Refereed Journals
2005 
  • S. Arcidiacono, J. H. Walther, D. Poulikakos, D. Passerone, P. Koumoutsakos, Solidification of gold nanoparticles in carbon nanotubes, Phys. Rev. Lett., 94(10), Art. No. 105502, 2005 (pdf)
  • A. Auger, Convergence results for (1, lambda)-SA-ES using the theory of phi-irreducible markov chains, Theoretical Computer Science, 334(1-3), 35 – 69, 2005 (pdf)
  • K. K. Baldridge, J. P. Greenberg, W. Sudholt, S. Mock, I. Altintas, C. Amoreira, Y. Potier, A. Birnbaum, K. Bhatia, M. Taufer, The computational chemistry prototyping environment, Proceedings of the IEEE, Special Issue on Grid Computing, 93(3), 2005 (pdf)
  • M. Bergdorf, G.-H. Cottet, P. Koumoutsakos, Multilevel adaptive particle methods for convection-diffusion equations, Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 4(1), 328-357 (pdf)
  • Th. Hou, P. Koumoutsakos, Special section on multiscale modeling in materials and life sciences, Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 4(1), 213-214, 2005
  • P. Koumoutsakos, Multiscale flow simulations using particles, Annu. Rev. Fluid Mech., 37, 457-87, 2005 (pdf)
  • T. Pfeiffer, S. Schuster, Game-theoretical approaches to studying the evolution of biochemical systems, TiBS, 30(1), 2005 (pdf)
  • T. Pfeiffer, C. Rutte, T. Killingback, M. Taborsky, S. Bonhoeffer, Evolution of cooperation by generalized reciprocity, proceedings B, Proc. R. Soc. B., 2005 (pdf)
  • P. Poncet, G-H. Cottet, P. Koumoutsakos, Control of three-dimensional wakes using evolution strategies, C. R.C. R. Acad. Sci. Paris, Mécanique, 333, 65 – 77, 2005 (pdf)
  • W. Sudholt, K. K. Baldridge, D. Abramson, C. Enticott, S. Garic, C. Kondric, D. Nguyen, Application of grid computing to parameter sweeps and optimizations in molecular modeling, Future Generation Computer Systems, 21, 27 – 35, 2005 (pdf)
  • T. Werder, J. H. Walther, P. Koumoutsakos, Hybrid atomistic-continuum method for the simulation of dense fluid flow, J. Comput. Phys., 205, 373 – 390, 2005 (pdf)
  • S. Wessel, S. Trebst, M. Troyer, Renormalization approach to simulations of quantum effects in nanoscale magnetic systems, Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 4(1), 237-249, 2005 (pdf)
2004
  • A. Abdulle, C. Schwab, Heterogeneous multi-scale FEM for diffusion problem on rough surfaces, SIAM MMS, 3(1), 195 – 220, 2004 (pdf)
  • S. Alder, S. Trebst, A. K. Hartmann, M. Troyer, Dynamics of the Wang-Landau algorithm and complexity of rare events for the three-dimensional bimodal Ising spin glass, J. Stat. Mech., P07008, 2004 (pdf)
  • F. Alet, E. Sorensen, The generic, incommensurate transition in the two-dimensional Boson Hubbard model, Phys. Rev. B 70 (2), 024513, 2004 (pdf)
  • D. Aktah, D. Passerone, M. Parrinello, Insights into the electronic dynamics in chemical reactions, J. Phys. Chem. A, 108 (5), 848 -854, 2004
  • S. Attinger, M. Dentz, W. Kinzelbach, Exact transverse macro dispersion coefficients for transport in heterogeneous porous media, Stochastic Environmental Research and Risk Assessment, 18 (1), 9-15, 2004 (pdf)
  • D. Bueche, N. Schraudolph, P. Koumoutsakos, 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, 32 (4), 2004 (pdf)
  • H.-D. Chen, S. Capponi, F. Alet, S.-Ch. Zhang, Global phase diagram of the high Tc Cuprates, Phys. Rev. B (2), 70, 024516, 2004 (pdf)
  • O. Chinellato, E. Acherman, O. Broeker, Including covariances in calibration to obtain better measurement uncertainty estimates, Siam Journal on Scientific Computing (Special Issue on Uncertainty Quantification), 26 (2), 523-536, 2004 (pdf)
