Computer Simulation of Liquids

Cites (1,395)

Items 201–400 of 1,390

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2. Statistical Mechanics: Theory and Molecular Simulation
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3. Parallel Tempering: Theory, Applications, and New Perspectives
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4. Parallel tempering algorithm for conformational studies of biological molecules
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5. Free energy reconstruction from nonequilibrium single-molecule pulling experiments
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6. The Principles of Statistical Mechanics
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7. Studies in Molecular Dynamics. VIII. The Transport Coefficients for a Hard-Sphere Fluid
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8. Experimental Demonstration of Violations of the Second Law of Thermodynamics for Small Systems and Short Time Scales
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9. Dynamic light scattering
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10. Novel Configurational-Bias Monte Carlo Method for Branched Molecules. Transferable Potentials for Phase Equilibria. 2. United-Atom Description of Branched Alkanes
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11. Strain fluctuations and elastic constants
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12. Parallel Tempering Algorithm for Conformational Studies of Biological Molecules
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13. Temperature-accelerated dynamics for simulation of infrequent events
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14. The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
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15. Interfacial Density Profile for Fluids in the Critical Region
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16. Lattice-Gas Cellular Automata and Lattice Boltzmann Models: An Introduction
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17. Fermion Monte Carlo without fixed nodes: A game of life, death, and annihilation in Slater determinant space
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18. Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach
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19. Large Slip Effect at a Nonwetting Fluid-Solid Interface
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20. Correlation Functions for Molecular Motion
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21. Trajectory Surface Hopping in the Time-Dependent Kohn-Sham Approach for Electron-Nuclear Dynamics
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22. Equation of state for the Lennard-Jones fluid
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23. Numerical calculation of the rate of crystal nucleation in a Lennard-Jones system at moderate undercooling
    Pieter Rein ten Wolde, Maria J. Ruiz-Montero, Daan Frenkel · 1996 · The Journal of Chemical Physics
24. Optimally smooth norm-conserving pseudopotentials
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25. Studies in Molecular Dynamics. II. Behavior of a Small Number of Elastic Spheres
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26. Empirical potential Monte Carlo simulation of fluid structure
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27. The Theory of Intermolecular Forces
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28. Equilibrium microstates which generate second law violating steady states
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29. Molecular-dynamics study of atomic motions in water
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30. Parallel programming in C with MPI and OpenMP
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31. Computer simulation and the statistical mechanics of adsorption
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32. The representation of van der Waals (vdW) interactions in molecular mechanics force fields: potential form, combination rules, and vdW parameters
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33. Neural network potential-energy surfaces in chemistry: a tool for large-scale simulations
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34. Monte Carlo simulation of a many-fermion study
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35. Electrical double layer forces. A Monte Carlo study
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36. Accuracy and efficiency of the particle mesh Ewald method
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37. Theory of Thermal Transport Coefficients
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38. Statistical thermodynamics of surfaces, interfaces, and membranes
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39. Structural transformation in supercooled water controls the crystallization rate of ice
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40. Fluctuation–dissipation: Response theory in statistical physics
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41. Atom dipole interaction model for molecular polarizability. Application to polyatomic molecules and determination of atom polarizabilities
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42. Accelerating molecular modeling applications with graphics processors
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43. Dipole moment fluctuation formulas in computer simulations of polar systems
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44. High-Strain-Rate Plastic Flow Studied via Nonequilibrium Molecular Dynamics
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45. Monte Carlo simulation of differences in free energies of hydration
    William L. Jorgensen, Ch. Ravimohan · 1985 · The Journal of Chemical Physics
46. Ring-Polymer Molecular Dynamics: Quantum Effects in Chemical Dynamics from Classical Trajectories in an Extended Phase Space
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47. Monte Carlo study of the isotropic and nematic phases of infinitely thin hard platelets
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48. Monte Carlo studies of the dielectric properties of water-like models
    John Adair Barker, R.O. Watts · 1973 · Molecular Physics
49. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
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50. Molecular dynamics of liquid alkanes
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51. A Fast Adaptive Multipole Algorithm in Three Dimensions
    Hongwei Cheng, Leslie Greengard, Vladimir Rokhlin · 1999 · Journal of Computational Physics
52. Generalized Verlet Algorithm for Efficient Molecular Dynamics Simulations with Long-range Interactions
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53. Error estimates on averages of correlated data
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54. Replica exchange with solute tempering: a method for sampling biological systems in explicit water.
