Computer Simulation of Liquids

Cited by (1,031)

Items 801–900 of 1,031

1. High-resolution protein–protein docking
   Jeffrey J. Gray · 2006 · Current Opinion in Structural Biology
2. Coarse-Grained Modeling of the Actin Filament Derived from Atomistic-Scale Simulations
   Jhih‐Wei Chu, Gregory A. Voth · 2005 · Biophysical Journal
3. The Formation and Dynamics of Proton Wires in Channel Environments
   Mark L. Brewer, Udo W. Schmitt, Gregory A. Voth · 2001 · Biophysical Journal
4. Microscopic expressions for the thermodynamic temperature
   Owen G. Jepps, Gary S. Ayton, Denis J. Evans · 2000 · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
5. Molecular dynamics simulation on bubble formation in a nanochannel
   Gyoko Nagayama, Takaharu Tsuruta, Ping Cheng C · 2006 · International Journal of Heat and Mass Transfer
6. Metal Cation Complexation with Natural Organic Matter in Aqueous Solutions: Molecular Dynamics Simulations and Potentials of Mean Force
   Eugenia Iskrenova-Tchoukova, Andrey G. Kalinichev, R. James Kirkpatrick · 2010 · Langmuir
7. Fractional Stokes-Einstein and Debye-Stokes-Einstein Relations in a Network-Forming Liquid
   Stephen Becker, Peter H. Poole, Francis W. Starr · 2006 · Physical Review Letters
8. Influence of periodic wall roughness on the slip behaviour at liquid/solid interfaces: molecular-scale simulations versus continuum predictions
   Nikolai V. Priezjev, Sandra M. Troian · 2006 · Journal of Fluid Mechanics
9. Molecular dynamics simulation of vaporization of an ultra-thin liquid argon layer on a surface
   Pan Yi, Dimos Poulikakos A, Jens Honoré Walther, G. Yadigaroglu · 2002 · International Journal of Heat and Mass Transfer
10. Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors
    Iman Jeddi, Leonor Saiz · 2017 · Scientific Reports
11. A 3-D discrete-element method for dry granular flows of ellipsoidal particles
    Loc Vu‐Quoc, X Zhang, Otis R. Walton · 2000 · Computer Methods in Applied Mechanics and Engineering
12. Adaptive Partitioning in Combined Quantum Mechanical and Molecular Mechanical Calculations of Potential Energy Functions for Multiscale Simulations
    Andreas Heyden, Hai Lin, Donald G. Truhlar · 2007 · The Journal of Physical Chemistry B
13. Molecular-dynamics simulations of methane hydrate dissociation
    Niall J. English, J. Karl Johnson, CHARLES E. TAYLOR · 2005 · The Journal of Chemical Physics
14. Heterogeneous multiscale method for the modeling of complex fluids and micro-fluidics
    Weiqing Ren, E Weinan · 2004 · Journal of Computational Physics
15. Identification and Validation of a Discrete Element Model for Concrete
    Sébastien Hentz, L. Daudeville, Frédéric‐Victor Donzé · 2004 · Journal of Engineering Mechanics
16. Algorithmic Challenges in Computational Molecular Biophysics
    Tamar Schlick A, Robert D. Skeel, Axel T. Brünger, Laxmikant V. Kalé, John A Board, Jan Hermans, Klaus J. Schulten · 1999 · Journal of Computational Physics
17. Beyond the Van Der Waals loop: What can be learned from simulating Lennard-Jones fluids inside the region of phase coexistence
    Kurt Binder, Benjamin Blöck, Peter Virnau, A. Tröster · 2012 · American Journal of Physics
18. Influence of particle shape on the packing and on the segregation of spherocylinders via Monte Carlo simulations
    Charlles R. A. Abreu, Frederico Wanderley Tavares, Marcelo Castier · 2003 · Powder Technology
19. Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation
    Mika A. Kastenholz, Philippe H. Hünenberger · 2006 · The Journal of Chemical Physics
20. A new empirical potential for simulating the formation of defects and their mobility in uranium dioxide
    N.-D. Morelon, D. Ghaleb, Jean‐Marc Delaye, L. Van Brutzel · 2003 · The Philosophical Magazine A Journal of Theoretical Experimental and Applied Physics
21. Rational design of liposomal drug delivery systems, a review: Combined experimental and computational studies of lipid membranes, liposomes and their PEGylation
    Alex Bunker, Aniket Magarkar, Tapani Viitala · 2016 · Biochimica et Biophysica Acta (BBA) - Biomembranes
22. Advances in nonequilibrium molecular dynamics simulations of lubricants and additives
    James Patrick Ewen, David M. Heyes, Daniele Dini · 2018 · Friction
23. A critical comparison of equilibrium, non-equilibrium and boundary-driven molecular dynamics techniques for studying transport in microporous materials
    Gaurav Arya, Hsueh‐Chia Chang, Edward Joseph Maginn · 2001 · The Journal of Chemical Physics
