Quiet high-resolution computer models of a plasma

Hockney, Roger W.; Goel, Saurav; Eastwood, J.W.

doi:10.1016/0021-9991(74)90010-2

Cited by 1,017 publications

(644 citation statements)

References 10 publications

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“…The simulations were conducted using the Groningen Machine for Chemical Simulations (GROMACS) simulation package, version 4.5.5. 24,25 The leapfrog algorithm 26 with time steps of 1 fs was implemented. Simulations were conducted for 100 ns of simulation time for all systems investigated.…”

Section: Simulation Models and Methodsologymentioning

confidence: 99%

N-octane diffusivity enhancement via carbon dioxide in silica slit-shaped nanopores – a molecular dynamics simulation

Ogbe

Striolo

et al. 2015

Molecular Simulation

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Equilibrium molecular dynamics simulations were conducted to study the competitive adsorption and diffusion of mixtures containing n-octane and carbon dioxide confined in slitshaped silica pores of width 1.9 nm. Atomic density profiles substantiate strong interactions between CO2 molecules and the protonated pore walls. Non-monotonic change in n-octane self-diffusion coefficients as a function of CO2 loading was observed. CO2 preferential adsorption to the pore surface is likely to attenuate the surface adsorption of n-octane, lower the activation energy for n-octane diffusivity, and consequently enhance n-octane mobility at low CO2 loading. This observation was confirmed by conducting test simulations for pure noctane confined in narrower pores. At high CO2 loading, n-octane diffusivity is hindered by molecular crowding. Thus, n-octane diffusivity displays a maximum. In contrast, within the concentration range considered here, the self-diffusion coefficient predicted for CO2 exhibits a monotonic increase with loading, which is attributed to a combination of effects including the saturation of the adsorption capacity of the silica surface. Test simulations suggest that the results are strongly dependent on the pore morphology, and in particular on the presence of edges that can preferentially adsorb CO2 molecules and therefore affect the distribution of these molecules equally on the pore surface, which is required to provide the effective enhancement of n-octane diffusivity.

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Section: Simulation Models and Methodsologymentioning

confidence: 99%

N-octane diffusivity enhancement via carbon dioxide in silica slit-shaped nanopores – a molecular dynamics simulation

Ogbe

Striolo

et al. 2015

Molecular Simulation

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“…Starting from independent and equilibrated configurations, four simulations are carried out for every molecular system, and the results are averaged across those four samples. The equations of motion are integrated by means of the leap-frog algorithm [51] with a time step of 1 fs for rigid (SPC, TIP4P, and SPC/E) and semi-flexible models (TraPPE-UA, OPLS and GAFF), and 0.2 fs for flexible force fields (F-SPC, Fw-SPC and MEAa). The trajectory of the molecules is read every 100 fs while the energy configuration is recorded every 50 fs.…”

Section: Simulation Detailsmentioning

confidence: 99%

Molecular dynamics simulations for the prediction of the dielectric spectra of alcohols, glycols and monoethanolamine

Cardona

Fartaria

Sweatman

et al. 2015

Molecular Simulation

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This version is available at https://strathprints.strath.ac.uk/54062/ Strathprints is designed to allow users to access the research output of the University of Strathclyde. Unless otherwise explicitly stated on the manuscript, Copyright © and Moral Rights for the papers on this site are retained by the individual authors and/or other copyright owners. Please check the manuscript for details of any other licences that may have been applied. You may not engage in further distribution of the material for any profitmaking activities or any commercial gain. You may freely distribute both the url (https://strathprints.strath.ac.uk/) and the content of this paper for research or private study, educational, or not-for-profit purposes without prior permission or charge.Any correspondence concerning this service should be sent to the The response of molecular systems to electromagnetic radiation in the microwave region (0.3-300 GHz) has been principally studied experimentally, using broadband dielectric spectroscopy. However, relaxation times corresponding to reorganisation of molecular dipoles due to their interaction with electromagnetic radiation at microwave frequencies are within the scope of modern molecular simulations. In this work, fluctuations of the total dipole moment of a molecular system, obtained through molecular dynamics simulations, are used to determine the dielectric spectra of water, a series of alcohols and glycols, and monoethanolamine. Although the force fields employed in this study have principally been developed to describe thermodynamic properties, most them give fairly good predictions of this dynamical property for these systems. However, the inaccuracy of some models and the long simulation times required for the accurate estimation of the static dielectric constant can sometimes be problematic. We show that the use of the experimental value for the static dielectric constant in the calculations, instead of the one predicted by the different models, yields satisfactory results for the dielectric spectra, and hence the heat absorbed from microwaves, avoiding the need for extraordinarily long simulations or re-calibration of molecular models.

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“…Simulations are run using GROMACS, version 4.5.3, 50 where LEWIS interactions are introduced as tabulated potentials. NPT and NVT ensembles are run in single precision leap-frog algorithm 51 and NVE in double precision Velocity-Verlet. 52 The neighbor list radius is 11 Å and the lists are updated every 25 steps (5 fs).…”

Section: Molecular Dynamicsmentioning

confidence: 99%

Natural polarizability and flexibility via explicit valency: The case of water

Kale

Herzfeld

2012

The Journal of Chemical Physics

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As the dominant physiological solvent, water drives the folding of biological macromolecules, influences conformational changes, determines the ionization states of surface groups, actively participates in catalytic events, and provides "wires" for long-range proton transfer. Elucidation of all these roles calls for atomistic simulations. However, currently available methods do not lend themselves to efficient simulation of proton transfer events, or even polarizability and flexibility. Here, we report that an explicit account of valency can provide a unified description for the polarizability, flexibility, and dissociability of water in one intuitive and efficient setting. We call this approach LEWIS, after the chemical theory that inspires the use of valence electron pairs. In this paper, we provide details of the method, the choice of the training set, and predictions for the neat ambient liquid, with emphasis on structure, dynamics, and polarization. LEWIS water provides a good description of bulk properties, and dipolar and quadrupolar responses.

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Quiet high-resolution computer models of a plasma

Cited by 1,017 publications

References 10 publications

N-octane diffusivity enhancement via carbon dioxide in silica slit-shaped nanopores – a molecular dynamics simulation

N-octane diffusivity enhancement via carbon dioxide in silica slit-shaped nanopores – a molecular dynamics simulation

Molecular dynamics simulations for the prediction of the dielectric spectra of alcohols, glycols and monoethanolamine

Natural polarizability and flexibility via explicit valency: The case of water

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