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Note: Molecular dynamics studies of high-density amorphous ice: Influence of long-range Coulomb interactions

Markus Seidl, Ferenc Karsai, Thomas Loerting, Gerhard Zifferer
2012 Journal of Chemical Physics  
Comparison of the critical point of the liquid-liquid transition of ST2 water regarding long-range Coulomb interactions by Ewald summation to a study with truncated electrostatic interactions 11 reveals  ...  The method adopted is described in Ref. 6 and only briefly reproduced here for convenience of the reader: Constant pressure and temperature molecular dynamics simulations (NpT) are performed by use of  ...  Comparison of the critical point of the liquid-liquid transition of ST2 water regarding long-range Coulomb interactions by Ewald summation to a study with truncated electrostatic interactions 11 reveals  ... 
doi:10.1063/1.3676058 pmid:22260617 fatcat:cgcxup2mgjehldnfjevxs4bnre

Learning intermolecular forces at liquid-vapor interfaces [article]

Samuel P. Niblett, Mirza Galib, David T. Limmer
2021 arXiv   pre-print
We demonstrate this perspective in a simple model of an asymmetric dipolar fluid where the exact long-ranged interaction is known, and in an ab initio water model where it is approximated.  ...  depend on unbalanced long-ranged interactions which build up in the presence of broken translation symmetry.  ...  Department of Energy, Office of Science, Of-  ... 
arXiv:2107.06208v2 fatcat:nn6gqxfctjd2libfsiv65o6txe

Molecular modeling of aqueous electrolytes at interfaces: effects of long-range dispersion forces and of ionic charge rescaling [article]

Guillaume Le Breton, Laurent Joly
2020 arXiv   pre-print
Molecular dynamics simulations of aqueous electrolytes generally rely on empirical force fields, combining dispersion interactions - described by a truncated Lennard-Jones (LJ) potential - and electrostatic  ...  repulsion at the liquid-vapor interface, and that the rescaling of LJ parameters in ECCR models - aimed at capturing local ion-ion and ion-water interactions in bulk - also describes well the formation  ...  INTRODUCTION Molecular dynamics (MD) is a very powerful tool to explore the structure and dynamics of aqueous electrolytes at the atomic scale.  ... 
arXiv:2004.07702v2 fatcat:jnhaw3womfcixofy733dlmqh6y

Realistic Modelling of Dynamics at Nanostructured Interfaces Relevant to Heterogeneous Catalysis

Kevin Rossi, Tzonka Mineva, Jean-Sebastien Filhol, Frederik Tielens, Hazar Guesmi
2022 Catalysts  
of its interaction with the support.  ...  This short review aims to offer the reader a birds-eye view of state-of-the-art methods that enable more realistic simulation of dynamical phenomena at nanostructured interfaces by exploiting resource-efficient  ...  [37] , who used multiscale quantum mechanics/molecular mechanics (QM/MM) simulations exploiting force fields and tight-binding methods to unravel the short-range and long-range arrangement of water molecules  ... 
doi:10.3390/catal12010052 fatcat:emst55tct5djxht4s5qu3moeva

Multi-scale Modeling of Structure, Dynamic and Thermodynamic Properties of Imidazolium-based Ionic Liquids: Ab initio DFT Calculations, Molecular Simulation and Equation of State Predictions

I. G. Economou, E. K. Karakatsani, G.-E. Logotheti, J. Ramos, A. A. Vanin
2008 Oil & Gas Science and Technology  
In this work, microscopic structure, dynamic and thermodynamic properties of imidazolium-based ionic liquids are calculated using theoretical models that cover a wide range of length and time scales, from  ...  Abstract -Multi-scale Modeling of Structure, Dynamic and Thermodynamic Properties of Imidazolium-based Ionic Liquids: Ab initio DFT Calculations, Molecular Simulation and Equation of State Predictions  ...  2 molecule with the IL were simulated as a summation of short-range Lennard-Jones interactions and of Coulombic interactions between charges using the Ewald summation method.  ... 
doi:10.2516/ogst:2008007 fatcat:dgzwpoifuvg3dblfvzbct2gbxi