24. Structure, dynamics, and thermodynamics of model (H2O)8 and (H2O)20 clusters
    David J. Wales, Iwao Ohmine · 1993 · The Journal of Chemical Physics
25. Cation Transport in Polymer Electrolytes: A Microscopic Approach
    Arijit Maitra, Andreas Heuer · 2007 · Physical Review Letters
26. Neighbor list collision-driven molecular dynamics simulation for nonspherical hard particles.
    Aleksandar Donev, Salvatore Torquato A, Frank H. Stillinger · 2004 · Journal of Computational Physics
27. Thermostating highly confined fluids
    Stefano Bernardi, Billy D. Todd, Debra J. Searles · 2010 · The Journal of Chemical Physics
28. Modelling of nanoparticles: approaches to morphology and evolution
    Amanda Susan Barnard · 2010 · Reports on Progress in Physics
29. Theory and simulation of jump dynamics, diffusion and phase equilibrium in nanopores
    Scott M. Auerbach · 2000 · International Reviews in Physical Chemistry
30. Molecular simulations of carbohydrates and protein–carbohydrate interactions: motivation, issues and prospects
    Elisa Fadda, Robert J. Woods · 2010 · Drug Discovery Today
31. Dynamics of fluid flow inside carbon nanotubes
    Robert E. Tuzun, Donald W. Noid, Bobby G. Sumpter, Ralph C. Merkle · 1996 · Nanotechnology
32. Molecular Dynamics Simulations of Lipid Membrane Electroporation
    Lucie Delemotte, Mounir Tarek · 2012 · The Journal of Membrane Biology
33. Potential models for simulations of the solvated proton in water
    Lars Ojamäe, Isaiah Shavitt, Sherwin J. Singer · 1998 · The Journal of Chemical Physics
34. Nuclear Quantum Effects and Enzyme Dynamics in Dihydrofolate Reductase Catalysis
    Pratul K. Agarwal, Salomon R. Billeter, Sharon Hammes‐Schiffer · 2002 · The Journal of Physical Chemistry B
35. Fragility and cooperative motion in a glass-forming polymer–nanoparticle composite
    Beatriz A. Pazmiño Betancourt, Jack F. Douglas, Francis W. Starr · 2012 · Soft Matter
36. Pseudo-random number generation for Brownian Dynamics and Dissipative Particle Dynamics simulations on GPU devices
    Carolyn L. Phillips, Joshua A. Anderson, Sharon C. Glotzer · 2011 · Journal of Computational Physics
37. A super-linear minimization scheme for the nudged elastic band method
    J. Chu, B. Trout, B. Brooks · 2003 · The Journal of Chemical Physics
38. Nano-engineering of construction materials using molecular dynamics simulations: Prospects and challenges
    Denvid Lau, Wei Jian, Zechuan Yu, David Hui · 2018 · Composites Part B Engineering
39. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples
    Michael Holst, Nathan Baker, F. Wang · 2000 · Journal of Computational Chemistry
40. Structural change and receptor binding in a chemokine mutant with a rearranged disulfide: X-ray structure of e38C/C50A IL-8 at 2 Å resolution
    Charles W. Eigenbrot, Henry B. Lowman, Linda Chee, Dean R. Artis · 1997 · Proteins Structure Function and Bioinformatics
41. Multidimensional infrared spectroscopy of water. II. Hydrogen bond switching dynamics
    Joseph J. Loparo, Sean T. Roberts, Andrei Tokmakoff · 2006 · The Journal of Chemical Physics
42. A computational investigation of thermodynamics, structure, dynamics and solvation behavior in modified water models
    Swaroop Chatterjee, Pablo G. Debenedetti, Frank H. Stillinger, Ruth Marion Lynden-Bell · 2008 · The Journal of Chemical Physics
43. Flow Effects on Melt Structure and Entanglement Network of Linear Polymers: Results from a Nonequilibrium Molecular Dynamics Simulation Study of a Polyethylene Melt in Steady Shear