  • J. Das, A.V. Mahajan, J. Bobroff, H. Alloul, F. Alet, E.S. Sorensen, Comparison of S=0 and S=1/2 impurities in Haldane chain compound, Y2BaNiO5 Phys. Rev. B, 69 (14), 144404, 2004 (pdf)
  • P. Dayal, S. Trebst, S. Wessel, D. Würtz, M. Troyer, S. Sabhapandit, S. N. Coppersmith, Performance limitations of flat histogram methods, Phys. Rev. Lett. 92, 097201, 2004 (pdf)
  • S. E. Hieber, J. H. Walther, P. Koumoutsakos, Remeshed smoothed particle hydrodynamics simulation of the mechanical behavior of human organs, Technology and Health Care, 12 (4), 305-314, 2004 (pdf)
  • P. Hitchcock, E. Sorensen, F. Alet, Dual geometric worm algorithm for two-dimensional classical lattice models, Phys. Rev. E 70 (1), 016702, 2004 (pdf)
  • R. L. Jaffe, P. Gonnet, T. Werder, J. H. Walther, P. Koumoutsakos, Water-carbon interactions 2: calibration of potentials using contact angle data for interaction models, Mol. Sim., 30 (4), 205-216, 2004 (pdf)
  • S. Kern, N. Hansen, S. Müller, D. Büche, J. Ocenasek, P. Koumoutsakos, Learning probability distributions in continuous evolutionary algorithms: A comparative review, Natural Computing 3(1), 77-112, 2004 (pdf)
  • E. M. Kotsalis, J. H. Walther, P. Koumoutsakos, Multiphase water flow inside carbon nanotubes, Int. J. Multiphase Flow, 30, 995-1010, 2004 (pdf)
  • T. Laino, D. Passerone, Pseudo-Dynamics and Band Optimizations: shedding light into Conical Intersection Seams, Chem. Phys. Lett., 369, 1, 2004
  • F. Marchal, K. Nagel, Modeling location choice of secondary activities with a social network of cooperative agents, Trans. Res. Rec., 2004 (pdf)
  • F. Marchal, A trip generation method for time-dependent large-scale simulations of transport and land-use, Networks and Spatial Economics, Kluwer Academic Publishers, 2004 (pdf)
  • F. Marchal, J. Hackney, K.W. Axhausen, Efficient map-matching of large GPS data sets – Tests on a speed monitoring experiment in Zurich, Trans. Res. Rec. 2004
  • M. Milano, P. Koumoutsakos, J. Schmidhueber, Optimization using self-organising maps, IEEE Trans. Neural Networks, 15 (3), 758-765, 2004
  • S. D. Mueller, I. Mezic, J. H. Walther, P. Koumoutsakos, Transverse momentum micromixer optimization with evolution strategies, Computers & Fluids, 33 (4), 521-531 2004
  • J. Ocenasek, S. Kern, N. Hansen, P. Koumoutsakos, A mixed Bayesian Optimization Algorithm with variance adaptation, Lect. Notes Comput. Sc., 3242, 352, 2004 (pdf)
  • T. Pfeiffer, S. Bonhoeffer, Evolution of crossfeeding in microbial populations, Am. Nat. 163, E126-35, 2004 (pdf)
  • G. Schmid, M. Troyer, Melting of bosonic stripes, Phys. Rev. Lett., 93 (6), 067003, 2004 (pdf)
  • W. Sudholt, K. K. Baldridge, D. Abramson, C. Enticott, S. Garic, Parameter Scan of an effective group difference pseudopotential using grid computing, New Generation Computing, 22(2): 137-146, 2004 (pdf)
  • S. Trebst, D. A. Huse, M. Troyer, Optimizing the ensemble for equilibration in broad-histogram Monte Carlo simulations, Phys. Rev. E 70, 046701, 2004 (pdf)
  • M. Troyer, F. Alet, S. Wessel, Histogram methods for quantum systems: from reweighting to Wang-Landau sampling, Braz. J. Phys. 34 (2A), 377-383, 2004 (pdf)
  • J. H. Walther, T. Werder, R. L. Jaffe, P. Koumoutsakos, Hydrodynamic properties of carbon nanotubes, Phys. Rev. E, 69, 062201, 2004 (pdf)
  • J. H. Walther, T. Werder, R. L. Jaffe, P. Gonnet, M. Bergdorf, U. Zimmerli, P. Koumoutsakos, Water-carbon interactions 3: the influence of surface and fluid impurities, Phys. Chem. Chem. Phys., 6, 1988-1995, 2004 (pdf)
  • J. H. Walther, R. L. Jaffe, E. Kotsalis, T. Werder, T. Halicioglu, P. Koumoutsakos, Hydrophobic hydration of C60 and carbon nanotubes in water, Carbon, 42 (5-6), 1185-1194, 2004 (pdf)
