• Yang Y., Walther J.H., Yan Y., Wen C., CFD modeling of condensation process of water vapor in supersonic flowsApplied Thermal Engineering, 115, pp. 1357-1362 (2017) (doi), (pdf)
  • Spietz H.J., Hejlesen M.M., Walther J.H., Iterative Brinkman penalization for simulation of impulsively started flow past a sphere and a circular disc, J. Comput. Phys., 336, pp. 261-274 (2017) (doi), (pdf)
  • Pang K.M., Karvounis N., Walther J.H., Schramm J, Glarborg P., Mayer S., Modelling of temporal and spatial evolution of sulphur oxides and sulphuric acid uder large, two-stroke marine engine-like conditions using integrated CFD-chemical kineticsApplied Energy, 193, pp. 60-73 (2017) (doi), (pdf)
  • Rasthofer U., Gravemeier V., Recent Developments in Variational Multiscale Methods for Large-Eddy Simulation of Turbulent FlowArch. Computat. Methods Eng., 11831-017-9209-4, pp. 1-44 (2017) (doi), (pdf)
  • Kim D., Bowman C., Del Bonis-O'Donnell J.T., Matzavinos A., Stein D., Giant Acceleration of DNA Diffusion in an Array of Entropic BarriersPhys. Rev. Lett., 118, 048002, pp. 1-5 (2017) (doi), (pdf)
  • Andersen A., Bohr T., Schnipper T., Walther J.H., Wake structure and thrust generation of a flapping foil in two-dimensional flowJ. Fluid Mech., 812, R4, pp. 1-12 (2017) (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)



  • 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
  • Hemmingsen C.S., Ingvorsen K.M., Mayer S., Walther J.H., LES And URANS simulations of the swirling flow in a dynamic model of a uniflow-scavenged cylinder, International Journal of Heat and Fluid Flow, 62, pp. 213-223 (2016) (doi), (pdf)
  • Karna N.K., Oyarzua E., Walther J.H., Zambrano H.A., Effect of the meniscus contact angle during early regimes of spontaneous imbibition in nanochannelsPhys. Chem. Chem. Phys., 18, 31997, pp. 1-5 (2016) (doi), (pdf)
  • Wen C., Yang Y., Walther J.H., Pang K.M., Feng Y., Effect of delta wing on the particle flow in a novel gas supersonic separatorPowder Technology, 304, pp. 261-267 (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)
  • Hovad E., Spangenberg J., Larsen P., Walther J.H., Thorborg J., Hattel J.H., Simulating the DISAMATIC process using the discrete element method - a dynamical study of granular flowPowder Technology, Vol. 303, pp. 228-240 (2016) (doi), (pdf)
  • Hejlesen M.M., Walther J.H., A multiresolution method for solving the Poisson equation using high order regularizationJ. Comput. Phys., Vol. 326, pp. 188-196 (2016) (doi), (pdf)
  • Wermelinger F., Hejazialhosseini B., Hadjidoukas P. E., Rossinelli D., Koumoutsakos P., An Efficient Compressible Multicomponent Flow Solver for Heterogeneous CPU/GPU ArchitecturesProceedings of the Platform for Advanced Scientific Computing Conference PASC'16 (2016) (doi) (pdf)
  • Kulakova L., Angelikopoulos P., Hadjidoukas P. E., Papadimitriou C., Koumoutsakos P., Approximate Bayesian Computation for Granular and Molecular Dynamics SimulationsProceedings of the Platform for Advanced Scientific Computing Conference PASC'16 (2016) (doi) (pdf)
  • Wen C., Li A., Walther J.H., Yang Y., 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) (doi), (pdf)
  • Zayernouri M, Matzavinos A., Fractional Adams-Bashforth/Moulton methods: An application to the fractional Keller-Segel chemotaxis systemJ. Comput. Phys., Vol. 317, pp. 1-14 (2016) (doi), (pdf)
  • Mishra S., Schwab C., Sukys J., Multi-level Monte Carlo finite volume methods for uncertainty quantification of acoustic wave propagation in random heterogeneous layered mediumJ. Comput. Phys., Vol. 312, pp. 192-217 (2016) (doi), (pdf)
  • Pang, K.M., Karvounis N., Walther J.H., Schramm J., 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) (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)
  • Andersen B.O., Nielsen N.F., Walther J.H., Numerical and experimental study of pulse-jet cleaning in fabric filters, Powder Technology, Vol. 291, 284–298 (2016) (doi), (pdf)



