Publications

 

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JOURNALS 

 

2017

  • Wu S., Angelikopoulos P., Papadimitriou C., Koumoutsakos P., Bayesian Annealed Sequential Importance Sampling (BASIS): an unbiased version of Transitional Markov Chain Monte Carlo, ASCE-ASME Journal of Risk and Uncertainty in Engineering Systems, Part B: Mechanical Engineering, (2017) (pdf)

     

  • Verma S., Abbati G., Novati G., Koumoutsakos P., Computing the force distribution on the surface of complex, deforming geometries using Vortex methods and Brinkman penalizationInt. J. Num. Meth. Fluids, Accepted, (doi), (pdf)
     
  • Novati G., Verma S., Alexeev D., Rossinelli D., van Rees W.M., Koumoutsakos P., Synchronisation through learning for two self-propelled swimmersBioinspir. Biomim., 2017, 12, 036001, (doi), (pdf)
     
  • Karathanasopoulos N., Angelikopoulos P., Papadimitriou C., Koumoutsakos P., Bayesian identification of the tendon fascicle's structural composition using finite element models for helical geometriesComputer Methods in Applied Mechanics and Engineering, 313, pp. 744-758 (2017) (doi), (pdf)

 

2016

  • Wu S., Angelikopoulos P., Tauriello G., Papadimitriou C., Koumoutsakos P., Fusing Heterogeneous Data for the Calibration of Molecular Dynamics Force Fields Using Hierarchical Bayesian Models, J. Chem. Phys., 145: 244112 (2016) (doi) (pdf
     
  • Chen J., Walther J.H., Koumoutsakos P., Ultrafast cooling by covalently bonded graphene-carbon nanotube hybrid immersed in waterNanotechnology, 27, 465705, pp. 1-8 (2016) (doi), (pdf)
     
  • Gazzola M., Tchieu A.A., Alexeev D., Brauer A. de, Koumoutsakos P., Learning to school in the presence of hydrodynamic interactions, J. Fluid Mech., Vol. 789, pp. 726-749 (2016) (doi), (pdf)

 

2015

  • Conti C., Rossinelli D., Alexeev D., Lykov K., Hadjidoukas P., Koumoutsakos P., The In-Silico Lab-on-a-Chip - Catching a Needle in a Flowing Haystack, APS Gallery of Fluid Motion, 2015 (doi) (movie)
     
  • Wu S., Angelikopoulos P., Papadimitriou C., Moser R., Koumoutsakos P., A hierarchical Bayesian framework for force field selection in molecular dynamics simulations, Phil. Trans. Royal Soc. A, Vol. - (2015) (doi) (pdf)
     

  • Tauriello G., Meyer H.M., Smith R.S., Koumoutsakos P., Roeder A.H. K., Variability and Constancy in Cellular Growth of Arabidopsis Sepals, Plant Physiology, Vol. 169, 2342-2358 (2015) (doi) (pdf)
     

  • Chen J., Walther J.H., Koumoutsakos P., Covalently Bonded Graphene-Carbon Nanotube Hybrid for High-Performance Thermal Interface, Advanced Funtional Materials (2015) (doi) (pdf)
     

  • Finley S.D., Angelikopoulos P., Koumoutsakos P., Popel A., Pharmacokinetics of Anti-VEGF Agent Aflibercept in Cancer Predicted by Data-Driven, Molecular-Detailed Model, CPT: Pharmacometrics & Systems Pharmacology, (2015) (doi) (pdf)
     

  • Popadic A., Praprotnik M., Koumoutsakos P., Walther J.H., Continuum simulations of water flow past fullerene moleculesEur. Phys. J. Special Topics, 224, 2321-2330 (2015) (doi) (pdf)
     

  • Alexeev D., Chen J., Walther J.H., Giapis K.P., Angelikopoulos P., Koumoutsakos P., Kapitza Resistance between Few-Layer Graphene and Water: Liquid Layering EffectsNano Letters, 2015 (doi) (pdf) (SI)
     

  • Jones P.R., Hao X., Cruz-Chu E.R., Rykaczewski K., Nandy K., Schutzius T.M., Varanasi K.K., Megaridis C.M., Walther J.H., Koumoutsakos P., Espinosa H.D., Patankar N.A., Sustaining dry surfaces under waterScientific Reports, 5:12311, 2015 (doi) (pdf)
     
  • Baumann M.U., Marti M., Durrer L., Koumoutsakos P., Angelikopoulos P., Bolla D., Acharya G., Bichsel U., Surbek D. V., Raio L., Placental plasticity in monochorionic twins: Impact on birth weight and placental weightPlacenta, 2015 (doi) (pdf)
     
  • Van Rees W.M., Gazzola M., Koumoutsakos P., Optimal morphokinematics for undulatory swimmers at intermediate Reynolds numbers J. Fluid Mech., Vol. 775, pp. 178-188 (2015) (doi), (pdf)
     
  • Hadjidoukas P.E., Angelikopoulos P., Kulakova L., Papadimitriou C., Koumoutsakos P., Exploiting Task-Based Parallelism in Bayesian Uncertainty QuantificationLecture Notes in Computer Science, 2015, 9233, 532-544 (doi) (pdf)
     
  • Van Rees W.M., Novati G., Koumoutsakos P., Self-propulsion of a counter-rotating cyllinder pair in a viscous fluidPhysics of Fluids, 2015, 27, 063102 (doi) (pdf)
     
  • Huhn F., van Rees W.M., Gazzola M., Rossinelli D., Haller G., Koumoutsakos P., Quantitative flow analysis of swimming dynamics with coherent Lagrangian vortices. Chaos, 25, 087405, 2015 (pdf)
     
