Strong scaling of general-purpose molecular dynamics simulations on GPUs

Glaser, Jens; Nguyen, Trung Dac; Anderson, Joshua A.; Lui, Pak; Spiga, Filippo; Millan, Jaime A.; Morse, David C.; Glotzer, Sharon C.

doi:10.1016/j.cpc.2015.02.028

Title: Strong scaling of general-purpose molecular dynamics simulations on GPUs

Journal Article · Wed Mar 11 00:00:00 EDT 2015 · Computer Physics Communications

DOI:https://doi.org/10.1016/j.cpc.2015.02.028· OSTI ID:1565293

Glaser, Jens ^[1]; Nguyen, Trung Dac ^[2]; Anderson, Joshua A. ^[1]; Lui, Pak ^[3];

^[4]; Millan, Jaime A. ^[1]; Morse, David C. ^[5];

^[1]

Univ. of Michigan, Ann Arbor, MI (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). National Center for Computational Sciences
Mellanox Technologies, Inc., Sunnyvale, CA (United States)
Univ. of Cambridge (United Kingdom). High Performance Computing Service
Univ. of Minnesota, Minneapolis, MN (United States). Dept. of Chemical Engineering and Materials Science

We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, 2013). Here, our approach is inspired by a traditional CPU-based code, LAMMPS (Plimpton, 1995), but is implemented within a code that was designed for execution on GPUs from the start (Anderson et al., 2008). The software supports short-ranged pair force and bond force fields and achieves optimal GPU performance using an autotuning algorithm. We are able to demonstrate equivalent or superior scaling on up to 3375 GPUs in Lennard-Jones and dissipative particle dynamics (DPD) simulations of up to 108 million particles. GPUDirect RDMA capabilities in recent GPU generations provide better performance in full double precision calculations. For a representative polymer physics application, HOOMD-blue 1.0 provides an effective GPU vs. CPU node speed-up of 12.5x.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1565293

Alternate ID(s):: OSTI ID: 1246983; OSTI ID: 1565294; OSTI ID: 1820890

Journal Information:: Computer Physics Communications, Vol. 192, Issue C; ISSN 0010-4655

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 478 works

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References (36)