  • Hadjidoukas P., Rossinelli D., Wermelinger F., Sukys J., Rasthofer U., Conti C., Hejazialhosseini B., Koumoutsakos P., High throughput simulations of two-phase flows on Blue Gene/Q, Parallel Computing: On the Road to Exascale, Proceedings of the International Conference on Parallel Computing ParCo '15 (2015) (doi) (pdf)
  • 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)
  • Rossinelli, D., Tang, Y.-H., Lykov, K., Alexeev, D., Bernaschi, M., Hadjidoukas, P., Bisson, M., Joubert, W., Conti, C., Karniadakis G., Fatica, M., Pivkin, I., Koumoutsakos, P., The In-Silico Lab-on-a-Chip: Petascale and High-Throughput Simulations of Microfluidics at Cell ResolutionACM 2015 Gordon Bell Award Finalist, Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC '15), 2015 (doi) (pdf)
  • 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)

  • Hejlesen M.M., Rasmussen J.T., Chatelain P., Walther J.H.High Order Poisson Solver for Unbounded Flows, Procedia IUTAM, 18 (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 molecules, Eur. Phys. J. Special Topics, 224, 2321-2330 (2015) (doi) (pdf)

  • Karathanasopoulos N., Angelikopoulos P. Optimal structural arrangements of multilayer helical assemblies, Int. J. Sol. Struct., (2015) (doi) (pdf)

  • Hejlesen M.M., Rasmussen J.T., Larsen A., Walther J.H., On estimating the aerodynamic admittance of bridge sections by a mesh-free vortex methodJ. Wind Eng. Ind. Aerodyn., 146 (2015) 117-127 (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)
  • Hadjidoukas P.E., Rossinelli D., Hejazialhosseini B., Koumoutsakos P., From 11 to 14.4 PFLOPs: Performance Optimization for Finite Volume Flow SolverProc. of the 3rd Intl. Conf. on Exascale Applications and Software (EASC 2015), 2015 (pdf)
  • Voglis C., Hadjidoukas, P.E., Parsopoulos K.E., Papageorgiou D.G., Lagaris I.E., Vrahatis M.N., p-MEMPSODE: Parallel and irregular memetic global optimization, Comput. Phys. Commun., 2015 (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)
  • Oyarzua E., Walther J.H.,  Mejia A., Zambrano H.A., Early regimes of water capillary flow in slitsilica nanochannelsPCCP, 2015, 17, 14731-14739 (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)
  • Fasil M., Plesner D., Walther J.H., Mijatovic N., Holbøll J., Numerical and Experimental Investigation of Heat Flow in Permanent Magnet Brushless DC Hub Motor. SAE Int. J. Alt. Power, 4(1), 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)



  • 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)
  • Zambrano H.A., Walther J.H., Jaffe R.L., Molecular dynamics simulations of water on a hydrophilic silica surface at high air pressures. J. Mol. Liq., 198:107–113, 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)
  • Ingvorsen K.M., Meyer K.E., Walther J.H., Mayer S., Turbulent swirling flow in a dynamic model of a uniflow-scavenged two-stroke engine, Exp. Fluids, 55:1748, 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)
  • Obeidat A., Schnipper t., Ingvorsen K.M., Haider S., Meyer K.E., Mayer S.., Walther J.H., Large eddy simulations of the influence of piston on the swirling flow in a model two-stroke diesel engine. International Journal of Numerical Methods for Heat & Fluid Flow Vol. 24 No. 2, 2014 325-341 (pdf)
  • Sigurdsson E., Ingvorsen K.M., Jensen M.V., Mayer S., Matlok S., Walther J.H., Numerical analysis of the scavenge flow and convective heat transfer in two-stroke marine diesel engines. Elsevier 123:37–46, 2014 (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)
  • Felter C.L., Walther J.H., Henriksen C., Moving least squares simulation of free surface flowsElsevier Computers & Fluids 91:47–56, 2014  (pdf)
  • Hadjidoukas P.E., Voglis C., Dimakopoulos V.V., Lagaris I.E., Papageorgiou D.G., Supporting adaptiave and irregular parallelism for non-linear numerical optimizationAppl. Math. Comput., 231:544–599, 2014. (pdf)
  • Hadjidoukas P.E, Angelikopoulos P., Voglis C., Papageorgiou D.G., Lagaris I.E., NDL-v2.0: A New Version of the Numerical Diff erentiation Library for Parallel Architectures, Comput. Phys. Commun., 185:2217-2219, 2014. (pdf) (report)