  • Barbier de Reuille P., Routier-Kierzkowska A.L., Kierzkowski D., Bassel G.W., Schüpbach T., Tauriello G., Bajpai N., Strauss S., Weber A., Kiss A., Burian A., Hofhuis H., Sapala A., Lipowczan M., Heimlicher M.B., Robinson S., Bayer E.M., Basler K., Koumoutsakos P., Roeder A.H.K., Aegerter-Wilmsen T., Nakayama N., Tsiantis M., Hay A., Kwiatkowska D., Xenarios I., Kuhlemeier C., Smith R.S., MorphoGraphX: A platform for quantifying morphogenesis in 4D. eLife, 4:e05864, 2015 (doi) (pdf)
     
  • Rossinelli D., Hejazialhosseini B., van Rees W.M., Gazzola M., Bergdorf M., Koumoutsakos P., MRAG-I2D: Multi-resolution adapted grids for remeshed vortex methods on multicore architectures. J. Comput. Phys., 288:1–8, 2015 (doi) (pdf)
     
  • Angelikopoulos P., Papadimitriou C., Koumoutsakos P., X-TMCMC: Adaptive Kriging for Bayesian inverse modelingComput. Methods Appl. Mech. Engrg., 289:409-428, 2015 (doi) (pdf)
     
  • Tauriello G., Koumoutsakos P., A comparative study of penalization and phase field methods for the solution of the diffusion equation in complex geometries. J. Comput. Phys., 283:388–407, 2015 (doi) (pdf)
     
  • Hejlesen M.M., Koumoutsakos P., Leonard A., Walther J.H., Iterative Brinkman penalization for remeshed vortex methods. J. Comput. Phys., 280:547–562, 2015 (doi) (pdf)
     
  • Hadjidoukas P.E., Angelikopoulos P., Papadimitriou C., Koumoutsakos P., Pi4U: A high performance computing framework for Bayesian uncertainty quantification of complex modelsJ. Comput. Phys., 284:1–21, 2015 (doi) (pdf)

 

2014

  • Popadic A., Walther J.H., Koumoutsakos P., Praprotnik M., Continuum simulations of water flow in carbon nanotube membranes. New J. Phys., 16(8):082001, 2014 (doi) (pdf)
     
  • Hadjidoukas P. E, Angelikopoulos P., Rossinelli D., Alexeev D., Papadimitriou C., Koumoutsakos P., Bayesian uncertainty quantification and propagation for discrete element simulations of granular materials. Comput. Methods Appl. Mech. Engrg. 282:218-238, 2014 (doi) (pdf)
     
  • Gazzola M., Hejazialhosseini B., Koumoutsakos P., Reinforcement Learning and Wavelet Adapted Vortex Methods for Simulations of Self-propelled SwimmersSIAM J. Sci. Comput., 36(3):B622–B639, 2014 (doi) (pdf)
     
  • Milde F., Tauriello G., Haberkern H., Koumoutsakos P., SEM++: A particle model of cellular growth, signaling and migration, Comp. Part. Mech., 1(2):211–227, 2014 (doi) (pdf)
     
  • van Rees W.M., Rossinelli D., Hadjidoukas P., Koumoutsakos P., High performance CPU/GPU multiresolution Poisson solver. In Advances in Parallel Computing Vol 25, IOS Press, 2014, 481-490 (pdf)
     
  • Chen J., Walther J. H., Koumoutsakos P., Strain Engineering of Kapitza Resistance in Few-Layer GrapheneNano Letters 14:819–825, 2014. (link) (pdf
     
  • Cruz-Chu E. R., Malafeev A., Pajarskas T., Pivkin I. V., Koumoutsakos P., Structure and Response to Flow of the Glycocalyx LayerBiophys. J., 6(1):232–243, 2014 (Abstract) (pdf)

 

2013

  • Tauriello G., Koumoutsakos P., Coupling Remeshed Particle and Phase Field Methods for the Simulation of Reaction-Diffusion on the Surface and the Interior of Deforming Geometries, SIAM J. Sci. Comput., 35(6):B1285–B1303, 2013 (Abstract) (pdf)
     
  • Milde F., Lauw S., Koumoutsakos P., Iruela-Arispe L.M., The mouse retina in 3D: quantification of vascular growth and remodeling. Integrative Biology, 5(12): 1426-1438, 2013 (doi) (pdf)
     
  • Angelikopoulos P., Papadimitriou C., Koumoutsakos P., Data driven, predictive molecular dynamics for nanoscale flow simulations under uncertaintyJournal of Physical Chemistry B, 117, 14808-14816, 2013. (pdf)
     
  • van Rees W.M., Gazzola M., Koumoutsakos P., Optimal shapes for anguilliform swimmers at intermediate Reynolds numbersJournal of Fluid Mechanics, 722, 2013. (pdf(Cover JFM)
     
  • Hejazialhosseini B., Rossinelli D., Koumoutsakos P., Vortex dynamics in 3D shock-bubble interactionPhysics of Fluids, 25, 110816, 2013 (pdf) (doi)
     
  • Hejazialhosseini B., Rossinelli D., Koumoutsakos P., 3D shock-bubble interaction, Physics of Fluids Gallery of Fluid Motion, 25, 091105, 2013 (pdf) (doi) (movie)
     
  • Hejazialhosseini B., Conti C., Rossinelli D., Koumoutsakos P., High performance CPU kernels for multiphase compressible flows, Lecture Notes in Computer Science, 7851, 216-225, Springer Berlin,  2013 (pdf)
     
  • Koumoutsakos P., Pivkin I., Milde F., The Fluid Mechanics of Cancer and Its Therapy. Annual Review of Fluid Mechanics, 45:325-55, 2013 (Abstract) (pdf)
     