Molecular modelling and simulation of electrolyte solutions, biomolecules, and wetting of component surfaces [article]

Martin Horsch and Stefan Becker and Juan Manuel Castillo and Stephan Deublein and Agnes Fröscher and Steffen Reiser and Stephan Werth and Jadran Vrabec and Hans Hasse
2013 arXiv   pre-print
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces.  ...  Thereby, Ewald summation methods are used to compute the long range electrostatic interactions.  ...  Acknowledgements The present work was carried out under the auspices of the Boltzmann-Zuse Society for Computational Molecular Engineering (BZS), and the molecular simulations were conducted on the XC4000  ... 
arXiv:1305.4048v1 fatcat:erqcyw2knng5jcufzbb6oczski

Molecular Modelling and Simulation of Electrolyte Solutions, Biomolecules, and Wetting of Component Surfaces [chapter]

M. Horsch, S. Becker, J. M. Castillo, S. Deublein, A. Fröscher, S. Reiser, S. Werth, J. Vrabec, H. Hasse
2013 High Performance Computing in Science and Engineering '13  
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces.  ...  Thereby, Ewald summation methods are used to compute the long range electrostatic interactions.  ...  Acknowledgements The present work was carried out under the auspices of the Boltzmann-Zuse Society for Computational Molecular Engineering (BZS), and the molecular simulations were conducted on the XC4000  ... 
doi:10.1007/978-3-319-02165-2_45 fatcat:5cipypohhvdpdm66a6y3i4jble

Comparison of Activation Energy and Pore Dynamics in Liquid and Gel Phases of Electroporated Lipid Bilayers using Temperature Dependent MD Simulations

Amit K. Majhi, Subbarao Kanchi, Venki Venkataraman, Ganapathy Ayappa, Prabal Maiti
2015 Biophysical Journal  
boiled (range 40 -70 C) or lysed in a 900-watt microwave on isolator-mounted microscope slides, both with and without the assistance of disjointed antenna gold bow-tie structures.  ...  PCR results suggest that low power microwave irradiation is ideal for PCR methods while higher microwave powers are required to generate DNA fragments 1586-Pos Board B537 Molecular Modeling of Self-Assembly  ...  We have performed molecular dynamics simulation(MDS) of electroporation at different temperatures to find activation energy as well as pore dynamics in the gel and liquid phases of POPC and DPPC lipid  ... 
doi:10.1016/j.bpj.2014.11.1715 fatcat:nztdcho4kjg23ksjnmfe4rd4bi

A temperature of maximum density in soft sticky dipole water

Ming-Liang Tan, Justin T. Fischer, Amalendu Chandra, Bernard R. Brooks, Toshiko Ichiye
2003 Chemical Physics Letters  
A temperature of maximum density near 260 K at 1 atm has been found for the soft sticky dipole (SSD) water model in molecular dynamics simulations.  ...  The parameters of SSD have been optimized to reproduce the density of water as well as other structural, thermodynamic, dielectric, and dynamic properties at room temperature and 1 atm.  ...  Acknowledgements We are grateful to the National Science Foundation for the support of this work through Grant number MCB-0131780.  ... 
doi:10.1016/s0009-2614(03)01044-3 fatcat:klm2ogjisfcktkcsxnfcwgfmnm

Pair correlation function integrals: Computation and use

Rasmus Wedberg, John P. O'Connell, Günther H. Peters, Jens Abildskov
2011 Journal of Chemical Physics  
We describe a method for extending radial distribution functions obtained from molecular simulations of pure and mixed molecular fluids to arbitrary distances.  ...  We describe the numerical implementation of the method in detail, and report numerical tests complementing previous results.  ...  ACKNOWLEDGMENTS The authors gratefully acknowledge access to the Danish Center of Scientific Computing at the University of Southern Denmark, Odense, Denmark. R.  ... 
doi:10.1063/1.3626799 pmid:21895165 fatcat:qd2mpkfzyrc6jpikl2hvihto5i