  • Rossinelli D., Hejazialhosseini B. , Hadjidoukas P., Bekas C., Curioni A., Bertsch A., Futral S., Schmidt S.J., Adams N.A., Koumoutsakos P., 11 PFLOP/s simulations of cloud cavitation collapseACM 2013 Gordon Bell Award WinnerProceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC '13), 2013 (doi) (pdf)
  • 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)
  • Papadimitriou C., Angelikopoulos P., Papadioti D.-C., Efficient techniques for Bayesian inverse modeling of large-order computational models. ICOSSAR 2013: 11th International Conference on Structural Safety & Reliability, 2013. (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)
  • Hejlesen M.M., Rasmussen J.T., Chatelain P., Walther J.H., A high order solver for the unbounded Poisson equationJournal of Computational Physics, 252, 458-467,  2013 (pdf)
  • 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)
  • Ingvorsen K.M., Meyer K.E., Walther J.H., Mayer S., Turbulent swirling flow in a model of a uniflow-scavenged two-stroke engine, Exp. Fluids, 54:1494, 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)
  • S. Haider, T. Schnipper, A. Obeidat, K.E.Meyer, V.L.Okulov, S.Mayer, 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 enginesJ Mar Sci Technol, 18:133–143, 2013. (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)
  • Jensen M.V., Walther J.H., Numerical Analysis of Jet Impingement Heat Transfer at High Jet Reynolds Number and Large Temperature Difference, Heat Transfer Engineering, 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)
  • Voglis C., Hadjidoukas P.E, Parsopoulos K.E., Papageorgiou D.G., Lagaris I.E., Adaptive memetic particle swarm optimization with variable local search pool size, GECCO '13: 15th Annual Conference on Genetic and Evolutionary Computation,  2013. (pdf)
  • Voglis C., Hadjidoukas P.E, Papageorgiou D.G., Lagaris I.E., A parallel hybrid optimization algorithm for fitting interatomic potentials, Appl. Soft. Comput., 13(12): 4481-4492, 2013. (pdf)



  • Hejazialhosseini B., Rossinelli D., Conti C., Koumoutsakos P., High throughput software for direct numerical simulations of compressible two-phase flows. In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC '12). IEEE Computer Society Press, Los Alamitos, CA, USA, Article 16, 2012. (Abstract) (pdf)
  • 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)

  • Rossinelli D., Chatagny L., Koumoutsakos P., Evolutionary optimization of scalar transport in cylinder arrays on multiGPU/multicore architecturesProc. EuroGen, pages 773–782, Capua, Italy, September 14–16 2011, (Abstract) (pdf)
  • Riisgård H.U., Jørgensen B.H., Lundgreen K., Storti F., Walther J.H., Meyer K.E., Larsen P.S., The exhalant jet of mussels, Mytilus edulis, Marine Ecology Progress Series, 437:147-164, 2011. (Abstract) (pdf)
  • Rasmussen J.T., Cottet G.-H., Walther J.H., A multiresolution remeshed vortex-in-cell algorithm using patches, Journal of Computational Physics, 230(17):6742–6755, 2011 (Abstract) (pdf)
  • 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 numbers,  Journal 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 processes, Journal 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 systems, Concurrency 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

  • 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-mantle, Physics 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)
  • Rasmussen J.T., Hejlesen M.M., Larsen A., Walther J.H., Discrete Vortex Method simulations of the aerodynamic admitance in bridge aerodynamics, J. of. Wind Eng. and Industrial Aerodynamics, 98(12), 754-766, 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)