  • Walther J.H., Ritos K., Cruz-Chu E., Megaridis C.M., Koumoutsakos P., Barriers to Superfast Water Transport for Carbon Nanotube Membranes, Nano Letters, 2013. (pdf)
     
  • Koumoutsakos P., Feigelman J., Multiscale stochastic simulations of chemical reactions with regulated scale separation, Journal of Computational Physics, 2013. (Abstract) (pdf)
     
  • Franco D., Milde F., Klingauf M., Orsenigo F., Dejana E., Poulikakos D., Cecchini M., Koumoutsakos P., Ferrari A., Kurtcuoglu V., Accelerated endothelial wound healing on microstructured substrates under flow. Biomaterials, 34(5):1488-1497, 2013. (Abstract) (pdf)
     
  • Koumoutsakos P., Feigelman J., Multiscale stochastic simulations of chemical reactions with regulated scale separation, Journal of Computational Physics, 2013. (Abstract) (pdf)

 

2012

  • Angelikopoulos P., Papadimitriou C., Koumoutsakos P., Bayesian uncertainty quantification and propagation in molecular dynamics simulations: A high performance computing frameworkJournal of Chemical Physics, 137(144103), 2012. (Abstract) (pdf)
     
  • Milde F., Franco D., Ferrari A., Kurtcuoglu V., Poulikakos D., Koumoutsakos P., Cell Image Velocimetry (CIV): boosting the automated quantification of cell migration in wound healing assaysIntegrative Biology,  4(11):1437-1447, 2012. (Abstract) (pdf)
     
  • Paolucci M., Kossman D., Conte R., Lukowicz P., Argyrakis P., Blandford A., Bonelli G., Anderson S., de Freitas S., Edmonds B., Gilbert N., Gross M., Kolhammer J., Koumoutsakos P. Krause A., Linner Bo., Slusallek P, Sorkne O., Sumner RW., Helbing D., Towards a Living Earth Simulator, European Phys. J., Vol. 214, pp:77-108, 2012
     

  • van Rees W.M., Hussain F., Koumoutsakos P., Vortex tube reconnection at Re=104. Physics of Fluids, 24(7):075105, 2012. (Abstract) (pdf)
     
  • Gazzola M., Mimeau C., Tchieu A.A., Koumoutsakos P., Flow mediated interactions between two cylinders at finite Re numbersPhysics of Fluids, 24(4):043103, 2012.  (Abstract) (pdf)  (Research Highlight)
     
  • Gazzola M., van Rees W.M., Koumoutsakos P., C-start: optimal start of larval fish. Journal of Fluid Mechanics, 698:5–18, 2012. (Abstract) (pdf(this article is featured in the JFM series: Focus on Fluids) (Cover of JFM)
     
  • Walther J.H., Praprotnik M., Kotsalis E.M., Koumoutsakos P., Multiscale simulation of water flow past a C-540 Fullerene, Journal of Computational Physics, 231(7):2677–2681, 2012. (Abstract) (pdf)
     
  • Conti C., Rossinelli D., Koumoutsakos P., GPU and APU computations of Finite Time Lyapunov Exponent fieldsJournal of Computational Physics, 231(5):2229–2244, 2012. (Abstract) (pdf)


2011

  • Gazzola M., Chatelain P., van Rees W.M., Koumoutsakos P., Simulations of single and multiple swimmers with non-divergence free deforming geometries, Journal of Computational Physics, 230(19):7093–7114, 2011. (Abstract) (pdf)
     
  • Koumoutsakos P., Bayati B., Milde F., Tauriello G., Particle Simulations of Morphogenesis, Math. Mod. Meth. Appl. S., 21, pp. 955-1006, 2011 (Abstract) (pdf)
     
  • Rossinelli D., Conti C., Koumoutsakos P., Mesh-particle interpolations on GPUs and multicore CPUs, Phil. Trans. R. Soc. A, 369, pp. 2164-2175, 2011 (Abstract) (pdf
     
  • Rossinelli D., Hejazialhosseini B., Spampinato D., Koumoutsakos P., Multicore/Multi-GPU Accelerated Simulations of Multiphase Compressible Flows Using Wavelet Adapted Grids, SIAM J. Sci. Comput., 33, pp. 512-540, 2011 (Abstract) (pdf
     
  • Chatelain P., Gazzola M., Kern S., Koumoutsakos P., Optimization of aircraft wake alleviation schemes through an evolution strategy, Lecture Notes in Computer Science, 6649:210, 2011 (Abstract) (pdf)
     
  • van Rees W.M., Leonard A., Pullin D.I., Koumoutsakos P., A comparison of vortex and pseudo-spectral methods for the simulation of periodic vortical flows at high Reynolds numbersJournal of Computational Physics, 230(8), 2794-2805, 2011 (Abstract) (pdf)
     
  • Schwank G., Tauriello G., Yagi R., Kranz E., Koumoutsakos P., Basler K., Antagonistic growth regulation by Dpp and Fat drives uniform cell proliferation, Developmental Cell, 20(1), 123-30, 2011 (Abstract) (pdf)
     
  • Bayati B., Chatelain P., Koumoutsakos P., Adaptive mesh refinement for stochastic reaction-diffusion processesJournal of Computational Physics, 230, 13-26, 2011 (Abstract) (pdf)
     
  • Rossinelli D., Hejazialhosseini B., Bergdorf M., Koumoutsakos P., Wavelet-adaptive solvers on multi-core architectures for the simulation of complex systemsConcurrency and Computation: Practice and Experience, 23(2), 172, 2011 (Abstract) (pdf
     