    Chunggi Baig, Vlasis George Mavrantzas, Martin Kröger · 2010 · Macromolecules
44. Allostery of actin filaments: Molecular dynamics simulations and coarse-grained analysis
    Jhih‐Wei Chu, Gregory A. Voth · 2005 · Proceedings of the National Academy of Sciences
45. Variable reaction coordinate transition state theory: Analytic results and application to the C2H3+H→C2H4 reaction
    Yuri Georgievskii, Stephen J. Klippenstein · 2003 · The Journal of Chemical Physics
46. Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulations of systems with square-well interactions
    Yaoqi Zhou, Martin Karplus, John M. Wichert, Carol K. Hall · 1997 · The Journal of Chemical Physics
47. Dynamics of prolate ellipsoidal particles in a turbulent channel flow
    Pal H. Mortensen, Helge I. Andersson, J. J. J. Gillissen, Bendiks Jan Boersma · 2008 · Physics of Fluids
48. Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method
    D. Das, Kirsten P. Eurenius, E. Billings, P. Sherwood, David C. Chatfield, M. Hodošček, B. Brooks · 2002 · The Journal of Chemical Physics
49. Energetics of atomic scale structure changes in graphene
    Stephen T. Skowron, Irina V. Lebedeva, А. М. Попов, Elena Besley · 2015 · Chemical Society Reviews
50. Langevin stabilization of molecular-dynamics simulations of polymers by means of quasisymplectic algorithms
    Luca Larini, R. Mannella, D. Leporini · 2007 · The Journal of Chemical Physics
51. Adsorption and separation of hydrogen isotopes in carbon nanotubes: Multicomponent grand canonical Monte Carlo simulations
    Sivakumar R. Challa, David S. Sholl, J. Karl Johnson · 2002 · The Journal of Chemical Physics
52. 111 years of Brownian motion
    Xin Bian, Changho Kim, George Em Karniadakis · 2016 · Soft Matter
53. Materials science in the artificial intelligence age: high-throughput library generation, machine learning, and a pathway from correlations to the underpinning physics
    Rama Krishnan Vasudevan, Kamal Kumar Choudhary, Apurva Mehta, Ryan P. Smith, Aaron Gilad Kusne, Francesca Tavazza, Lukáš Vlček, Maxim A Ziatdinov, Sergei V. Kalinin, Jason R. Hattrick-Simpers · 2019 · MRS Communications
54. A highly distorted ultraelastic chemically complex Elinvar alloy
    Quanfeng He, J. G. Wang, Hsin‐An Chen, Zhaoyi Ding, Ziqing Zhou, Lianghua Xiong, Junhua Luan, J.M. Pelletier, J.C. Qiao, Qiang Wang et al. · 2022 · Nature
55. A QM/MM simulation method applied to the solution of Li+ in liquid ammonia
    Teerakiat Kerdcharoen, Klaus Roman Liedl, Bernd Michael Rode · 1996 · Chemical Physics
56. Determination of symmetries and idealized cell parameters for simulated structures
    Rudolf Hundt, J. Christian Scho ̈n, A. Hannemann, Martin Jansen · 1999 · Journal of Applied Crystallography
57. Absolute entropies from molecular dynamics simulation trajectories
    Heiko Schäfer, Alan Edward Mark, Wilfred F. Van Gunsteren A · 2000 · The Journal of Chemical Physics
58. Atomic packing in multicomponent aluminum-based metallic glasses
    H. W. Sheng, Yongqiang Q. Cheng, P. L. Lee, S. D. Shastri, Evan Ma · 2008 · Acta Materialia
59. Interaction potentials for alumina and molecular dynamics simulations of amorphous and liquid alumina
    Priya D. Vashishta, Rajiv K. Kalia, Aiichiro Nakano, José Pedro Rino · 2008 · Journal of Applied Physics
60. Ion Conduction and Selectivity in K + Channels
    Benoı̂t Roux · 2005 · Annual Review of Biophysics and Biomolecular Structure
61. Solvent effects in emission spectroscopy: A Monte Carlo quantum mechanics study of the n←π* shift of formaldehyde in water