  • 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)
  • Zambrano H.A., Walther J.H., Jaffe R.L.,Thermally driven molecular linear motors: A molecular dynamics study, Journal of Chemical Physics, 131, 241104, 2009 (Abstract) (pdf)
  • 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 delays, Journal of Computational Physics, 228, 5908-5916, 2009 (Abstract) (pdf)
  • Gebäck T., Koumoutsakos P., Edge detection in microscopy images using curvelets, BMC Bioinformatics, 10,75, 2009 (Abstract) (pdf)
  • Mjolsness E., Orendorff D., Chatelain P., Koumoutsakos P., An exact accelerated stochastic simulation algorithm, Journal 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)
  • Walther J.H., Sbalzarini I.F., Large-scale parallel discrete element simulations of granular flow, International Journal for Computer-Aided Engineering and Software, 26, 6, 688-697, 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)

  • 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 tissue,  J. Computational Physics, 227, 9195-9215, 2008 (Abstract) (pdf)
  • Milde F., Bergdorf M., Koumoutsakos P., A Hybrid Model for 3D Simulations of Sprouting Angiogenesis,  Biophysical 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)


  • 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)
  • Morgenthal G., Walther J.H., An Immersed interface method for the Vortex-In-Cell algorithm, Computers & Structures, 85, 11-14, 712-726, 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)


  • 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 Surfaces. Biophysical 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 Nanotubes. Nano Letters, 2006 (Abstract) (pdf)
  • Fukagata K., Kasagi N., Koumoutsakos P., A theoretical prediction of friction drag reduction in turbulent flow by superhydrophobic surfaces. Physics of Fluids, 18:051703-1:051703-4, 2006 (Abstract) (pdf)
  • Hansen N., An analysis of mutative sigma-self-adaptation on linear fitness functions. Evolutionary Computation, 14, 255-275, 2006 (Abstract) (pdf)
  • Zimmermann S., Bauer P., Held R., Kinzelbach W., and Walther J.H., Salt transport on islands in the Okavango delta: Numerical investigation. Advances Water Research, 29(1):11-29, 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 Strategies. Lecture Notes in Computer Science, 4193, 939-948, Springer Berlin, 2006 (Abstract) (pdf)