  • Gazzola M., Vasilyev O.V., Koumoutsakos P., Shape optimization for drag reduction in linked bodies using evolution strategies, Computers and Structures, 6649:210, 2011 (Abstract) (pdf

2010
  • Hanasaki I., Walther J.H., Kawano S., Koumoutsakos P., Coarse-grained molecular dynamics simulations of shear-induced instabilities of lipid bilayer membranes in water, Physical Review E., 82, 051602-1 - 051602-6, 2010 (Abstract) (pdf)
     
  • Bayati B., Owhadi H., Koumoutsakos P., A cutoff phenomenon in accelerated stochastic simulations of chemical kinetics via flow averaging (FLAVOR-SSA)J. of Chemical Physics, 133, 2441171-2441176, 2010 (Abstract) (pdf) (AIP)
     
  • Hejazialhosseini B., Rossinelli D., Bergdorf M., Koumoutsakos P., 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, Volume 229, Issue 22, Pages 8364-8383, 2010 (Abstract) (pdf)
     
  • Morra G., Yuen D.A., Boschi L., Chatelain P., Koumoutsakos P., Tackley P.J., The fate of the slabs interacting with a density/viscosity hill in the mid-mantlePhysics of the Earth and Planetary Interiors , 180, 271-282, 2010 (Abstract) (pdf)
     
  • Kotsalis E.M., Hanasaki I., Walther J.H., Koumoutsakos P., Non-periodic Molecular Dynamics simulations of coarse grained lipid bilayer in water, Computers and Mathematics with Applications, 59, 2370-2373, 2010 (Abstract) (pdf)
     
  • Chatelain P., Koumoutsakos P., A Fourier-based elliptic solver for vortical flows with periodic and unbounded directions, Journal of Computational Physics, 229, 7, 2425-2431, 2010 (Abstract) (pdf)
     
  • Rossinelli D., Bergdorf M., Cottet G-H., Koumoutsakos P., GPU accelerated simulations of bluff body flows using vortex particle methods, Journal of Computational Physics, 229, 9, 3316-3333, 2010 (Abstract) (pdf)
     
  • Bergdorf M., Sbalzarini I. F., Koumoutsakos P., A Lagrangian particle method for reaction–diffusion systems on deforming surfaces, Journal of Mathematical Biology Physics, 61, 5, 649-663, 2010 (Abstract) (pdf)


2009

  • Rossinelli D., Bergdorf M., Hejazialhosseini B., Koumoutsakos P., Wavelet based adaptive simulation of complex systems on multicore architectures, Lecture Notes In Computer Science, 5704, 10, 721-734, (Abstract) (pdf) (Distinguished Paper Award in Euro-Par 2009)
     
  • Gazzola M., Burckhardt C.J., Bayati B., Engelke M., Greber U.F., Koumoutsakos P., A Stochastic Model for Microtubule Motors Describes the In Vivo Cytoplasmic Transport of Human Adenovirus, PLoS Computational Biology, 5, 12, e1000623, 2009 (Abstract) (pdf)
     
  • Falcón B.L., Hashizume H., Koumoutsakos P., Chou J., Bready J.V.,  Coxon A.,  Oliner J.D., McDonald D.M., Contrasting Actions of Selective Inhibitors of Angiopoietin-1 and Angiopoietin-2 on the Normalization of Tumor Blood Vessels, The American Journal of Pathology, 175, 5, 2009 (Abstract) (pdf)
     
  • Bayati B., Chatelain P., Koumoutsakos P., D-leaping: Accelerating stochastic simulation algorithms for reactions with delaysJournal of Computational Physics, 228, 5908-5916, 2009 (Abstract) (pdf)
     
  • Gebäck T., Koumoutsakos P., Edge detection in microscopy images using curveletsBMC Bioinformatics, 10,75, 2009 (Abstract) (pdf)
     
  • Mjolsness E., Orendorff D., Chatelain P., Koumoutsakos P., An exact accelerated stochastic simulation algorithmJournal of Chemical Physics, 130, 14, 2009 (Abstract) (pdf)
     
  • Gebäck T., Schulz M.M.P., Koumoutsakos P., Detmar M.,TScratch: a novel and simple software tool for automated analysis of monolayer wound healing assays, Bio Techniques, 46, 265-274, 2009 (Abstract) (pdf)
     
  • Morra G., Chatelain P., Tackley P., Koumoutsakos P., Earth curvature effects on subduction morphology: Modeling subduction in a spherical setting,  Acta Geotechnica, 4, 95-105, 2009 (Abstract) (pdf)
     
  • Kotsalis E.M., Walther J.H., Kaxiras E., Koumoutsakos P., Control algorithm for multiscale flow simulations of water, Physical Review E, 79,4, 2009 (Abstract) (pdf)
     
  • Gonnet P., Walther J.H., Koumoutsakos P., ϑ-SHAKE: An extension to SHAKE for the explicit treatment of angular constraints, Computer Physics Communications, 180, 360–364, 2009 (Abstract) (pdf)
     
  • Zambrano H.A., Walther J.H., Koumoutsakos P., Sbalzarini I.F., Thermophoretic Motion of Water Nanodroplets Confined inside Carbon Nanotubes, Nano Letters, 9,1,66-71, 2009 (Abstract) (pdf)
     
  • Hansen N., Niederberger A.S.P., Guzzella L., Koumoutsakos P., A Method for Handling Uncertainty in Evolutionary Optimization With an Application to Feedback Control of Combustion, IEEE Transactions on Evolutionary Computation, 180-197, 13, 2009 (Abstract) (pdf)

