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Note: Molecular dynamics studies of high-density amorphous ice: Influence of long-range Coulomb interactions
2012
Journal of Chemical Physics
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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]
2021
arXiv
pre-print
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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]
2020
arXiv
pre-print
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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
2022
Catalysts
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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
2008
Oil & Gas Science and Technology
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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]
2013
arXiv
pre-print
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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]
2013
High Performance Computing in Science and Engineering '13
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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
2015
Biophysical Journal
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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
2003
Chemical Physics Letters
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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
2011
Journal of Chemical Physics
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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
2015
Journal of Chemical Theory and Computation
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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
2015
Proceedings of the National Academy of Sciences of the United States of America
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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]
2019
arXiv
pre-print
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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
2019
Computational and Structural Biotechnology Journal
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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
2016
Journal of Computational Physics
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2016 pre-print arXiv:1609.03077v1 fatcat:2pbrypqalnf57gzytlwilk6bem
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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