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55. Predicting slow structural transitions in macromolecular systems: Conformational flooding
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56. Mixed quantum-classical dynamics
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57. Choosing a Point from the Surface of a Sphere
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58. Transition-path theory and path-finding algorithms for the study of rare events.
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59. A Liouville-operator derived measure-preserving integrator for molecular dynamics simulations in the isothermal–isobaric ensemble
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60. How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines
    Markus Deserno, Christian Holm · 1998 · The Journal of Chemical Physics
61. Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics
    Christopher J. Fennell, J. Daniel Gezelter · 2006 · The Journal of Chemical Physics
62. Strong scaling of general-purpose molecular dynamics simulations on GPUs
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63. Theory of Simple Liquids: with Applications to Soft Matter
    J. P. Hansen, Ian R. McDonald · 2013
64. Concurrent coupling of length scales: Methodology and application
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65. The relative entropy is fundamental to multiscale and inverse thermodynamic problems
    M. Scott Shell · 2008 · The Journal of Chemical Physics
66. A Hamiltonian electrostatic coupling scheme for hybrid Car–Parrinello molecular dynamics simulations
    Alessandro Laio, Joost VandeVondele, Ursula Röthlisberger · 2002 · The Journal of Chemical Physics
67. Non-Newtonian molecular dynamics
    Denis J. Evans, O.P. Morriss · 1984 · Computer Physics Reports
68. Two-Step Melting in Two Dimensions: First-Order Liquid-Hexatic Transition
    Etienne P. Bernard, Werner Krauth · 2011 · Physical Review Letters
69. Multiscale coarse graining of liquid-state systems
    Sergei Izvekov, Gregory A. Voth · 2005 · The Journal of Chemical Physics
70. The potential calculation and some applications
    Roger W. Hockney · 1970 · Methods in computational physics
71. Direct evaluation of phase coexistence by molecular simulation via integration along the saturation line
    David A. Kofke · 1993 · The Journal of Chemical Physics
72. Molecular dynamics of liquid n-butane near its boiling point
    Jean-Paul Ryckaert, A. Bellemans · 1975 · Chemical Physics Letters
73. Finite-size scaling at first-order phase transitions
    Kurt Binder, D. P. Landau · 1984 · Physical review. B, Condensed matter
74. Good Practices in Free-Energy Calculations
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75. Colloids and the Depletion Interaction
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76. Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm
    G. Lamoureux, B. Roux · 2003 · The Journal of Chemical Physics
77. Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
    Michael Feig, Alexey V. Onufriev, Michael S. Lee, Wonpil Im, David Andrew Case, Charles L. Brooks · 2003 · Journal of Computational Chemistry
78. Mesoscopic Undulations and Thickness Fluctuations in Lipid Bilayers from Molecular Dynamics Simulations
    Erik R. Lindahl, Olle Edholm · 2000 · Biophysical Journal
79. Liquid argon: Monte carlo and molecular dynamics calculations
    John Adair Barker, R.A. Fisher, R.O. Watts · 1971 · Molecular Physics
80. A Fast Adaptive Multipole Algorithm for Particle Simulations
    J. Carrier, Leslie Greengard, Vladimir Rokhlin · 1988 · SIAM Journal on Scientific and Statistical Computing
81. A Multiscale Red Blood Cell Model with Accurate Mechanics, Rheology, and Dynamics
    Dmitry A. Fedosov, Bruce Caswell, George Em Karniadakis · 2010 · Biophysical Journal
82. Time-Dependent Density-Functional Theory: Concepts and Applications
    Carsten A. Ullrich · 2019
83. Membrane protein sequestering by ionic protein–lipid interactions
    van den Bogaart, Geert, Meyenberg, Karsten, Risselada, H. Jelger, Amin, Hayder, Willig, Katrin I., Hubrich, Barbara E., Dier, Markus, Hell, Stefan W., Grubmüller, Helmut, Diederichsen, Ulf et al. · 2011 · Nature
