Computer Simulation of Liquids

Scalable molecular dynamics with NAMD

Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914

The Amber biomolecular simulation programs

Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20290 · Cited by 9,535

CHARMM‐GUI: A web‐based graphical user interface for CHARMM

Jo, S., Kim, T., Iyer, V. G., & Im, W. (2008) · Journal of Computational Chemistry · doi:10.1002/jcc.20945 · Cited by 9,284

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., et al. (2000) · Accounts of Chemical Research · doi:10.1021/ar000033j · Cited by 4,978

Transport in Proton Conductors for Fuel-Cell Applications: Simulations, Elementary Reactions, and Phenomenology

Kreuer, K.-D., Paddison, S. J., Spohr, E., & Schuster, M. (2004) · Chemical Reviews · doi:10.1021/cr020715f · Cited by 2,187

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

Laio, A., & Gervasio, F. L. (2008) · Reports on Progress in Physics · doi:10.1088/0034-4885/71/12/126601 · Cited by 1,619

Deriving effective mesoscale potentials from atomistic simulations

Reith, D., Pütz, M., & Müller‐Plathe, F. (2003) · Journal of Computational Chemistry · doi:10.1002/jcc.10307 · Cited by 1,314

Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME

Godoy, P., Hewitt, N. J., Albrecht, U., Andersen, M. E., Ansari, N., Bhattacharya, S., Bode, J. G., Bolleyn, J., Borner, C., Böttger, J., et al. (2013) · Archives of Toxicology · doi:10.1007/s00204-013-1078-5 · Cited by 1,280

Thermal Contraction and Disordering of the Al(110) Surface

Marzari, N., Vanderbilt, D., De Vita, A., & Payne, M. C. (1999) · Physical Review Letters · doi:10.1103/physrevlett.82.3296 · Cited by 1,255

How Ions Affect the Structure of Water

Hribar, B., Southall, N. T., Vlachy, V., & Dill, K. A. (2002) · Journal of the American Chemical Society · doi:10.1021/ja026014h · Cited by 860

Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach

Lyubartsev, A. P., & Laaksonen, A. (1995) · Physical Review E · doi:10.1103/physreve.52.3730 · Cited by 852

Molecular dynamics simulation of a polymer melt with a nanoscopic particle

Starr, F. W., Schrøder, T. B., & Glotzer, S. C. (2002) · Macromolecules · doi:10.1021/ma010626p · Cited by 511

F ROM F OLDING T HEORIES TO F OLDING P ROTEINS: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding

Shea, J.-E., & Brooks III, C. L. (2001) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.52.1.499 · Cited by 481

Untitled work

(2009) · JuSER (Forschungszentrum Jülich) · Cited by 465

Automatic Method for Identifying Reaction Coordinates in Complex Systems

Ma, A., & Dinner, A. R. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp045546c · Cited by 400

Zinc binding in proteins and solution: A simple but accurate nonbonded representation

Stote, R. H., & Karplus, M. (1995) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340230104 · Cited by 354

Dielectric Constant of Water Confined in a Nanocavity

Senapati, S., & Chandra, A. (2001) · The Journal of Physical Chemistry B · doi:10.1021/jp011058i · Cited by 302

Mapping atomistic simulations to mesoscopic models: A systematic coarse-graining procedure for vinyl polymer chains

Milano, G., & Müller-Plathe, F. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp0523571 · Cited by 260

Molecular dynamics simulation of orientation and crystallization of polyethylene during uniaxial extension

Lavine, M. S., Waheed, N., & Rutledge, G. C. (2003) · Polymer · doi:10.1016/s0032-3861(03)00017-x · Cited by 219

Dynamics of polystyrene melts through hierarchical multiscale simulations

Harmandaris, V. A., & Kremer, K. (2009) · Macromolecules · doi:10.1021/ma8018624 · Cited by 215

Molecular simulation of water confined in nanoporous silica

Bonnaud, P. A., Coasne, B., & Pellenq, R. J.-M. (2010) · Journal of Physics: Condensed Matter · doi:10.1088/0953-8984/22/28/284110 · Cited by 182

Molecular Dynamics Studies of Interfacial Water at the Alumina Surface

Argyris, D., Ho, T., Cole, D. R., & Striolo, A. (2011) · The Journal of Physical Chemistry C · doi:10.1021/jp109244c · Cited by 167

Detailed modeling of hydrodynamics, mass transfer and chemical reactions in a bubble column using a discrete bubble model

Darmana, D., Deen, N. G., & Kuipers, J. A. M. (2005) · Chemical Engineering Science · doi:10.1016/j.ces.2005.01.025 · Cited by 159

Molecular modeling of protein materials: case study of elastin

Tarakanova, A., & Buehler, M. J. (2013) · Modelling and Simulation in Materials Science and Engineering · doi:10.1088/0965-0393/21/6/063001 · Cited by 160

Microstructure of Catalyst Layers in PEM Fuel Cells Redefined: A Computational Approach