  • P. Koumoutsakos, Multiscale flow simulations using particles, Annual Review Fluid Mechanics, 37, 457-87, 2005 (Abstract) (pdf)
  • S. E. Hieber and P. Koumoutsakos. A Lagrangian particle level set method. J. Computational Physics, 210:342-367, 2005 (Abstract) (pdf)
  • T. Werder, J. H. Walther, P. Koumoutsakos, Hybrid atomistic-continuum method for the simulation of dense fluid flow, J. Computational Physics, 205, 373 - 390, 2005 (Abstract) (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, 2005 (Abstract) (pdf)
  • H. Ewers, A. E. Smith, I. F. Sbalzarini, H. Lilie, P. Koumoutsakos, and A. Helenius. 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)
  • U. Zimmerli, P. G. Gonnet, J. H. Walther, P. Koumoutsakos, Curvature Induced L-Defects in Water Conduction in Carbon Nanotubes, Nano Letters, 5(6), 1017-1022, 2005 (Abstract) (pdf)
  • I. F. Sbalzarini and P. Koumoutsakos. Feature point tracking and trajectory analysis for video imaging in cell biology. J. Structural Biology, 151(2):182-195, 2005 (Abstract) (pdf)
  • I. F. Sbalzarini, A. Mezzacasa, A. Helenius, and P. Koumoutsakos. Effects of organelle shape on fluorescence recovery after photobleaching. Biophysical J., 89(3):1482-1492, 2005 (Abstract) (pdf)
  • S. Arcidiacono, J. H. Walther, D. Poulikakos, D. Passerone, P. Koumoutsakos, Solidification of gold nanoparticles in carbon nanotubes, Physical Review Letters, 94(10), Art. No. 105502, 2005 (Abstract) (pdf)
  • 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, 412(4-6):250-254, 2005 (Abstract) (pdf)
  • T. 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 (Abstract) (pdf)
  • C. Luedeke, S. B. Frei, I. F. Sbalzarini, H. Schwarz, A. Spang, Y. Barral, Septin-dependent compartmentalization of the endoplasmic reticulum during yeast polarized growth, J. Cell Biology, 169(6), 897-908, 2005 (Abstract) (pdf)
  • P. Poncet, P. Koumoutsakos, Optimization of vortex shedding in 3-D wakes using belt actuators, Int. J. Offshore and Polar Engn., 15(1), 2005 (Abstract) (pdf)
  • P. Poncet, G-H. Cottet, P. Koumoutsakos, Control of three-dimensional wakes using evolution strategies, C. R. Acad. Sci. Paris, Mécanique, 333, 65-77, 2005 (Abstract) (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, 35, 2, 183-194, 2005 (Abstract) (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 (Abstract) (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 different interaction models, Mol. Sim, 30(4), 205-216, 2004 (Abstract) (pdf)
  • S. Kern, S. D. Mueller, N. Hansen, D. Bueche, J. Ocenasek, P. Koumoutsakos, Learning probability distributions in continuous evolutionary algorithms - a comparative review, Natural Computing, 3(1), 77-112, 2004 (Abstract) (pdf)
  • E. M. Kotsalis, J. H. Walther, P. Koumoutsakos, Multiphase water flow inside carbon nanotubes, Int. J. Multiphase Flow, 30, 995-1010, 2004 (Abstract) (pdf)
  • P. Gonnet, K. Rudd, F. Lisacek, Fine-tuning the prediction of sequences cleaved by signal peptidase II: a curated set of proven and predicted LipoProteins of E. coli K-12, PROTEOMICS, 4(6), 1597-1613, 2004 (Abstract) (pdf)
  • F. Lisacek, C. Chichester, P. Gonnet, O. Jaillet, S. Kappus, F. Nikitin, P. Roland, G. Rossier, L. Truong, R. Appel, Shaping biological knowledge: applications in proteomics, Comparative and Functional Genomics, 5(2), 190-195, 2004 (Abstract) (pdf)
  • M. Milano, J. Schmidhueber, P. Koumoutsakos, Self-organizing nets for optimization, IEEE Transactions on Neural Networks, 15(3), 758-765, 2004 (Abstract) (pdf)
  • S. D. Mueller, I. Mezic, J. H. Walther, P. Koumoutsakos, Transverse momentum micromixer optimization with evolution strategies, Computers & Fluids, 33(4), 521-531, 2004 (Abstract) (pdf)
  • 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., 6, 1988-1995, 2004 (Abstract) (pdf)
  • J. H. Walther, R. L. Jaffe, E. M. Kotsalis, T. Werder, T. Halicioglu, P. Koumoutsakos, Hydrophobic hydration of C60 and carbon nanotubes in water, Carbon, 42(5-6), 1185-1194, 2004 (Abstract) (pdf)
  • J. H. Walther, T. Werder, J. Jaffe, P. Koumoutsakos, Hydrodynamic properties of carbon nanotubes, Phys. Rev. E., 69, 062201, 2004 (Abstract) (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 (Abstract) (pdf)


  • M. Bergdorf, Ch. Peter, Ph. H. Hunenberger, Influence of cut-off truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions: A continuum electrostatics study, J. Chem. Phys. 119, 9129-9144, 2003 (Abstract) (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 (Abstract) (pdf)
  • J. H. Walther, An influence matrix particle-particle particle-mesh algorithm with exact particle-particle correction, J. Comput. Phys., 184, 670-678, 2003 (Abstract) (pdf)
  • T. Werder, J. H. Walther, R. L. Jaffe, T. Halicioglu, P. Koumoutsakos, 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)
  • F. Gers, N. N. Schraudolph, J. Schmidhuber, Learning precise timing with LSTM recurrent networks, J. Mach. Learn. Res., 3, 115-143, 2003 (Abstract) (pdf)