    Kaline Coutinho, Sylvio Canuto · 2000 · The Journal of Chemical Physics
62. A critical study of the simulation of the liquid-vapour interface of a Lennard-Jones fluid
    Cynthia D. Holcomb, Paulette Clancy, John A. Zollweg · 1993 · Molecular Physics
63. Nonadiabatic Excited-State Molecular Dynamics Modeling of Photoinduced Dynamics in Conjugated Molecules
    Tammie Nelson, Sebastian Fernández-Alberti, Vladimir Chernyak, Adrián E. Roitberg, Sergei Tretiak · 2011 · The Journal of Physical Chemistry B
64. Large-scale powder mixer simulations using massively parallel GPUarchitectures
    Charles A. Radeke, Benjamin J. Glasser, Johannes Khinast · 2010 · Chemical Engineering Science
65. Structure and dynamics of water confined in silica nanopores
    Anatoli A. Milischuk, Branka M. Ladanyi · 2011 · The Journal of Chemical Physics
66. Molecular dynamics simulations of thermal resistance at the liquid-solid interface
    BoHung Kim, Ali Beşkök, Tahir Cagin B · 2008 · The Journal of Chemical Physics
67. Predicting Hydrogen Storage in Mofs via Machine Learning
    Alauddin Ahmed, Donald J. Siegel · 2020 · Patterns
68. Structural modification aimed for improving solubility of lead compounds in early phase drug discovery
    Bhanuranjan Das, Anurag T. K. Baidya, Alen T. Mathew, Ashok Kumar Yadav, Rajnish Kumar · 2022 · Bioorganic & Medicinal Chemistry
69. Fusion pathways of vesicles: A Brownian dynamics simulation
    Hiroshi Noguchi, Masako Takasu · 2001 · The Journal of Chemical Physics
70. Molecular simulation of water confined in nanoporous silica
    Bonnaud, P A, Coasne, B, Pellenq, R J-M · 2010 · Journal of Physics: Condensed Matter
71. A smoothed particle hydrodynamics model for miscible flow in three-dimensional fractures and the two-dimensional Rayleigh–Taylor instability
    Alexandre M. Tartakovsky, Paul Meakin · 2005 · Journal of Computational Physics
72. Molecular dynamics simulation of hydroxyapatite–polyacrylic acid interfaces
    Rahul Bhowmik, Kalpana S. Katti, Dinesh R. Katti · 2006 · Polymer
73. Amorphous ices: experiments and numerical simulations
    Thomas Loerting, Nicolás Giovambattista · 2006 · Journal of Physics Condensed Matter
74. Towards in Silico Liquid Crystals. Realistic Transition Temperatures and Physical Properties for n‐Cyanobiphenyls via Molecular Dynamics Simulations
    Giustiniano Tiberio, Luca Muccioli, Roberto Berardi, Claudio Zannoni A · 2008 · ChemPhysChem
75. Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the Ewald potential
    Stephen Bogusz, Thomas E. Cheatham, Bernard R. Brooks · 1998 · The Journal of Chemical Physics
76. From Topographies to Dynamics on Multidimensional Potential Energy Surfaces of Atomic Clusters
    Keith D. Ball, R. Stephen Berry, Ralph E. Kunz, Feng‐Yin Li, Ana Proykova, David J. Wales · 1996 · Science
77. α‐Helix formation: Discontinuous molecular dynamics on an intermediate‐resolution protein model
    Anne Voegler Smith, Carol K. Hall · 2001 · Proteins Structure Function and Bioinformatics
78. A smoothed particle hydrodynamics model for reactive transport and mineral precipitation in porous and fractured porous media
    Alexandre M. Tartakovsky, Paul Meakin, Tim Scheibe, Brian D. Wood · 2007 · Water Resources Research
79. Pressure-driven water flow through carbon nanotubes: Insights from molecular dynamics simulation
    John A. Thomas, Alan J. H. McGaughey, Ottoleo Kuter-Arnebeck · 2009 · International Journal of Thermal Sciences
80. Symmetry breaking and morphological instabilities in core-shell metallic nanoparticles