84. Thermostat Algorithms for Molecular Dynamics Simulations
    Philippe H. Hünenberger · 2005 · Advances in polymer science
85. Analysis of separable potentials
    Gonze, Xavier, Stumpf, Roland, Scheffler, Matthias · 1991 · Physical Review B
86. Preliminary Results from a Recalculation of the Monte Carlo Equation of State of Hard Spheres
    William W. Wood, J. D. Jacobson · 1957 · The Journal of Chemical Physics
87. Computing time scales from reaction coordinates by milestoning.
    Anton Faradjian, R. Elber · 2004 · Journal of Chemical Physics
88. Transport Properties of Polymer Chains in Dilute Solution: Hydrodynamic Interaction
    Hiromi Yamakawa · 1970 · The Journal of Chemical Physics
89. Molecular dynamics without effective potentials via the Car-Parrinello approach
    Dahlia K. Remler, Paul Anthony Madden · 1990 · Molecular Physics
90. Ordering in Two Dimensions
    J. Michael Kosterlitz · 1980 · Springer eBooks
91. Shape transitions of fluid vesicles and red blood cells in capillary flows
    Hiroshi Noguchi, Gerhard Gompper · 2005 · Proceedings of the National Academy of Sciences
92. Microcanonical Monte Carlo Simulation
    Michael J. Creutz · 1983 · Physical Review Letters
93. New Monte Carlo algorithm: Entropic sampling
    Jooyoung Lee · 1993 · Physical Review Letters
94. Towards an exact description of electronic wavefunctions in real solids
    George H. Booth, Andreas Grüneis, Georg Kresse, Ali Alavi · 2012 · Nature
95. Isothermal molecular dynamics calculations for liquid salts
    Leslie V. Woodcock · 1971 · Chemical Physics Letters
96. Liquids and liquid mixtures
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97. Helium at zero temperature with hard-sphere and other forces
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98. A novel path sampling method for the calculation of rate constants
    Titus S. van Erp, Daniele Moroni, Peter G. Bolhuis · 2003 · The Journal of Chemical Physics
99. Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer
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100. Computer ‘‘experiment’’ for nonlinear thermodynamics of Couette flow
     D.J. Evans · 1983 · The Journal of Chemical Physics
101. Algorithms for brownian dynamics
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102. Method for Computing the Anisotropy of the Solid-Liquid Interfacial Free Energy
     J.J. Hoyt, Mark Asta, Alain Karma · 2001 · Physical Review Letters
103. Computer simulations of bilayer membranes: Self-assembly and interfacial tension
     Rüdiger Goetz, Reinhard Lipowsky · 1998 · The Journal of Chemical Physics
104. Numerical Evidence for bcc Ordering at the Surface of a Critical fcc Nucleus
     Pieter Rein ten Wolde, Maria J. Ruiz-Montero, Daan Frenkel · 1995 · Physical Review Letters
105. Gaussian Model Potentials for Molecular Interactions
     B. J. Berne, Philip Pechukas · 1972 · The Journal of Chemical Physics
106. Polarizable force fields
     Thomas A. Halgren, Wolfgang Damm · 2001 · Current Opinion in Structural Biology
107. Theory of Dielectrics: Dielectric Constant and Dielectric Loss
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108. Optimum Monte-Carlo sampling using Markov chains
     Peter H. Peskun · 1973 · Biometrika
109. Efficient molecular dynamics and hybrid Monte Carlo algorithms for path integrals
     Mark E. Tuckerman, B. J. Berne, Glenn J. Martyna, Michael Lawrence Klein · 1993 · The Journal of Chemical Physics
110. Potential-distribution theory and the statistical mechanics of fluids
     B. Widom · 1982 · The Journal of Physical Chemistry
111. How to Mesh up Ewald Sums. I. A Theoretical and Numerical Comparison of Various Particle Mesh Routines
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112. Computer simulation study of gas–liquid nucleation in a Lennard-Jones system
     Pieter Rein ten Wolde, Daan Frenkel · 1998 · The Journal of Chemical Physics
113. Applications of the Monte Carlo Method in Statistical Physics
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114. Grand canonical ensemble Monte Carlo for a Lennard-Jones fluid
     David J. Adams · 1975 · Molecular Physics
115. Ornstein–Zernike Relation and Percus–Yevick Approximation for Fluid Mixtures