General purpose molecular dynamics simulations fully implemented on graphics processing units Anderson, Joshua A.; Lorenz, Chris D.; Travesset, A. Journal of Computational Physics, Vol. 227, Issue 10 https://doi.org/10.1016/j.jcp.2008.01.047	journal	May 2008
Fast Parallel Algorithms for Short-Range Molecular Dynamics Plimpton, Steve Journal of Computational Physics, Vol. 117, Issue 1 https://doi.org/10.1006/jcph.1995.1039	journal	March 1995
Implementing molecular dynamics on hybrid high performance computers – short range forces Brown, W. Michael; Wang, Peng; Plimpton, Steven J. Computer Physics Communications, Vol. 182, Issue 4 https://doi.org/10.1016/j.cpc.2010.12.021	journal	April 2011
Accelerating dissipative particle dynamics simulations on GPUs: Algorithms, numerics and applications Tang, Yu-Hang; Karniadakis, George Em Computer Physics Communications, Vol. 185, Issue 11 https://doi.org/10.1016/j.cpc.2014.06.015	journal	November 2014
A flexible algorithm for calculating pair interactions on SIMD architectures Páll, Szilárd; Hess, Berk Computer Physics Communications, Vol. 184, Issue 12 https://doi.org/10.1016/j.cpc.2013.06.003	journal	December 2013
Accelerating molecular modeling applications with graphics processors Stone, John E.; Phillips, James C.; Freddolino, Peter L. Journal of Computational Chemistry, Vol. 28, Issue 16 https://doi.org/10.1002/jcc.20829	journal	January 2007
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation Eastman, Peter; Friedrichs, Mark S.; Chodera, John D. Journal of Chemical Theory and Computation, Vol. 9, Issue 1 https://doi.org/10.1021/ct300857j	journal	November 2012
ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale Harvey, M. J.; Giupponi, G.; Fabritiis, G. De Journal of Chemical Theory and Computation, Vol. 5, Issue 6 https://doi.org/10.1021/ct9000685	journal	May 2009
Lattice Boltzmann simulations on GPUs with ESPResSo Roehm, D.; Arnold, A. The European Physical Journal Special Topics, Vol. 210, Issue 1 https://doi.org/10.1140/epjst/e2012-01639-6	journal	August 2012
Highly accelerated simulations of glassy dynamics using GPUs: Caveats on limited floating-point precision Colberg, Peter H.; Höfling, Felix Computer Physics Communications, Vol. 182, Issue 5 https://doi.org/10.1016/j.cpc.2011.01.009	journal	May 2011
Universality of Block Copolymer Melts Glaser, Jens; Medapuram, Pavani; Beardsley, Thomas M. Physical Review Letters, Vol. 113, Issue 6 https://doi.org/10.1103/PhysRevLett.113.068302	journal	August 2014
GPU Based Molecular Dynamics Simulations of Polymer Rings in Concentrated Solution: Structure and Scaling Reith, Daniel; Mirny, Leonid; Virnau, Peter Progress of Theoretical Physics Supplement, Vol. 191 https://doi.org/10.1143/PTPS.191.135	journal	January 2011
Micellization Studied by GPU-Accelerated Coarse-Grained Molecular Dynamics Levine, Benjamin G.; LeBard, David N.; DeVane, Russell Journal of Chemical Theory and Computation, Vol. 7, Issue 12 https://doi.org/10.1021/ct2005193	journal	October 2011
Anomalous structure and scaling of ring polymer brushes Reith, D.; Milchev, A.; Virnau, P. EPL (Europhysics Letters), Vol. 95, Issue 2 https://doi.org/10.1209/0295-5075/95/28003	journal	June 2011
Decreasing Polymer Flexibility Improves Wetting and Dispersion of Polymer-Grafted Particles in a Chemically Identical Polymer Matrix Lin, Brandon; Martin, Tyler B.; Jayaraman, Arthi ACS Macro Letters, Vol. 3, Issue 7 https://doi.org/10.1021/mz500274w	journal	June 2014
Rupture mechanism of liquid crystal thin films realized by large-scale molecular simulations Nguyen, Trung Dac; Carrillo, Jan-Michael Y.; Matheson, Michael A. Nanoscale, Vol. 6, Issue 6 https://doi.org/10.1039/C3NR05413F	journal	January 2014
Coexistence of spinodal instability and thermal nucleation in thin-film rupture: Insights from molecular levels Nguyen, Trung Dac; Fuentes-Cabrera, Miguel; Fowlkes, Jason D. Physical Review E, Vol. 89, Issue 3 https://doi.org/10.1103/PhysRevE.89.032403	journal	March 2014
Crossover to surface flow in supercooled unentangled polymer films Lam, Chi-Hang; Tsui, Ophelia K. C. Physical Review E, Vol. 88, Issue 4 https://doi.org/10.1103/PhysRevE.88.042604	journal	October 2013
