Numerical simulations support this recommendation and demonstrate that the new error bound can be used for the purpose of model selection.

`@article{larsen1998a, author = {Allan Larsen and Jens H. Walther}, doi = {10.1016/s0167-6105(98)00175-5}, journal = {Journal of Wind Engineering and Industrial Aerodynamics}, month = {sep}, pages = {591--602}, publisher = {Elsevier {BV}}, title = {Discrete vortex simulation of flow around five generic bridge deck sections}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/larsen1998a.pdf}, volume = {77-78}, year = {1998} }`

### 1997

- A. Larsen and J. H. Walther, “Aeroelastic analysis of bridge girder sections based on discrete vortex simulations," Journal of wind engineering and industrial aerodynamics, vol. 67-68, pp. 253-265, 1997.

[BibTeX] [Abstract] [PDF] [DOI]

Two-dimensional viscous incompressible flow past bridge girder cross-sections are simulated using the discrete vortex method. The flow around stationary cross-sections as well as cross-sections undergoing cross-wind vertical (bending) and rotary (torsional) motions are investigated for assessment of drag coefficient, Strouhal number and aerodynamic derivatives for application in aeroelastic analyses. Good to excellent agreement with wind tunnel test results is demonstrated for analyses of forced wind loading, flutter wind speed and vertical vortex-induced response of four practical girder cross-sections. The success of the simulations is attributed to the bluff nature of the cross-sections and to the two-dimensional (2-D) nature of flow around bridge girders.

`@article{larsen1997a, author = {Allan Larsen and Jens H. Walther}, doi = {10.1016/s0167-6105(97)00077-9}, journal = {Journal of Wind Engineering and Industrial Aerodynamics}, month = {apr}, pages = {253--265}, publisher = {Elsevier {BV}}, title = {Aeroelastic analysis of bridge girder sections based on discrete vortex simulations}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/larsen1997a.pdf}, volume = {67-68}, year = {1997} }`

- L. Milano, F. Barone, and M. Milano, “Time domain amplitude and frequency detection of gravitational waves from coalescing binaries," Physical review d, vol. 55, iss. 8, pp. 4537-4554, 1997.

[BibTeX] [Abstract] [PDF] [DOI]

We propose a multistep procedure for the on-line detection and analysis of gravitational wave signals emitted during the coalescence of compact binaries. This procedure, based on a hierarchical strategy, consists of a rough analysis of the gravitational wave signal using adaptive line enhancers (ALE) filters and the controlled random search (CRS) optimization algorithm Followed by a refined analysis using the classic matched-filtering technique. The results of simulations far the rough analysis are quite promising both for the relatively small computational power needed and for the robustness of the algorithms used, so that it could be very helpful far gravitational wave detection with very large baseline interferometric detectors like LIGO and VIRGO.

`@article{milano1997a, author = {L. Milano and F. Barone and M. Milano}, doi = {10.1103/physrevd.55.4537}, journal = {Physical Review D}, month = {apr}, number = {8}, pages = {4537--4554}, publisher = {American Physical Society ({APS})}, title = {Time domain amplitude and frequency detection of gravitational waves from coalescing binaries}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/milano1997a.pdf}, volume = {55}, year = {1997} }`

- L. Milano, F. Barone, and M. Milano, “Detection of gravitational waves from coalescing binaries in the time domain," Classical and quantum gravity, vol. 14, iss. 6, pp. 1531-1536, 1997.

[BibTeX] [Abstract] [PDF] [DOI]

We propose a multistep procedure for the on-line detection and analysis of the gravitational wave signals emitted during the coalescence of compact binaries. This procedure, based on a hierarchical strategy, consists of a rough on-line analysis of the gravitational wave signal using adaptive line enhancers filters and a fast off-line parameter estimate, using the controlled random search optimization algorithm. A more refined off-line analysis using the classic matched-filtering technique, with a greatly reduced computational burden, can follow to further improve the parameter estimate. The results of simulations for the rough analysis are quite promising both for the relatively small computational power needed and for the robustness of the algorithms used, so that it could be very helpful for gravitational wave detection with very large baseline interferometric detectors such as LIGO and VIRGO.

`@article{milano1997b, author = {L Milano and F Barone and M Milano}, doi = {10.1088/0264-9381/14/6/023}, journal = {Classical and Quantum Gravity}, month = {jun}, number = {6}, pages = {1531--1536}, publisher = {{IOP} Publishing}, title = {Detection of gravitational waves from coalescing binaries in the time domain}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/milano1997b.pdf}, volume = {14}, year = {1997} }`

- J. H. Walther and A. Larsen, “Two dimensional discrete vortex method for application to bluff body aerodynamics," Journal of wind engineering and industrial aerodynamics, vol. 67-68, pp. 183-193, 1997.

[BibTeX] [Abstract] [PDF] [DOI]

Two-dimensional viscous incompressible flow past a flat plate of finite thickness and length is simulated using the discrete vortex method. Both a fixed plate and a plate undergoing a harmonic heave and pitch motion are studied. The Reynolds number is 10(4) and the reduced onset flow speed, U/fc is in the range 2-14. The fundamental kinematic relation between the velocity and the vorticity is used in a novel approach to determine the surface vorticity. An efficient influence matrix technique is used in a fast adaptive multipole algorithm context to obtain a mesh-free method. The numerical results are compared with the steady-state Blasius solution, and with the inviscid solution for the flow past an oscillating plate by Theodorsen

`@article{walther1997a, author = {Jens Honor{\'{e}} Walther and Allan Larsen}, doi = {10.1016/s0167-6105(97)00072-x}, journal = {Journal of Wind Engineering and Industrial Aerodynamics}, month = {apr}, pages = {183--193}, publisher = {Elsevier {BV}}, title = {Two dimensional discrete vortex method for application to bluff body aerodynamics}, url = {http://www.cse-lab.ethz.ch/wp-content/papercite-data/pdf/walther1997a.pdf}, volume = {67-68}, year = {1997} }`