Malek, K., Mashio, T., & Eikerling, M. (2011) · Electrocatalysis · doi:10.1007/s12678-011-0047-0 · Cited by 151

Osmolyte Trimethylamine-N-Oxide Does Not Affect the Strength of Hydrophobic Interactions: Origin of Osmolyte Compatibility

Athawale, M. V., Dordick, J. S., & Garde, S. (2005) · Biophysical Journal · doi:10.1529/biophysj.104.056671 · Cited by 153

A general-purpose coarse-grained molecular dynamics program

Aoyagi, T., Sawa, F., Shoji, T., Fukunaga, H., Takimoto, J.-I., & Doi, M. (2002) · Computer Physics Communications · doi:10.1016/s0010-4655(02)00271-0 · Cited by 138

Automatic coarse graining of polymers

Faller, R. (2004) · Polymer · doi:10.1016/j.polymer.2003.11.053 · Cited by 115

Rigidity Strengthening: A Mechanism for Protein–Ligand Binding

Nguyen, D. D., Xiao, T., Wang, M., & Wei, G.-W. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00226 · Cited by 105

From mesoscale back to atomistic models: A fast reverse-mapping procedure for vinyl polymer chains

Santangelo, G., Di Matteo, A., Müller-Plathe, F., & Milano, G. (2007) · The Journal of Physical Chemistry B · doi:10.1021/jp066212l · Cited by 104

Influence of Hydrophilic Surface Specificity on the Structural Properties of Confined Water

Malani, A., Ayappa, K. G., & Murad, S. (2009) · The Journal of Physical Chemistry B · doi:10.1021/jp902562v · Cited by 97

Zeolite screening for the separation of gas mixtures containing SO 2 , CO 2 and CO

Matito-Martos, I., Martin-Calvo, A., Gutiérrez-Sevillano, J. J., Haranczyk, M., Doblare, M., Parra, J. B., Ania, C. O., & Calero, S. (2014) · Physical Chemistry Chemical Physics · doi:10.1039/c4cp00109e · Cited by 95

Properties of cell death models calibrated and compared using Bayesian approaches

Eydgahi, H., Chen, W. W., Muhlich, J. L., Vitkup, D., Tsitsiklis, J. N., & Sorger, P. K. (2013) · Molecular Systems Biology · doi:10.1038/msb.2012.69 · Cited by 84

Computational screening of porous carbons, zeolites, and metal organic frameworks for desulfurization and decarburization of biogas, natural gas, and flue gas

Peng, X., & Cao, D. (2013) · AIChE Journal · doi:10.1002/aic.14046 · Cited by 92

Multicentered Gaussian-based potentials for coarse-grained polymer simulations: Linking atomistic and mesoscopic scales

Milano, G., Goudeau, S., & Müller‐Plathe, F. (2005) · Journal of Polymer Science Part B: Polymer Physics · doi:10.1002/polb.20380 · Cited by 90

Relating interactions between neurofilaments to the structure of axonal neurofilament distributions through polymer brush models

Kumar, S., Yin, X., Trapp, B. D., Hoh, J. H., & Paulaitis, M. E. (2002) · Biophysical Journal · doi:10.1016/s0006-3495(02)75581-1 · Cited by 89

Molecular dynamics simulation of structural formation of short polymer chains

Fujiwara, S., & Sato, T. (1998) · Physical Review Letters · doi:10.1103/physrevlett.80.991 · Cited by 87

Crossover from unentangled to entangled dynamics in a systematically coarse-grained polystyrene melt

Sun, Q., & Faller, R. (2006) · Macromolecules · doi:10.1021/ma0514774 · Cited by 85

Molecular dynamics simulation of linear polyethylene blends: Effect of molar mass bimodality on topological characteristics and mechanical behavior

Moyassari, A., Gkourmpis, T., Hedenqvist, M. S., & Gedde, U. W. (2019) · Polymer · doi:10.1016/j.polymer.2018.12.012 · Cited by 82

Rod-like colloids and polymers in shear flow: A multi-particle-collision dynamics study

Winkler, R. G., Mussawisade, K., Ripoll, M., & Gompper, G. (2004) · Journal of Physics: Condensed Matter · doi:10.1088/0953-8984/16/38/012 · Cited by 81

How thick is the interphase in an ultrathin polymer film? Coarse grained molecular dynamics simulations of polyamide-6, 6 on graphene

Eslami, H., & Müller-Plathe, F. (2013) · The Journal of Physical Chemistry C · doi:10.1021/jp400142h · Cited by 76

Structure, dimensions, and entanglement statistics of long linear polyethylene chains

Foteinopoulou, K., Karayiannis, N. C., Laso, M., & Kröger, M. (2009) · The Journal of Physical Chemistry B · doi:10.1021/jp808287s · Cited by 74

Primitive chain network study on uncrosslinked and crosslinked cis-polyisoprene polymers