2008
  • Chatelain P., Curioni A., Bergdorf M., Rossinelli D., Andreoni W., Koumoutsakos P., Vortex Methods for Massively Parallel Computer Architectures, Lecture Notes in Computer Science, 5336, 479-489, 2008 (Abstract) (pdf)
     
  • Fukagata K., Kern S., Chatelain P., Koumoutsakos P., Kasagi N., Evolutionary optimization of an anisotropic compliant surface for turbulent friction drag reduction, J. Turbulence, 9, 35, 1-17, 2008 (Abstract) (pdf)
     
  • Bayati B., Chatelain P., Koumoutsakos P., Multiresolution stochastic simulations of reaction-diffusion processes, Physical Chemistry Chemical Physics, 10, 39, 5963-5966, 2008 (Abstract) (pdf)
     
  • Hieber S.E., Koumoutsakos P., A Lagrangian particle method for the simulation of linear and nonlinear elastic model of soft tissueJ. Computational Physics, 227, 9195-9215, 2008 (Abstract) (pdf)
     
  • Milde F., Bergdorf M., Koumoutsakos P., A Hybrid Model for 3D Simulations of Sprouting AngiogenesisBiophysical J., 95, 7, 3146–3160, 2008 (Abstract) (pdf)
     
  • Hieber S.E., Koumoutsakos P., An immersed boundary method for smoothed particle hydrodynamics of self-propelled swimmers, J. of Computational Physics, 227, 19, 8636-8654, 2008 (Abstract) (pdf)
     
  • Kotsalis E.M., Koumoutsakos P., A Control Algorithm for Multiscale Simulations of Liquid Water, Lecture Notes in Computer Science, 5102, 234-241, Springer Berlin, 2008 (Abstract) (pdf)
     
  • Milde F., Bergdorf M., Koumoutsakos P., A Hybrid Model of Sprouting Angiogenesis, Lecture Notes in Computer Science, 5102, 167-176, Springer Berlin, 2008 (Abstract) (pdf)
     
  • Rossinelli D., Koumoutsakos P., Vortex Methods for incompressible Flow Simulations on the GPU, Visual Computer, 24, 7-9, 699-708, 2008 (Abstract) (pdf)
     
  • Zimmerli U., Koumoutsakos P., Simulations of Electrophoretic RNA Transport through Transmembrane Carbon Nanotubes, Biophysical J. , 94, 7, 2546-2557, 2008 (Abstract) (pdf)
     
  • Poncet Ph., Hildebrand R., Cottet G.H., Koumoutsakos P., Spatially distributed control for optimal drag reduction of the flow past a circular cylinder, J. Fluid Mechanics, 599, 111-120, 2008 (Abstract). (pdf(bw), pdf(color))
     
  • Rossinelli D., Bayati B., Koumoutsakos P., Accelerated Stochastic and Hybrid Methods for Spatial Simulations of Reaction-Diffusion Systems, Chemical Physics Letters, 451, 1-3, 136-140, 2008. (Abstract) (pdf)
     
  • Chatelain P., Curioni A., Bergdorf M., Rossinelli D., Andreoni W., Koumoutsakos P., Billion Vortex Particle Direct Numerical Simulations of Aircraft Wakes, Computer Methods in Applied Mechanics and Engineering, 197, 13-16, 1296-1304, 2008 (Abstract) (pdf)
     
  • Morra G., Chatelain P., Tackley P., Koumoutsakos P., Earth curvature effects on subduction morphology: Modeling Subduction in a spherical setting, Acta Geotechnica, DOI 10.1007/s11440-008-0060-5, 2008 (Abstract) (pdf)
     
  • Dupuis A., Chatelain P., Koumoutsakos P., An Immersed Boundary-Lattice Boltzmann Method for the Simulation of the Flow Past an Impulsively Started Cylinder, J. Computational Physics, 227, 9, 4486-4498, 2008 (Abstract) (pdf)


2007

  • Altenhoff A., Walther J.H., Koumoutsakos P., A Stochastic Boundary Forcing for Dissipative Particle Dynamics, J. Computational Physics, 225, 1125-1136, 2007 (Abstract) (pdf)
     
  • Bergdorf M., Koumoutsakos P., Leonard A., Direct Numerical Simulations of Vortex Rings at Re=7,500, J. Fluid Mechanics, 581, 495-505, 2007 (Abstract) (pdf)
     
  • Dupuis A., Kotsalis E.M, Koumoutsakos P., Coupling Lattice Boltzmann and Molecular Dynamics Models for Dense Fluids, Physical Review E, 75, 046704, 2007 (Abstract) (pdf)
     
  • Kotsalis E.M., Walther J.H., Koumoutsakos P., Control of density fluctuations in atomistic-continuum simulations of dense liquids, Physical Review E, 76, 016709, 2007 (Abstract) (pdf)
     
  • Schoen P.A.E., Walther J.H., Poulikakos D., Koumoutsakos P., Phonon assisted thermophoretic motion of gold nanoparticles inside carbon nanotubes, Applied Physics Letters, 90, 24, 2007 (Abstract) (pdf)
     
  • Kern S., Koumoutsakos P., Eschler K., Optimization of anguiliform swimming, Physics of Fluids (Gallery of Fluid Motion), 19, 091102-1, 2007 (pdf)
     
  • Chatelain P., Cottet G.H., Koumoutsakos P., Particle Mesh Hydrodynamics for Astrophysics Simulations, Int. J. Modern Physics C, 18, 4, 610-618, 2007 (Abstract) (pdf)
     
  • Dupuis A., Koumoutsakos P., Effects of Atomistic Domain Size on Hybrid Lattice Boltzmann-Molecular Dynamics Simulations of Dense Fluids, Int. J. Modern Physics C, 18, 4, 644-651, 2007 (Abstract) (pdf)
     