Highly Scalable and Memory Efficient Ultra-Coarse-Grained Molecular Dynamics Simulations Grime, John. M. A.; Voth, Gregory A. Journal of Chemical Theory and Computation, Vol. 10, Issue 1 https://doi.org/10.1021/ct400727q	journal	November 2013
Stability of the double gyroid phase to nanoparticle polydispersity in polymer-tethered nanosphere systems Phillips, Carolyn L.; Iacovella, Christopher R.; Glotzer, Sharon C. Soft Matter, Vol. 6, Issue 8 https://doi.org/10.1039/b911140a	journal	January 2010
Langevin dynamics simulations of a two-dimensional colloidal crystal under confinement and shear Wilms, D.; Virnau, P.; Sengupta, S. Physical Review E, Vol. 85, Issue 6 https://doi.org/10.1103/PhysRevE.85.061406	journal	June 2012
Probing the limitations of isotropic pair potentials to produce ground-state structural extremes via inverse statistical mechanics Zhang, G.; Stillinger, F. H.; Torquato, S. Physical Review E, Vol. 88, Issue 4 https://doi.org/10.1103/PhysRevE.88.042309	journal	October 2013
Thermal and athermal three-dimensional swarms of self-propelled particles Nguyen, Nguyen H. P.; Jankowski, Eric; Glotzer, Sharon C. Physical Review E, Vol. 86, Issue 1 https://doi.org/10.1103/PhysRevE.86.011136	journal	July 2012
Viral genome structures are optimal for capsid assembly Perlmutter, Jason D.; Qiao, Cong; Hagan, Michael F. eLife, Vol. 2 https://doi.org/10.7554/eLife.00632	journal	June 2013
Effects of supercoiling on enhancer–promoter contacts Benedetti, Fabrizio; Dorier, Julien; Stasiak, Andrzej Nucleic Acids Research, Vol. 42, Issue 16 https://doi.org/10.1093/nar/gku759	journal	August 2014
Folding and stability of helical bundle proteins from coarse-grained models: Generic Coarse-Grained Model for Proteins Kapoor, Abhijeet; Travesset, Alex Proteins: Structure, Function, and Bioinformatics, Vol. 81, Issue 7 https://doi.org/10.1002/prot.24269	journal	April 2013
Constant pressure molecular dynamics algorithms Martyna, Glenn J.; Tobias, Douglas J.; Klein, Michael L. The Journal of Chemical Physics, Vol. 101, Issue 5 https://doi.org/10.1063/1.467468	journal	September 1994
Explicit reversible integrators for extended systems dynamics Martyna, Glenn J.; Tuckerman, Mark E.; Tobias, Douglas J. Molecular Physics, Vol. 87, Issue 5 https://doi.org/10.1080/00268979600100761	journal	April 1996
Pseudo-random number generation for Brownian Dynamics and Dissipative Particle Dynamics simulations on GPU devices Phillips, Carolyn L.; Anderson, Joshua A.; Glotzer, Sharon C. Journal of Computational Physics, Vol. 230, Issue 19 https://doi.org/10.1016/j.jcp.2011.05.021	journal	August 2011
Implementing molecular dynamics on hybrid high performance computers – Particle–particle particle-mesh Brown, W. Michael; Kohlmeyer, Axel; Plimpton, Steven J. Computer Physics Communications, Vol. 183, Issue 3 https://doi.org/10.1016/j.cpc.2011.10.012	journal	March 2012
An optimized united atom model for simulations of polymethylene melts Paul, Wolfgang; Yoon, Do Y.; Smith, Grant D. The Journal of Chemical Physics, Vol. 103, Issue 4 https://doi.org/10.1063/1.469740	journal	July 1995
The development of Mellanox/NVIDIA GPUDirect over InfiniBand—a new model for GPU to GPU communications Shainer, Gilad; Ayoub, Ali; Lui, Pak Computer Science - Research and Development, Vol. 26, Issue 3-4 https://doi.org/10.1007/s00450-011-0157-1	journal	April 2011
MVAPICH2-GPU: optimized GPU to GPU communication for InfiniBand clusters Wang, Hao; Potluri, Sreeram; Luo, Miao Computer Science - Research and Development, Vol. 26, Issue 3-4 https://doi.org/10.1007/s00450-011-0171-3	journal	April 2011
GPU-Aware MPI on RDMA-Enabled Clusters: Design, Implementation and Evaluation Wang, Hao; Potluri, Sreeram; Bureddy, Devendar IEEE Transactions on Parallel and Distributed Systems, Vol. 25, Issue 10 https://doi.org/10.1109/TPDS.2013.222	journal	October 2014
Scalable molecular dynamics with NAMD Phillips, James C.; Braun, Rosemary; Wang, Wei Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802 https://doi.org/10.1002/jcc.20289	journal	January 2005
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation Hess, Berk; Kutzner, Carsten; van der Spoel, David Journal of Chemical Theory and Computation, Vol. 4, Issue 3 https://doi.org/10.1021/ct700301q	journal	February 2008