    Riccardo Ferrando · 2014 · Journal of Physics Condensed Matter
81. Simulation of binary mixture adsorption of methane and CO2 at supercritical conditions in carbons
    Yohanes Kurniawan, Suresh K. Bhatia, Victor Rudolph · 2005 · AIChE Journal
82. A simulation technique for many spheres in quasi-static motion under frame-invariant pair drag and Brownian forces
    R. C. Ball, J. R. Melrose · 1997 · Physica A Statistical Mechanics and its Applications
83. Machine learning with force-field-inspired descriptors for materials: Fast screening and mapping energy landscape
    Kamal Kumar Choudhary, Brian DeCost, Francesca Tavazza · 2018 · Physical Review Materials
84. Folding Rate Prediction Using Total Contact Distance
    Hongyi Zhou, Yaoqi Zhou · 2002 · Biophysical Journal
85. Prediction of the thermodynamic properties of associating Lennard-Jones fluids: Theory and simulation
    Walter G. Chapman · 1990 · The Journal of Chemical Physics
86. Structural solution using molecular dynamics: Fundamentals and a case study of epoxy-silica interface
    Oral Büyüköztürk, Markus J. Buehler, Denvid Lau, Chakrapan Tuakta · 2011 · International Journal of Solids and Structures
87. Theory of binless multi-state free energy estimation with applications to protein-ligand binding
    Zhiqiang Tan, Emilio Gallicchio, Mauro Lapelosa, Ronald M. Levy · 2012 · The Journal of Chemical Physics
88. Flow patterns in the sedimentation of an elliptical particle
    Zhenhua Xia, Kevin W. Connington, Saikiran Rapaka, Pengtao Yue, James J. Feng, Shiyi Chen · 2009 · Journal of Fluid Mechanics
89. Normal and Shear Forces Between Polymer Brushes
    Gary S. Grest · 1999 · Advances in polymer science
90. Simulations of ice and liquid water over a range of temperatures using the fluctuating charge model
    Steven W. Rick · 2001 · The Journal of Chemical Physics
91. Electrostatic DFT Map for the Complete Vibrational Amide Band of NMA
    Tomoyuki Hayashi, Wei Zhuang, Shaul Mukamel · 2005 · The Journal of Physical Chemistry A
92. On the computation of crystalline microstructure
    Mitchell Luskin · 1996 · Acta Numerica
93. Structure calculation of biological macromolecules from NMR data
    Peter Güntert · 1998 · Quarterly Reviews of Biophysics
94. Computational modeling and simulation of nanoparticle self-assembly in polymeric systems: Structures, properties and external field effects
    Li‐Tang Yan, Xu‐Ming Xie · 2012 · Progress in Polymer Science
95. Research progress, models and simulation of electrospinning technology: a review
    Yajin Guo, Xinyu Wang, Ying Shen, Kuo Dong, Linyi Shen, Asmaa Ahmed Abdullah Alzalab · 2021 · Journal of Materials Science
96. A quantum molecular-dynamics study of proton-transfer reactions along asymmetrical H bonds in solution
    H. Azzouz, Daniel Borgis · 1993 · The Journal of Chemical Physics
97. First-Order Disorder-to-Order Transition in an Isolated Homopolymer Model
    Yaoqi Zhou, Carol K. Hall, Martin Karplus · 1996 · Physical Review Letters
98. Particle mesh Ewald method for three-dimensional systems with two-dimensional periodicity
    Masaaki Kawata, Umpei Nagashima · 2001 · Chemical Physics Letters
99. Poromechanics of microporous media
    Laurent Brochard, Matthieu Vandamme, Roland J.‐M. Pellenq · 2012 · Journal of the Mechanics and Physics of Solids
100. Force Field for Molecular Dynamics Computations in Flexible ZIF-8 Framework
     Bin Zheng, Marco Sant, Pierfranco Demontis, Giuseppe B. Suffritti · 2011 · The Journal of Physical Chemistry C