  • Helmuth J.A., Burckhardt Ch.J., Koumoutsakos P., Greber U.F., Sbalzarini I., A novel supervised trajectory segmentation algorithm identifies distinct types of human adenovirus motion in host cells, J. Structural Biology, 159, 3, 347-358, 2007 (Abstract) (pdf)


2006

  • Bergdorf M., Koumoutsakos P., A Lagrangian Particle-Wavelet Method, Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 5(3), 980-995, 2006 (Abstract) (pdf)
     
  • Kern S., Koumoutsakos P., Simulations of optimized anguilliform swimming, J. Experimental Biology, 209, 4841-4857, 2006 (Abstract) (pdf)
     
  • Auger A., Chatelain P., Koumoutsakos P., R-leaping: Accelerating the stochastic simulation algorithm by reaction leaps, J. Chemical Physics, 125, 84103, 2006 (Abstract) (pdf)
     
  • Sbalzarini I.F., Hayer A., Helenius A., Koumoutsakos. P., Simulations of (An)Isotropic Diffusion on Curved Biological SurfacesBiophysical J., 90:878-885, 2006 (Abstract) (pdf)
     
  • Sbalzarini I.F., Walther J.H., Bergdorf M., Hieber S.E., Kotsalis E.M., Koumoutsakos P., PPM - A highly efficient parallel particle-mesh library for the simulation of continuum systems, J. Computational Physics, 215:566-588, 2006 (Abstract) (pdf)
     
  • Schoen P.A.E., Walther J.H., Arcidiacono S., Poulikakos D., Koumoutsakos P., Nanoparticle Traffic on Helical Tracks: Thermophoretic Mass Transport through Carbon NanotubesNano Letters, 2006 (Abstract) (pdf)
     
  • Fukagata K., Kasagi N., Koumoutsakos P., A theoretical prediction of friction drag reduction in turbulent flow by superhydrophobic surfacesPhysics of Fluids, 18:051703-1:051703-4, 2006 (Abstract) (pdf)
     
  • Sbalzarini I.F., Walther J.H., Polasek B., Chatelain P., Bergdorf M., Hieber S.E., Kotsalis E.M., Koumoutsakos P., A Software Framework for Portable Parallelization of Particle-Mesh Simulations, Lecture Notes in Computer Science, 4128, 730-739, Springer Berlin, 2006 (Abstract) (pdf)
     
  • Koumoutsakos P., Muller S.D., Flow optimization using stochastic algorithms, Lecture Notes in Control and Information Sciences, 330, 213-229, Springer Berlin, 2006 (Abstract) (pdf)
     
  • Hansen N., Gemperle F., Auger A., Koumoutsakos P., When Do Heavy-Tail Distributions Help?, Lecture Notes in Computer Science, 4193, 62-71, Springer Berlin, 2006 (Abstract) (pdf)
     
  • Kern S., Hansen N., Koumoutsakos P., Local Meta-models for Optimization Using Evolution StrategiesLecture Notes in Computer Science, 4193, 939-948, Springer Berlin, 2006 (Abstract) (pdf)


2005

  • Koumoutsakos P., Multiscale flow simulations using particles, Annual Review Fluid Mechanics, 37, 457-87, 2005 (Abstract) (pdf)
     
  • Hieber S.E., Koumoutsakos P., A Lagrangian particle level set method, J. Computational Physics, 210:342-367, 2005 (Abstract) (pdf)
     
  • Werder T., Walther J.H., Koumoutsakos P., Hybrid atomistic-continuum method for the simulation of dense fluid flow, J. Computational Physics, 205, 373 - 390, 2005 (Abstract) (pdf)
     
  • Bergdorf M., Cottet G.H., Koumoutsakos P., Multilevel adaptive particle methods for convection-diffusion equations, Multiscale Modeling and Simulation: A SIAM, Interdisciplinary Journal, 4(1), 328-357, 2005 (Abstract) (pdf)

  • Ewers H., Smith A.E., Sbalzarini I.F., Lilie H., Koumoutsakos  P., Helenius A., Single particle-tracking of murine polyomavirus-like particles on live cells and artificial membranes, Proc. National Academy Sciences USA, 102(42):15110-15115, 2005 (Abstract) (pdf)
     
  • Zimmerli U., Gonnet  P.G., Walther  J.H., Koumoutsakos P., Curvature Induced L-Defects in Water Conduction in Carbon Nanotubes, Nano Letters, 5(6), 1017-1022, 2005 (Abstract) (pdf)
     
  • Sbalzarini I.F., Koumoutsakos P., Feature point tracking and trajectory analysis for video imaging in cell biology, J. Structural Biology, 151(2):182-195, 2005 (Abstract) (pdf)
     
  • Sbalzarini I.F., Mezzacasa A., Helenius  A., Koumoutsakos P., Effects of organelle shape on fluorescence recovery after photobleaching, Biophysical J., 89(3):1482-1492, 2005 (Abstract) (pdf)
     
  • Arcidiacono S., Walther  J.H., Poulikakos D., Passerone D., Koumoutsakos P., Solidification of gold nanoparticles in carbon nanotubes, Physical Review Letters, 94(10), Art. No. 105502, 2005 (Abstract) (pdf)
     
  • Kotsalis E.M., Demosthenous E., Walther J.H., Kassinos S.C., Koumoutsakos P., Wetting of doped carbon nanotubes by water droplets, Chemical Physics Letters, 412(4-6):250-254, 2005 (Abstract) (pdf)
     
  • Hou T., Koumoutsakos P., Special section on multiscale modeling in materials and life sciences, Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 4(1), 213-214, 2005 (Abstract) (pdf)
     