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Self-diffusion in single-component Yukawa fluids Khrapak, Sergey; Klumov, Boris; Couedel, Lenaic Journal of Physics Communications, Vol. 2, Issue 4 https://doi.org/10.1088/2399-6528/aaba23	journal	April 2018
Clathrate colloidal crystals Lin, Haixin; Lee, Sangmin; Sun, Lin Science, Vol. 355, Issue 6328 https://doi.org/10.1126/science.aal3919	journal	March 2017
Inverse design of simple pair potentials for the self-assembly of complex structures Adorf, Carl S.; Antonaglia, James; Dshemuchadse, Julia The Journal of Chemical Physics, Vol. 149, Issue 20 https://doi.org/10.1063/1.5063802	journal	November 2018
Cross-stream migration of a Brownian droplet in a polymer solution under Poiseuille flow Howard, Michael P.; Truskett, Thomas M.; Nikoubashman, Arash Soft Matter, Vol. 15, Issue 15 https://doi.org/10.1039/c8sm02552e	journal	January 2019
Chromatin Loop Extrusion and Chromatin Unknotting Racko, Dusan; Benedetti, Fabrizio; Goundaroulis, Dimos Polymers, Vol. 10, Issue 10 https://doi.org/10.3390/polym10101126	journal	October 2018
Self-assembly of lobed particles into amorphous and crystalline porous structures Paul, Sanjib; Vashisth, Harish Soft Matter, Vol. 16, Issue 5 https://doi.org/10.1039/c9sm01878f	journal	January 2020
RUMD: A general purpose molecular dynamics package optimized to utilize GPU hardware down to a few thousand particles Bailey, Nicholas; Ingebrigtsen, Trond; Hansen, Jesper Schmidt SciPost Physics, Vol. 3, Issue 6 https://doi.org/10.21468/scipostphys.3.6.038	journal	January 2017
Rapid sampling of stochastic displacements in Brownian dynamics simulations Fiore, Andrew M.; Balboa Usabiaga, Florencio; Donev, Aleksandar The Journal of Chemical Physics, Vol. 146, Issue 12 https://doi.org/10.1063/1.4978242	journal	March 2017
Freezing on a sphere Guerra, Rodrigo E.; Kelleher, Colm P.; Hollingsworth, Andrew D. Nature, Vol. 554, Issue 7692 https://doi.org/10.1038/nature25468	journal	February 2018
FastNBL: fast neighbor lists establishment for molecular dynamics simulation based on bitwise operations Li, Kun; Li, Shigang; Huang, Shan The Journal of Supercomputing, Vol. 76, Issue 7 https://doi.org/10.1007/s11227-019-02860-3	journal	April 2019
Air separation with graphene mediated by nanowindow-rim concerted motion Vallejos-Burgos, Fernando; Coudert, François-Xavier; Kaneko, Katsumi Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-04224-6	journal	May 2018
Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials Dubbeldam, David; Walton, Krista S.; Vlugt, Thijs J. H. Advanced Theory and Simulations, Vol. 2, Issue 11 https://doi.org/10.1002/adts.201900135	journal	September 2019
Self-Diffusion in a Spatially Modulated System of Electrons on Helium Moskovtsev, K.; Dykman, M. I. Journal of Low Temperature Physics, Vol. 195, Issue 3-4 https://doi.org/10.1007/s10909-019-02148-z	journal	February 2019
Static and dynamic properties of large polymer melts in equilibrium Hsu, Hsiao-Ping; Kremer, Kurt The Journal of Chemical Physics, Vol. 144, Issue 15 https://doi.org/10.1063/1.4946033	journal	April 2016
Excitation spectra in fluids: How to analyze them properly Kryuchkov, Nikita P.; Mistryukova, Lukiya A.; Brazhkin, Vadim V. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-46979-y	journal	July 2019
Doping colloidal bcc crystals — interstitial solids and meta-stable clusters Higler, Ruben; Sprakel, Joris Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-12730-8	journal	October 2017