  • S. Attinger, Parametrizing macro-dispersivity: first pick a length scale, Hydrol. Proc., 16, 1685-1687, 2002 (Abstract) (pdf)
  • S. Attinger, J. Eberhard, N. Neuss, Filtering procedures for flow in heterogeneous porous media: numerical results, Comput. Visual Sci., 2(5), 67-72, 2002 (pdf) (Abstract)
  • D. Bueche, P. Stoll, R. Dornberger, P. Koumoutsakos, 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)
  • A. K. Chaniotis, D. Poulikakos, P. Koumoutsakos, Remeshed smoothed particle hydrodynamics for the simulation of viscous and heat conducting flows, J. Comput. Phys., 182(1), 67-90, 2002 (Abstract) (pdf)
  • M. Dentz, H. Kinzelbach, S. Attinger, W. Kinzelbach, Temporal behaviour of a solute cloud in a heterogeneous porous medium - 3. Numerical simulations, Water Resour. Res., 38(7), 23-1-23-13, 2002 (Abstract) (pdf)
  • R. Gämperle, S.D. Müller, P. Koumoutsakos A parameter study for differential evolution, Advances in intelligent systems, fuzzy systems, evolutionary computation, 10 (2002): 293-298 (pdf)
  • P. Gonnet, F. Lisacek. Probabilistic alignment of motifs with sequences, Bioinformatics 18(8), 1091-1101, 2002 (Abstract) (pdf)
  • R. Herbrich, T. Graepel, A PAC-Bayesian margin bound for linear classifiers, IEEE T. Inform. Theory, 3140-3150, 2002 (Abstract) (pdf)
  • I. Lunati, S. Attinger, W. Kinzelbach, Macrodispersivity for transport in arbitrary nonuniform flow fields: asymptotic and preasymptotic results, Water Resour. Res., 38(10), 5-1-5-11, 2002 (Abstract) (pdf)
  • M. Milano, P. Koumoutsakos, Neural net modeling for near wall turbulent flows, J. Comput. Phys., 182(1), 1-26, 2002 (Abstract) (pdf)
  • M. Milano, P. Koumoutsakos, A clustering genetic algorithm for cylinder drag optimization, J. Comput. Phys., 175(1), 79-107, 2002 (Abstract) (pdf)
  • S. D. Mueller, J. Marchetto, S. Airaghi, P. Koumoutsakos, Optimization based on bacterial chemotaxis, IEEE T. Evolut. Comput., 6(1), 16-29, 2002 (Abstract) (pdf)
  • P. Yi, D. Poulikakos, J. Walther, G. Yadigaroglu, Molecular Dynamics simulation of vaporization on an ultra-thin liquid argon layer on a surface, Int. J. Heat Mass Transfer, 45, 2087-2100, 2002 (Abstract) (pdf)
  • N. N. Schraudolph, Fast curvature matrix-vector products for second-order gradient descent, Neural Computation, 14(7), 1723-1738, 2002 (Abstract) (pdf)
  • F. Stauffer, S. Attinger, S. Zimmermann, W. Kinzelbach, Uncertainty estimation of well catchments in heterogeneous aquifers, Water. Resour. Res., 38(11), 20-1-20-8, 2002 (Abstract) (pdf)
  • J. H. Walther, G. Morgenthal, An immersed interface method for the vortex-in-cell algorithm, J. Turbulence, 3, 039, 2002 (Abstract) (pdf)


  • N. Hansen, A. Ostermeier, Completely derandomized self-adaptation in evolution strategies, Evol. Comput., 9(2), 159-195, 2001 (Abstract) (pdf)
  • P. Koumoutsakos, J. Freund, D. Parekh, Evolution strategies for automatic optimization of jet mixing, AIAA Journal, 39(5), 967-969, 2001(Abstract) (pdf)
  • S. D. Mueller, J. H. Walther, P. Koumoutsakos, Evolution strategies for film cooling optimization, AIAA Journal, 39(3), 537-539, 2001 (Abstract) (pdf)
  • J. H. Walther, P. Koumoutsakos, Molecular dynamics simulation of nanodroplet evaporation, J. Heat Transfer., 123 (4), 741 - 748, 2001 (Abstract) (pdf)
  • J. H. Walther, P. Koumoutsakos, Three-dimensional vortex methods for particle-laden flows with two-way coupling, J. Comput. Phys., 167, 39-71, 2001 (Abstract) (pdf)
  • J. H. Walther, T. Halicioglu, R. Jaffe and P. Koumoutsakos, Carbon nanotubes in water: structural characteristics and energetics, J. Phys. Chem. B., 105, 9980-9987, 2001 (Abstract) (pdf)
  • T. Werder, K. Gerdes, D. Schoetzau, C. Schwab, hp-discontinuous galerkin time stepping for parabolic problems, Computer Methods in Applied Mathematics and Engineering, 190(49-50), 6685- 708, 2001 (Abstract) (pdf)
  • T. Werder, J. H. Walther, R. L. Jaffe, T. Halicioglu, F. Noca, P. Koumoutsakos, Molecular dynamics simulations of contact angles of water droplets in carbon nanotubes, Nano Lett., 1(12), 697-702, 2001 (Abstract) (pdf)
  • S. Zimmermann, P. Koumoutsakos, W. Kinzelbach, Simulation of pollutant transport using a particle method, J. Comput. Phys., 173, 322-347, 2001 (Abstract) (pdf)