  • Poncet P., Koumoutsakos P., Optimization of vortex shedding in 3-D wakes using belt actuators, Int. J. Offshore and Polar Engn., 15(1), 2005 (Abstract) (pdf)
     
  • Poncet P., Cottet G.H., Koumoutsakos P., Control of three-dimensional wakes using evolution strategies, C. R. Acad. Sci. Paris, Mécanique, 333, 65-77, 2005 (Abstract) (pdf)
     
  • Bueche D., Schraudolph N., Koumoutsakos P., Accelerating evolutionary algorithms with Gaussian process fitness function models, IEEE Transactions on Systems, Man and Cybernetics, Part C, Special Issue on Knowledge Extraction and Incorporation in Evolutionary Computation, 35, 2, 183-194, 2005 (Abstract) (pdf)


2004

  • Hieber S.E., Walther J.H., Koumoutsakos P., Remeshed smoothed particle hydrodynamics simulation of the mechanical behavior of human organs, Technology and Health Care, 12(4), 305-314, 2004 (Abstract) (pdf)
     
  • Jaffe R.L., Gonnet P., Werder T., Walther J.H., Koumoutsakos P., Water-carbon interactions 2: calibration of potentials using contact angle data for different interaction models, Mol. Sim, 30(4), 205-216, 2004 (Abstract) (pdf)
     
  • Kern S., Mueller S.D., Hansen N., Bueche D., Ocenasek J., Koumoutsakos P., Learning probability distributions in continuous evolutionary algorithms - a comparative review, Natural Computing, 3(1), 77-112, 2004 (Abstract) (pdf)
     
  • Kotsalis E.M., Walther  J.H., Koumoutsakos P., Multiphase water flow inside carbon nanotubes, Int. J. Multiphase Flow, 30, 995-1010, 2004 (Abstract) (pdf)
     
  • Milano M., Schmidhueber J., Koumoutsakos P., Self-organizing nets for optimization, IEEE Transactions on Neural Networks, 15(3), 758-765, 2004 (Abstract) (pdf)
     
  • Mueller S.D., Mezic I., Walther J.H., Koumoutsakos P., Transverse momentum micromixer optimization with evolution strategies, Computers & Fluids, 33(4), 521-531, 2004 (Abstract) (pdf)
     
  • Walther J.H., Werder T., Jaffe R.L., Gonnet P., Bergdorf M., Zimmerli U., Koumoutsakos P., Water-carbon interactions III: the influence of surface and fluid impurities, Phys. Chem., 6, 1988-1995, 2004 (Abstract) (pdf)
     
  • Walther J.H., Jaffe R.L., Kotsalis E.M., Werder T., Halicioglu T., Koumoutsakos P., Hydrophobic hydration of C60 and carbon nanotubes in water, Carbon, 42(5-6), 1185-1194, 2004 (Abstract) (pdf)
     
  • Walther J.H., Werder T., Jaffe R.L., Koumoutsakos  P., Hydrodynamic properties of carbon nanotubes, Phys. Rev. E., 69, 062201, 2004 (Abstract) (pdf)
     
  • Zimmerli U., Parrinello M., Koumoutsakos P., Dispersion corrections to density functional theory for water aromatic interaction, J. Chem. Phys., 120(6), 2693-2699, 2004 (Abstract) (pdf)


2003

  • Hansen N., Mueller S.D., Koumoutsakos P., Reducing the time complexity of the derandomized evolution strategy with covariance matrix adaptation (CMA-ES), Evol. Comput., 11(1), 1-18, 2003 (Abstract) (pdf)
     
  • Werder T., Walther J.H., Jaffe R.L., Halicioglu T., Koumoutsakos P., On the water-carbon interaction for use in MD simulations of graphite and carbon nanotubes, J. Phys. Chem. B., 107, 1345-1352, 2003 (Abstract) (pdf)

 

2002

  • Bueche D., Stoll P., Dornberger R., Koumoutsakos P., Multi-objective evolutionary algorithm for the optimization of noisy combustion problems, IEEE Transactions on Systems, Man and Cybernetics, Part C, 32(4), 460-473, 2002 (Abstract) (pdf)
     
  • Chaniotis A.K., Poulikakos D., Koumoutsakos P., Remeshed smoothed particle hydrodynamics for the simulation of viscous and heat conducting flows, J. Comput. Phys., 182(1), 67-90, 2002 (Abstract) (pdf)
     
  • Gämperle R., Müller S.D., Koumoutsakos P., A parameter study for differential evolutionAdvances in intelligent systems, fuzzy systems, evolutionary computation, 10 (2002): 293-298 (pdf)
     
  • Milano M., Koumoutsakos P., Neural net modeling for near wall turbulent flows, J. Comput. Phys., 182(1), 1-26, 2002 (Abstract) (pdf)
     
  • Milano M., Koumoutsakos P., A clustering genetic algorithm for cylinder drag optimization, J. Comput. Phys., 175(1), 79-107, 2002 (Abstract) (pdf)
     
  • Mueller S.D., Marchetto J., Airaghi S., Koumoutsakos P., Optimization based on bacterial chemotaxis, IEEE T. Evolut. Comput., 6(1), 16-29, 2002 (Abstract) (pdf)

 

2001

  • Koumoutsakos P., Freund J., Parekh D., Evolution strategies for automatic optimization of jet mixing, AIAA Journal, 39(5), 967-969, 2001(Abstract) (pdf)
     
  • Mueller S.D., Walther J.H., Koumoutsakos P., Evolution strategies for film cooling optimization, AIAA Journal, 39(3), 537-539, 2001 (Abstract) (pdf)
     