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116. Mobility and Elasticity of Self-Assembled Membranes
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117. Structure of water; A Monte Carlo calculation
     John Adair Barker, R.O. Watts · 1969 · Chemical Physics Letters
118. Molecular dynamics simulation of rigid molecules
     Giovanni Ciccotti, Jean-Paul Ryckaert · 1986 · Computer Physics Reports
119. The Analysis of Time Series: An Introduction
     Chris Chatfield · 1984 · Springer eBooks
120. Brownian dynamics as smart Monte Carlo simulation
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121. Water Confined in Nanotubes and between Graphene Sheets: A First Principle Study
     Giancarlo Cicero, Jeffrey C. Grossman, Eric Schwegler, François Gygi, Giulia Galli · 2008 · Journal of the American Chemical Society
122. Computer simulations of liquid/vapor interface in Lennard-Jones fluids: Some questions and answers
     Andrij Trokhymchuk, José Alejandre · 1999 · The Journal of Chemical Physics
123. Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations
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124. Reaction coordinates and rates from transition paths
     Robert B. Best, Gerhard Hummer · 2005 · Proceedings of the National Academy of Sciences
125. Implementing molecular dynamics on hybrid high performance computers – Particle–particle particle-mesh
     W. Michael Brown, Axel Kohlmeyer, Steven J. Plimpton, Arnold Tharrington · 2011 · Computer Physics Communications
126. Stochastic rotation dynamics: A Galilean-invariant mesoscopic model for fluid flow
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127. A molecular dynamics study of liquid drops
     Shannon M. Thompson, Keith E. Gubbins, Jeremy P. R. B. Walton, R. A. R. Chantry, John Shipley Rowlinson · 1984 · The Journal of Chemical Physics
128. Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations
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129. Structure of molten 1,3-dimethylimidazolium chloride using neutron diffraction
     Christopher Hardacre, John D. Holbrey, S. E. Jane McMath, Daniel T. Bowron, Alan K. Soper · 2002 · The Journal of Chemical Physics
130. A polarizable model for water using distributed charge sites
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131. Solute molecular dynamics in a mesoscale solvent
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132. On path integral Monte Carlo simulations
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133. Inadequacy of the Lorentz-Berthelot combining rules for accurate predictions of equilibrium properties by molecular simulation
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134. Ensemble Dependence of Fluctuations with Application to Machine Computations
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135. Singularity free algorithm for molecular dynamics simulation of rigid polyatomics
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136. Phase diagrams of Lennard-Jones fluids
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137. Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 2. A benchmark for the objective comparison of alternative force fields
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138. Thermodynamic Properties of the Fluid and Solid Phases for Inverse Power Potentials
     William Graham Hoover, Steven G. Gray, Keith W. Johnson · 1971 · The Journal of Chemical Physics
139. How van der Waals interactions determine the unique properties of water
     Tobias Morawietz, Andreas Singraber, Christoph Dellago, Jörg Behler · 2016 · Proceedings of the National Academy of Sciences
140. Versatile object-oriented toolkit for coarse-graining applications
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141. Transition Path Sampling
     Christoph Dellago, Peter G. Bolhuis, Phillip L. Geissler · 2002 · Advances in chemical physics
142. Dense-fluid shear viscosity via nonequilibrium molecular dynamics
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143. Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution
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144. An Introduction to Probability Theory and its Applications.