Hemoglobin-driven iron-directed assembly of gold nanoparticles Egan, Jacquelyn G.; Drossis, Nicole; Ebralidze, Iraklii I. RSC Advances, Vol. 8, Issue 28 https://doi.org/10.1039/c8ra01996g	journal	January 2018
Self-assembly of semiflexible polymers confined to thin spherical shells Khadilkar, Mihir R.; Nikoubashman, Arash Soft Matter, Vol. 14, Issue 33 https://doi.org/10.1039/c8sm01170b	journal	January 2018
Harnessing entropy to enhance toughness in reversibly crosslinked polymer networks Tito, Nicholas B.; Creton, Costantino; Storm, Cornelis Soft Matter, Vol. 15, Issue 10 https://doi.org/10.1039/c8sm02577k	journal	January 2019
Patchy particles by self-assembly of star copolymers on a spherical substrate: Thomson solutions in a geometric problem with a color constraint Hain, Tobias M.; Schröder-Turk, Gerd E.; Kirkensgaard, Jacob J. K. Soft Matter, Vol. 15, Issue 46 https://doi.org/10.1039/c9sm01460h	journal	January 2019
Enhanced gel formation in binary mixtures of nanocolloids with short-range attraction Harden, James L.; Guo, Hongyu; Bertrand, Martine The Journal of Chemical Physics, Vol. 148, Issue 4 https://doi.org/10.1063/1.5007038	journal	January 2018
Collective modes of two-dimensional classical Coulomb fluids Khrapak, Sergey A.; Kryuchkov, Nikita P.; Mistryukova, Lukia A. The Journal of Chemical Physics, Vol. 149, Issue 13 https://doi.org/10.1063/1.5050708	journal	October 2018
Configurational entropy of glass-forming liquids Berthier, Ludovic; Ozawa, Misaki; Scalliet, Camille The Journal of Chemical Physics, Vol. 150, Issue 16 https://doi.org/10.1063/1.5091961	journal	April 2019
Characterization of colloidal nanocrystal surface structure using small angle neutron scattering and efficient Bayesian parameter estimation Winslow, Samuel W.; Shcherbakov-Wu, Wenbi; Liu, Yun The Journal of Chemical Physics, Vol. 150, Issue 24 https://doi.org/10.1063/1.5108904	journal	June 2019
Universal folding pathways of polyhedron nets Dodd, Paul M.; Damasceno, Pablo F.; Glotzer, Sharon C. Proceedings of the National Academy of Sciences, Vol. 115, Issue 29 https://doi.org/10.1073/pnas.1722681115	journal	July 2018
The race to the bottom: approaching the ideal glass? Royall, C. Patrick; Turci, Francesco; Tatsumi, Soichi Journal of Physics: Condensed Matter, Vol. 30, Issue 36 https://doi.org/10.1088/1361-648x/aad10a	journal	August 2018
Charged hydrophobic colloids at an oil–aqueous phase interface Kelleher, Colm P.; Wang, Anna; Guerrero-García, Guillermo Iván Physical Review E, Vol. 92, Issue 6 https://doi.org/10.1103/physreve.92.062306	journal	December 2015
The alchemical energy landscape for a pentameric cluster. Morgan, John; Glotzer, Sharon C. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.47568	text	January 2020
Flow behavior of chain and star polymers and their mixtures Srivastva, Deepika; Nikoubashman, Arash MDPI https://doi.org/10.25358/openscience-652	text	January 2018
ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL Wutz, Gordana; Ladurner, Rene; St Hilaire, Brian Glenn eLife, Vol. 9 https://doi.org/10.7554/elife.52091	journal	February 2020
Adsorption characteristics of glycols on calcite and hematite Olsen, Richard; Leirvik, Kim N.; Kvamme, Bjørn AIChE Journal, Vol. 65, Issue 11 https://doi.org/10.1002/aic.16728	journal	July 2019