  • Walther J.H., Koumoutsakos P., Molecular dynamics simulation of nanodroplet evaporation, J. Heat Transfer., 123 (4), 741 - 748, 2001 (Abstract) (pdf)
     
  • Walther J.H., Koumoutsakos P., Three-dimensional vortex methods for particle-laden flows with two-way coupling, J. Comput. Phys., 167, 39-71, 2001 (Abstract) (pdf)
     
  • Walther J.H., Halicioglu T., Jaffe L.R., Koumoutsakos P., Carbon nanotubes in water: structural characteristics and energetics, J. Phys. Chem. B., 105, 9980-9987, 2001 (Abstract) (pdf)
     
  • Werder T., Walther J.H., Jaffe R.L., Halicioglu T., Noca F., Koumoutsakos P., Molecular dynamics simulations of contact angles of water droplets in carbon nanotubes, Nano Lett., 1(12), 697-702, 2001 (Abstract) (pdf)
     
  • Zimmermann S., Koumoutsakos P., Kinzelbach W., Simulation of pollutant transport using a particle method, J. Comput. Phys., 173, 322-347, 2001 (Abstract) (pdf)


2000

  • Cottet G.H., Koumoutsakos P., Salihi M.L., Vortex methods with spatially varying cores, J. Comput. Phys., 162(1), 164-185, 2000 (Abstract) (pdf)
     
  • Noca F., Hoenk M., Hunt B., Koumoutsakos P., Walther J.H., Werder T., Bio-inspired acoustic sensors based on artificial stereocilia, J. Acoust. Soc. Am., 108(5), 2494, 2000 (Abstract) (pdf)
     
  • Walther J.H., Lee S.S., Koumoutsakos  P., Simulation of particle laden flows using particle methods, Phys. Fluids, 12(9), 2000 (Abstract) (pdf)


1999

  • Koumoutsakos P., Vorticity flux control in a turbulent channel flow, Phys. Fluids, 11(2), 248-250, 1999 (Abstract) (pdf)
     
  • Lundgren T.S., Koumoutsakos P., On the generation of vorticity at a free surface, J. Fluid Mech., 382, 351-366, 1999 (Abstract) (pdf)
     
  • Walther J.H., P. Koumoutsakos P., Particle methods for incompressible flow simulations, Speedup Journal, 12(2), 27-32, 1999 (Abstract) (pdf)
     
  • Walther J.H., Pan Y., Poulikakos D., Koumoutsakos P., Molecular dynamics simulations of evaporation and coalescence of nano size droplet, J. Heat Transfer (gallery award), 121(3), 1999


1997

  • Koumoutsakos P., Active control of vortex-wall interactions, Phys. Fluids, 9(12), 3808-3816, 1997 (Abstract) (pdf)
     
  • Koumoutsakos P., Inviscid axisymmetrization of an elliptical vortex, J. Comput. Phys., 138(2), 821-857, 1997 (Abstract) (pdf)

 

1996

  • Koumoutsakos P., Shiels D., Simulations of the viscous flow normal to an impulsively started and uniformly accelerated flat plate, J. Fluid Mech., 328, 177-227, 1996 (Abstract) (pdf)


1995

  • Koumoutsakos P., Leonard A., High Resolution Simulations of the Flow Around and Impulsively Started Cylinder Using Vortex Methods, J. Fluid Mech., 296, 1-38, 1995 (Abstract) (pdf)


1994

  • Koumoutsakos P., Leonard A., Pepin F., Boundary Conditions for Viscous Vortex Methods, J. Computational Physics, 113, 1, 52-61, 1994 (Abstract) (pdf)


1993

  • Leonard A., Koumoutsakos P., High Resolution Vortex Simulations of Bluff Body Flows, J. Wind Engineering and Industrial Aerodynamics, 46-7, 315-325, 1993 (Abstract) (pdf)
     
  • Koumoutsakos P., Leonard A., Improved Integral Method for Inviscid Boundary Condition Applications, AIAA J, 31, 2, 401-404, 1993,(Abstract), (pdf)

 

MONOGRAPH

  • CottetG.H., Koumoutsakos P., Vortex Methods: Theory and Practice, Cambridge University Press, 2000 (Abstract) (pdf)
     

EDITED VOLUMES
  • Koumoutsakos P., Mezic I., Control of Fluid Flow, Lecture Notes in Control and Information, Springer-Verlag, 2006 (pdf)
     
  • Attinger S., Koumoutsakos P., Multiscale Modeling and Simulation,  Lecture Notes in Computational Science and Engineering, Springer-Verlag, 2004 (pdf)
     
  • Gyr A., Koumoutsakos P., Burr U., Science and Art Symposium 2000: 3rd International Conference on Flow Interaction of Science and Art with Exhibition/Lectures on Interaction of Science & Art, 28.2-3.3 200 at the ETH Zurich, Springer Science+Business Media Dordrecht, 2000 (pdf)
 
BOOK CHAPTERS
  • Bergdorf M., Milde F., Koumoutsakos P., 2012. Particle Simulations of Growth: Application to TumorigenesisIn: Jackson T.L., editor. Modeling Tumor Vasculature. Springer New York. pages 261-303. (Abstract) (pdf)
     
  • Milde F., Bergdorf M., Koumoutsakos P., 2012. Particle Simulations of Growth: Application to Angiogenesis. In: Jackson T.L., editor. Modeling Tumor Vasculature. Springer New York. pages 305-334. (Abstract) (pdf)
     
  • Bergdorf M., Milde F., Koumoutsakos P., 2010. Continuum Models of Mesenchymal Cell Migration and Sprouting Angiogenesis. In: Deisboeck T.S., Stamatakos G.S., editors. Multiscale Cancer Modeling. CRC Press. pages 213-235. (pdf)