  • A. Wille, P. Zimmermann, E. Vranova, A. Fürholz, O. Laule, S. Bleuler, L. Hennig, A. Prelic, P. von Rohr, L. Thiele, E. Zitzler, W. Gruissem, P. Bühlmann, Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana, Genome Biol., 5 (11), R92, 2004 (pdf)
  • U. Zimmerli, M. Parrinello, P. Koumoutsakos, Dispersion corrections to density functional theory for water aromatic interaction, J. Chem. Phys., 120(6), 2693-2699, 2004 (pdf) 
2003
  • A. Abdulle, W. E, Finite difference HMM for homogenization problem, J. Comput. Phys., 191 (1), 18-39, 2003
  • A. Abdulle, G. Wanner, 200 let metody nejmensich ctvercu Pokroky matematiky, fyziky a astronomie, rocnik 48, c.2, 2003. (200 years of least squares method. In Czech)
  • F. Alet, E. S. Sorensen, Directed geometrical worm algorithm applied to the quantum rotor model, Phys. Rev. E 68 (2), 026702, 2003 (pdf)
  • F. Alet, E. S. Sorensen, Cluster Monte Carlo algorithm for the quantum rotor model, Phys. Rev. E 67 (1), 015701
  • S. Attinger, J. D. Micha, W. Kinzelbach, Multi-Scale Modeling of Nonlinearly Adsorbing Solute Transport, Multiscale Modelling and Simulation, 1 (3), 408-431, 2003 (pdf)
  • O. A. Cirpka, S. Attinger, Effective dispersion in heterogeneous media under random transient flow conditions, Water Res. Res., 39(9), 1257, 2003 (pdf)
  • N. Hansen, S. D. Mueller, P. Koumoutsakos, Reducing the time complexity of the derandomized evolution strategy with covariance matrix adaptation (CMA-ES), Evol. Comput. 11(1):1-18, 2003 (pdf)
  • K. Harada, N. Kawashima, M. Troyer, Néel and Spin-Peierls ground states of two-dimensional SU(N) quantum antiferromagnets, Phys. Rev. Lett. 90 (11), 117203, 2003 (pdf)
  • M. Pelikan, D. E. Goldberg, Hierarchical BOA Solves Ising Spin Glasses and MAXSAT, Lect. Notes Comput. Sci., 2724, 1271-1282, 2003
  • T. Pfeiffer, S. Bonhoeffer, An evolutionary scenario for the transition to undifferentiated multicellularity, PNAS 2003, 100(3), 1095-1098
  • M. Troyer, S. Wessel, F. Alet, Flat histogram methods for quantum systems: algorithms to overcome tunneling problems and calculate the free energy Phys. Rev. Lett. 90 (12), 120201, 2003 (pdf)
  • A. Wille, J. Hoh, J. Ott, Sum statistics for the joint detection of multiple disease loci in case-control association studies with SNP markers, Genet. Epidemiol, 25(4), 350-9, 2003

Refereed Conferences

  • S. Mostaghim and J. Teich. A new approach on many objective diversity measure. In Dagstuhl Proceedings number 04461, Dagstuhl, Germany, 2005.
  • A. Auger, M. Schoenauer, O. Teytaud, Local and Global Order 3/2 Convergence of a Surrogate Evolutionary Algorithm, Proceedings of GECCO 2005, Genetic and Evolutionary Computation Conference (pdf)
  • A. Auger, N. Hansen, A Restart CMA Evolution Strategy With Increasing Population Size, Proceedings of the IEEE Congress on Evolutionary Computation, CEC 2005 (erratum) (pdf)
  • A. Auger, N. Hansen, Performance Evaluation of an Advanced Local Search Evolutionary Algorithm, Proceedings of the IEEE Congress on Evolutionary Computation, CEC, 2005 (erratum) (pdf)
  • S. Trebst, The ALPS Project: Open Source Software for Strongly Correlated Systems, Einstein Spring Meeting of the German Physical Society, Berlin, Germany, 2005
  • S. Trebst, Adiabatic construction of d-wave RVB states of ultracold fermionic atoms in optical lattices, APS March Meeting, Los Angeles, CA, 2005
  • S. Trebst, Optimal ensemble Monte Carlo simulations of dense Lennard-Jones fluids, Conference on Computational Physics 2005, Los Angeles, CA, 2005