  • D. Bueche, N. Sukumar, B. Moran, Dispersive properties of the natural element method, Comput. Mech., 25(2/3), 207-139, 2000 (Abstract) (pdf)
  • G.-H. Cottet, P. Koumoutsakos, M. L. Salihi, Vortex methods with spatially varying cores, J. Comput. Phys., 162(1), 164-185, 2000 (Abstract) (pdf)
  • L. Glielmo, M. Milano, S. Santini, A machine learning approach to modeling and identification of automotive three-way catalytic converters, IEEE Trans. on Mechatronics, 5(2), 132-141, 2000 (Abstract) (pdf)
  • F. Noca, M. Hoenk, B. Hunt, P. Koumoutsakos, J.H. Walther, T. Werder, Bio-inspired acoustic sensors based on artificial stereocilia, J. Acoust. Soc. Am., 108(5), 2494, 2000 (Abstract) (pdf)
  • J. H. Walther, S.-S. Lee, P. Koumoutsakos, Simulation of particle laden flows using particle methods, Phys. Fluids, 12(9), 2000 (Abstract) (pdf)


  • P. Koumoutsakos, Vorticity flux control in a turbulent channel flow, Phys. Fluids, 11(2), 248-250, 1999 (Abstract) (pdf)
  • T. S. Lundgren, P. Koumoutsakos, On the generation of vorticity at a free surface, J. Fluid Mech., 382, 351-366, 1999 (Abstract) (pdf)
  • P. Marino, M. Milano, F. Vasca, Linear quadratic state feedback and robust neural network estimator for field oriented controlled induction motors, IEEE Trans. on Industrial Electronics, 46(1), 150-161, 1999 (Abstract) (pdf)
  • J. H. Walther, P. Koumoutsakos, Particle methods for incompressible flow simulations, Speedup Journal, 12(2), 27-32, 1999 (Abstract) (pdf)
  • J. H. Walther, Y. Pan, D. Poulikakos, P. Koumoutsakos, Molecular dynamics simulations of evaporation and coalescence of nano size droplet, J. Heat Transfer (gallery award), 121(3), 1999


  • A. Larsen, J. H. Walther, Discrete vortex simulation of flow around five generic bridge deck sections, J. Wind Eng. Ind. Aerodyn., 77-78, 591-602, 1998 (Abstract) (pdf)


  • P. Koumoutsakos, Active control of vortex-wall interactions, Phys. Fluids, 9(12), 3808-3816, 1997 (Abstract) (pdf)
  • P. Koumoutsakos, Inviscid axisymmetrization of an elliptical vortex, J. Comput. Phys., 138(2), 821-857, 1997 (Abstract) (pdf)
  • A. Larsen, J.H. Walther, Aeroelastic analysis of bridge sections based on discrete vortex simulations, J. Wind Eng. Ind. Aerodyn., 67-69, 253-265, 1997 (Abstract) (pdf)
  • M. Milano, F. Barone, L. Milano, Detection of gravitational waves from coalescing binaries in the time domain, Class. Quantum Grav., 14, 1531-1536, 1997 (Abstract) (pdf)
  • M. Milano, F. Barone, L. Milano, Time domain amplitude and frequency detection of gravitational waves from coalescing binaries, Phys. Rev. D, 55(8), 4537-4554, 1997 (Abstract) (pdf)
  • J. H. Walther, A. Larsen, Discrete vortex method for application to bluff body aerodynamics, J. Wind Eng. Ind. Aerodyn., 67-68, 183-193, 1997 (Abstract) (pdf)


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


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


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


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



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

  • P. Koumoutsakos and I. Mezic, Control of Fluid Flow, Lecture Notes in Control and Information, Springer-Verlag, 2006 (pdf)
  • S. Attinger and P. Koumoutsakos, Multiscale Modeling and Simulation,  Lecture Notes in Computational Science and Engineering, Springer-Verlag, 2004 (pdf)
  • 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, 28.2-3.3 200 at the ETH Zurich, Springer Science+Business Media Dordrecht, 2000 (pdf)

  • 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)