Li, Y., Kröger, M., & Liu, W. K. (2011) · Polymer · doi:10.1016/j.polymer.2011.10.044 · Cited by 70

Cryogenic Separation of Hydrogen Isotopes in Single-Walled Carbon and Boron-Nitride Nanotubes: Insight into the Mechanism of Equilibrium Quantum Sieving in Quasi-One-Dimensional Pores

Kowalczyk, P., Gauden, P. A., & Terzyk, A. P. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp800735k · Cited by 62

Coarse-grained computer simulation of nanoconfined polyamide-6, 6

Eslami, H., Karimi-Varzaneh, H. A., & Müller-Plathe, F. (2011) · Macromolecules · doi:10.1021/ma102320v · Cited by 61

Entanglements and dynamics of polymer melts near a SWCNT

Karatrantos, A., Composto, R. J., Winey, K. I., Kröger, M., & Clarke, N. (2012) · Macromolecules · doi:10.1021/ma3007637 · Cited by 53

Thermomechanical properties of the WCA–Lennard-Jones model system in its fluid and solid states

Hess, S., Kröger, M., & Voigt, H. (1998) · Physica A: Statistical Mechanics and its Applications · doi:10.1016/s0378-4371(97)00612-2 · Cited by 52

Linear viscoelastic behavior of unentangled polymer melts via non-equilibrium molecular dynamics

Cifre, J. G. H., Hess, S., & Kröger, M. (2004) · Macromolecular Theory and Simulations · doi:10.1002/mats.200400021 · Cited by 46

Monte Carlo Simulations Probing the Adsorptive Separation of Hydrogen Sulfide/Methane Mixtures Using All-Silica Zeolites

Shah, M. S., Tsapatsis, M., & Siepmann, J. I. (2015) · Langmuir · doi:10.1021/acs.langmuir.5b03015 · Cited by 46

Computational amphiphilic materials for drug delivery

Thota, N., & Jiang, J. (2015) · Frontiers in Materials · doi:10.3389/fmats.2015.00064 · Cited by 38

Modeling particulate self-healing materials and application to uni-axial compression

Herbst, O., & Luding, S. (2008) · International Journal of Fracture · doi:10.1007/s10704-008-9299-y · Cited by 37

Charge Transfer Models of Zinc and Magnesium in Water

Soniat, M., Hartman, L., & Rick, S. W. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/ct501173n · Cited by 34

Anergy in self-directed B lymphocytes: A statistical mechanics perspective

Agliari, E., Barra, A., Del Ferraro, G., Guerra, F., & Tantari, D. (2015) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2014.05.006 · Cited by 34

Crucial Importance of Water Structure Modification on Trimethylamine N-Oxide Counteracting Effect at High Pressure

Sarma, R., & Paul, S. (2013) · The Journal of Physical Chemistry B · doi:10.1021/jp311102v · Cited by 33

Multiscale simulation of polymer melt viscoelasticity: Expanded-ensemble Monte Carlo coupled with atomistic nonequilibrium molecular dynamics

Baig, C., & Mavrantzas, V. G. (2009) · Physical Review B · doi:10.1103/physrevb.79.144302 · Cited by 30

Computer simulation of the rheology of concentrated star polymer suspensions

Padding, J. T., van Ruymbeke, E., Vlassopoulos, D., & Briels, W. J. (2010) · Rheologica Acta · doi:10.1007/s00397-009-0406-4 · Cited by 30

Self-healing of damaged particulate materials through sintering

Luding, S., & Suiker, A. S. J. (2008) · Philosophical Magazine · doi:10.1080/14786430802438176 · Cited by 26

Atomistic Simulation of Bulk Mechanics and Local Dynamics of Amorphous Polymers

Lyulin, A. V., Li, J., Mulder, T., Vorselaars, B., & Michels, M. A. J. (2006) · Macromolecular Symposia · doi:10.1002/masy.200650512 · Cited by 23

ON THE SIMULATION OF UNIAXIAL, COMPRESSIVE BEHAVIOR OF AMORPHOUS, GLASSY POLYMERS WITH MOLECULAR DYNAMICS

MAHAJAN, D. K., & BASU, S. (2010) · International Journal of Applied Mechanics · doi:10.1142/s1758825110000639 · Cited by 20

Gas Adsorption in Zeolites and Related Materials

(2007) · Studies in Surface Science and Catalysis · doi:10.1016/s0167-2991(07)80805-6 · Cited by 16

Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts

Soltanikazemi, E., Quadir, F., Roy, R. S., Guo, Z., & Cheng, J. (2022) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26269 · Cited by 15

Towards extreme scale dissipative particle dynamics simulations using multiple GPGPUs

Castagna, J., Guo, X., Seaton, M., & O’Cais, A. (2020) · Computer Physics Communications · doi:10.1016/j.cpc.2020.107159 · Cited by 10

Solute diffusion in nonionic liquids--effects of gravity

Smith, R. W., Scott, P. J., & Szpunar, B. (2009) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2008.04329.x · Cited by 3