OSPREY 3.0: Open‐source protein redesign for you, with powerful new features Hallen, Mark A.; Martin, Jeffrey W.; Ojewole, Adegoke Journal of Computational Chemistry, Vol. 39, Issue 30 https://doi.org/10.1002/jcc.25522	journal	October 2018
Principle of corresponding states for hard polyhedron fluids Vo, Thi; Glotzer, Sharon C. Molecular Physics, Vol. 117, Issue 23-24 https://doi.org/10.1080/00268976.2019.1640906	journal	July 2019
Implementing molecular dynamics simulation on the Sunway TaihuLight system with heterogeneous many-core processors: Implementing molecular dynamics simulation on the Sunway TaihuLight system with heterogeneous many-core processors Dong, Wenqian; Li, Kenli; Kang, Letian Concurrency and Computation: Practice and Experience, Vol. 30, Issue 16 https://doi.org/10.1002/cpe.4468	journal	April 2018
Two-time correlations for probing the aging dynamics of glassy colloids Robe, Dominic; Boettcher, Stefan Soft Matter, Vol. 14, Issue 46 https://doi.org/10.1039/c8sm02191k	journal	January 2018
Molecular height measurement by cell surface optical profilometry (CSOP) Son, Sungmin; Takatori, Sho C.; Belardi, Brian Proceedings of the National Academy of Sciences, Vol. 117, Issue 25 https://doi.org/10.1073/pnas.1922626117	journal	June 2020
Chromatin-loop extrusion and chromatin unknotting Racko, Dusan; Benedetti, Fabrizio; Goundaroulis, Dimos Polymers https://doi.org/10.1101/411629	journal	September 2018
Routine million-particle simulations of epoxy curing with dissipative particle dynamics Thomas, Stephen; Alberts, Monet; Henry, Michael M. Journal of Theoretical and Computational Chemistry, Vol. 17, Issue 03 https://doi.org/10.1142/s0219633618400059	journal	May 2018
Principle of corresponding states for hard polyhedron fluids Vo, Thi; Glotzer, Sharon C. Taylor & Francis https://doi.org/10.6084/m9.figshare.8948711.v1	text	January 2019
Biomolecular simulations: from dynamics and mechanisms to computational assays of biological activity Huggins, David Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.30464	text	January 2019
Exploring the zone of anisotropy and broken symmetries in DNA-mediated nanoparticle crystallization O’Brien, Matthew N.; Girard, Martin; Lin, Hai-Xin Proceedings of the National Academy of Sciences, Vol. 113, Issue 38 https://doi.org/10.1073/pnas.1611808113	journal	September 2016
Alchemical molecular dynamics for inverse design Zhou, Pengji; Proctor, James C.; van Anders, Greg Molecular Physics, Vol. 117, Issue 23-24 https://doi.org/10.1080/00268976.2019.1680886	journal	October 2019
OSPREY 3.0: Open-Source Protein Redesign for You, with Powerful New Features Hallen, Mark A.; Martin, Jeffery W.; Ojewole, Adegoke Journal of Computational Chemistry https://doi.org/10.1101/306324	journal	April 2018
RUMD: A general purpose molecular dynamics package optimized to utilize GPU hardware down to a few thousand particles Bailey, Nicholas P.; Ingebrigtsen, Trond S.; Hansen, Jesper Schmidt arXiv https://doi.org/10.48550/arxiv.1506.05094	text	January 2015
Anomalous dynamics of interstitial dopants in soft crystals Tauber, Justin; Higler, Ruben; Sprakel, Joris arXiv https://doi.org/10.48550/arxiv.1611.08845	text	January 2016
Rapid Sampling of Stochastic Displacements in Brownian Dynamics Simulations Fiore, A. M.; Usabiaga, F. Balboa; Donev, A. arXiv https://doi.org/10.48550/arxiv.1611.09322	text	January 2016
Inverse Design of Simple Pair Potentials for the Self-Assembly of Complex Structures Adorf, Carl S.; Antonaglia, James; Dshemuchadse, Julia arXiv https://doi.org/10.48550/arxiv.1711.04153	text	January 2017