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145. Reversing the perturbation in nonequilibrium molecular dynamics: An easy way to calculate the shear viscosity of fluids
     Florian Müller‐Plathe · 1999 · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
146. Forward flux sampling for rare event simulations
     Rosalind J. Allen, Chantal Valeriani, Pieter Rein ten Wolde · 2009 · Journal of Physics Condensed Matter
147. Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations
     Joseph E. Basconi, Michael R. Shirts · 2013 · Journal of Chemical Theory and Computation
148. The role of local structure in dynamical arrest
     C. Patrick Royall, Stephen R. Williams · 2014 · Physics Reports
149. The Nosé–Poincaré Method for Constant Temperature Molecular Dynamics
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150. Monte Carlo calculation of the surface tension for two- and three-dimensional lattice-gas models
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151. Untitled work
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152. Acceleration of convergence for lattice sums
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153. Good Parameters and Implementations for Combined Multiple Recursive Random Number Generators
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154. Hydrodynamic interactions and Brownian forces in colloidal suspensions: Coarse-graining over time and length scales
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155. Monte Carlo Equation of State of Molecules Interacting with the Lennard-Jones Potential. I. A Supercritical Isotherm at about Twice the Critical Temperature
     William W. Wood, F. R. Parker · 1957 · The Journal of Chemical Physics
156. Pressure tensor for inhomogeneous fluids
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157. Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N‐methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases
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158. A uniqueness theorem for fluid pair correlation functions
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159. Accurate sampling using Langevin dynamics
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160. Efficient stochastic thermostatting of path integral molecular dynamics
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161. Monte Carlo simulations: Hidden errors from ‘‘good’’ random number generators
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162. Gaussian split Ewald: A fast Ewald mesh method for molecular simulation
     Yibing Shan, John L. Klepeis, Michael P. Eastwood, Ron O. Dror, David Elliot Shaw · 2005 · The Journal of Chemical Physics
163. Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly
     Matej Praprotnik, Luigi Delle Site, Kurt Kremer · 2005 · The Journal of Chemical Physics
164. Fluctuation-Dissipation: Response Theory in Statistical Physics
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165. The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models
     William G. Noid, Pu Liu, Yanting Wang, Jhih‐Wei Chu, Gary S. Ayton, Sergei Izvekov, Hans C. Andersen, Gregory A. Voth · 2008 · The Journal of Chemical Physics
166. Nonlinear-response theory for steady planar Couette flow
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167. Chemical reaction rates from ring polymer molecular dynamics
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168. Simulation of a single polymer chain in solution by combining lattice Boltzmann and molecular dynamics
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169. On the Calculation of Time Correlation Functions
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170. A quantum-statistical Monte Carlo method; path integrals with boundary conditions
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171. Obtaining reaction coordinates by likelihood maximization
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172. From transition paths to transition states and rate coefficients
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173. The role of long ranged forces in determining the structure and properties of liquid water
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174. To milliseconds and beyond: challenges in the simulation of protein folding
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175. Statistical Associating Fluid Theory: A Successful Model for the Calculation of Thermodynamic and Phase Equilibrium Properties of Complex Fluid Mixtures
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176. Homogeneous NEMD algorithm for thermal conductivity—Application of non-canonical linear response theory
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177. Soft-Sphere Equation of State
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178. Hydrodynamic boundary conditions, correlation functions, and Kubo relations for confined fluids
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179. Numerical integration of the Langevin equation: Monte Carlo simulation
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180. The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition
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181. Chemical potential of hard-sphere fluids by Monte Carlo methods
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182. Test-area simulation method for the direct determination of the interfacial tension of systems with continuous or discontinuous potentials
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183. A Course in Statistical Mechanics
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184. Simulating rare events in equilibrium or nonequilibrium stochastic systems
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185. Simulation of polymer dynamics. I. General theory
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186. Gibbs-Duhem integration: a new method for direct evaluation of phase coexistence by molecular simulation
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187. Statistical mechanics of inhomogeneous fluids
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188. Brownian motion in thin sheets of viscous fluid
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189. Polarizable Force Fields: History, Test Cases, and Prospects
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