A Stochastic Algorithm for the Isobaric–Isothermal Ensemble with Ewald Summations for All Long Range Forces

Michele Di Pierro, Ron Elber, Benedict Leimkuhler
2015 Journal of Chemical Theory and Computation  
We present an algorithm, COMPEL, (COnstant Molecular Pressure with Ewald sum for Long range forces) to conduct simulations in the NPT ensemble.  ...  COMPEL exploits the concepts of molecular pressure, rapid stochastic relaxation to equilibrium, exact calculation of the contribution to the pressure of long range non-bonded forces with Ewald summation  ...  Thanks also to Alfredo Cardenas and Daniel Walker for helping with the set up of the systems and some simulations.  ... 
doi:10.1021/acs.jctc.5b00648 pmid:26616351 pmcid:PMC4890727 fatcat:gtix4rjuibh7heqgmxofkol5oe

Signature properties of water: Their molecular electronic origins

Vlad P. Sokhan, Andrew P. Jones, Flaviu S. Cipcigan, Jason Crain, Glenn J. Martyna
2015 Proceedings of the National Academy of Sciences of the United States of America  
It exhibits a uniquely rich phenomenology including dramatic variations in behavior over the wide temperature range of the liquid into water's crystalline phases and amorphous states.  ...  Water challenges our fundamental understanding of emergent materials properties from a molecular perspective.  ...  Finitetemperature condensed phase simulation of the QDO model in the NVT, NpT, and NpT-flex ensembles were performed using the adiabatic path integral molecular dynamics for QDOs (APIMD-QDO) method (19  ... 
doi:10.1073/pnas.1418982112 pmid:25941394 pmcid:PMC4443379 fatcat:76meljwagjebnogzvrulteaewq

Nanoscale ice fracture by molecular dynamics simulations [article]

A. Afshar, J. Zhong, D. S. Thompson, D. Meng
2019 arXiv   pre-print
In this work, we conducted molecular dynamics simulations to study the fracture mechanism of ice crystals in a bulk phase and at ice-ice interfaces at the atomistic scale.  ...  This result illustrates the dominant role played by the small amount of disordered water molecules at interface in altering mechanical strength of an interfacial structure.  ...  Acknowledgments The authors gratefully acknowledge the National Aeronautics and Space Administration (NASA) for the sponsor and financial support in the project of "Multiscale Physics-Based Modeling of  ... 
arXiv:1907.09018v1 fatcat:fuld5gvorvgp3obcfrmy6e4ufq

Studies on molecular dynamics of intrinsically disordered proteins and their fuzzy complexes: A mini-review

Kota Kasahara, Hiroki Terazawa, Takuya Takahashi, Junichi Higo
2019 Computational and Structural Biotechnology Journal  
Recent advances in MD methods, and computational power make it possible to dissect the molecular details of realistic molecular systems involving the dynamic behavior of IDRs.  ...  Then, several examples of the applications of MD to investigate molecular interactions of IDRs in terms of the two kinds of complex formations; coupled-folding and binding and fuzzy complex.  ...  A major concern in using non-Ewald methods is that artifacts arise from the cutoff truncation of long-range electrostatic potential.  ... 
doi:10.1016/j.csbj.2019.06.009 pmid:31303975 pmcid:PMC6603302 fatcat:pvcx57a7djclbanmfwrvslujrm

Electronic coarse graining enhances the predictive power of molecular simulation allowing challenges in water physics to be addressed

Flaviu S. Cipcigan, Vlad P. Sokhan, Jason Crain, Glenn J. Martyna
2016 Journal of Computational Physics  
One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field.  ...  , Curtiss and Bird [The Molecular Theory of Gases and Liquids (1954)].  ...  ab initio methods and all-atom molecular dynamics.  ... 
doi:10.1016/j.jcp.2016.08.030 fatcat:ka7kenk3kjfitf6bih3rpqbjoi
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