The race to the bottom: approaching the ideal glass? Royall, C. Patrick; Turci, Francesco; Tatsumi, Soichi arXiv https://doi.org/10.48550/arxiv.1711.04739	text	January 2017
Freezing on a Sphere Guerra, Rodrigo E.; Kelleher, Colm P.; Hollingsworth, Andrew D. arXiv https://doi.org/10.48550/arxiv.1802.04341	text	January 2018
Collective modes of two-dimensional classical Coulomb fluids Khrapak, S. A.; Kryuchkov, N. P.; Mistryukova, L. A. arXiv https://doi.org/10.48550/arxiv.1810.04435	text	January 2018
Bulk structural informations from density functionals for patchy particles Stopper, Daniel; Hirschmann, Frank; Oettel, Martin arXiv https://doi.org/10.48550/arxiv.1811.09388	text	January 2018
Strain field in graphene induced by nanopillar mesh Milovanovic, S. P.; Covaci, L.; Peeters, F. M. arXiv https://doi.org/10.48550/arxiv.1811.10345	text	January 2018
Phase behavior of flexible and semiflexible polymers in solvents of varying quality Midya, Jiarul; Egorov, Sergei A.; Binder, Kurt arXiv https://doi.org/10.48550/arxiv.1905.06789	text	January 2019
Attractive versus truncated repulsive supercooled liquids: The dynamics is encoded in the pair correlation function Landes, François P.; Biroli, Giulio; Dauchot, Olivier arXiv https://doi.org/10.48550/arxiv.1906.01103	text	January 2019
Patchy particles by self-assembly of star copolymers on a spherical substrate: Thomson solutions in a geometric problem with a color constraint Hain, Tobias M.; Schröder-Turk, Gerd E.; Kirkensgaard, Jacob J. K. arXiv https://doi.org/10.48550/arxiv.1907.08103	preprint	January 2019
Active binary mixtures of fast and slow hard spheres Kolb, Thomas; Klotsa, Daphne arXiv https://doi.org/10.48550/arxiv.1909.02919	preprint	January 2019
Activity-controlled Annealing of Colloidal Monolayers Ramananarivo, Sophie; Ducrot, Etienne; Palacci, Jeremie arXiv https://doi.org/10.48550/arxiv.1909.07382	text	January 2019
Self-Consistent Field Lattice Model for Polymer Networks Tito, Nicholas B.; Storm, Cornelis; Ellenbroek, Wouter G. Macromolecules, Vol. 50, Issue 24 https://doi.org/10.1021/acs.macromol.7b01284	journal	December 2017
Langevin Dynamics Simulations of the Exchange of Complex Coacervate Core Micelles: The Role of Nonelectrostatic Attraction and Polyelectrolyte Length Bos, Inge; Sprakel, Joris Macromolecules, Vol. 52, Issue 22 https://doi.org/10.1021/acs.macromol.9b01442	journal	November 2019
Disentangling the Role of Chain Conformation on the Mechanics of Polymer Tethered Particle Materials Midya, Jiarul; Cang, Yu; Egorov, Sergei A. Nano Letters, Vol. 19, Issue 4 https://doi.org/10.1021/acs.nanolett.9b00817	journal	March 2019
Segregation in Drying Binary Colloidal Droplets Liu, Wendong; Midya, Jiarul; Kappl, Michael ACS Nano, Vol. 13, Issue 5 https://doi.org/10.1021/acsnano.9b00459	journal	March 2019
Thermal crumpling of perforated two-dimensional sheets Yllanes, David; Bhabesh, Sourav S.; Nelson, David R. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01551-y	journal	November 2017
Evolutionary drivers of protein shape Shannon, Gareth; Marples, Callum R.; Toofanny, Rudesh D. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-47337-8	journal	August 2019
Semiflexible Polymers in the Bulk and Confined by Planar Walls Egorov, Sergei; Milchev, Andrey; Binder, Kurt Polymers, Vol. 8, Issue 8 https://doi.org/10.3390/polym8080296	journal	August 2016

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