Role of Viscosity in Deviations from the Nernst-Einstein Relation

Finite Size Effect ◽

Einstein Relation ◽

Experimental Measurements ◽

<p> </p><div> <div> <div> <p>Deviations from the Nernst-Einstein relation are commonly attributed to ion-ion correlation and ion-pairing. Despite the fact that these de- viations can be quantified by either experimental measurements or molecular dynamics simulations, there is no rule of thumb to tell the extent of deviations. Here, we show that deviations from the Nernst-Einstein relation is proportional to the inverse viscosity by exploring the finite-size effect on the transport properties in periodic boundary conditions. This conclusion is in accord with established experimental results of ionic liquids. </p> </div> </div> </div><br><p></p>

Role of Viscosity in Deviations from the Nernst-Einstein Relation

10.26434/chemrxiv.8217152.v1 ◽

2019 ◽

Author(s):

Yunqi Shao ◽

Keisuke Shigenobu ◽

Masayoshi Watanabe ◽

Chao Zhang

Keyword(s):

Molecular Dynamics ◽

Periodic Boundary ◽

Cross Correlation ◽

Finite Size ◽

Finite Size Effect ◽

Einstein Relation ◽

Experimental Measurements ◽

<div><div><div><p>Deviations from the Nernst-Einstein rela- tion are commonly attributed to ion-ion (cross)correlation and ion-pairing. Despite the fact that these deviations can be quantified by either experimental measurements or molecular dynamics simulations, there is no rule of thumb to tell the extent of deviations. Here, we show that deviations from the Nernst-Einstein relation scale linearly with the inverse viscosity by exploring the finite-size effect in periodic boundary conditions. This conclusion is in accord with published experimental results of ionic liquids.</p></div></div></div>

Role of Viscosity in Deviations from the Nernst-Einstein Relation

10.26434/chemrxiv.8217152.v2 ◽

2019 ◽

Cited By ~ 1

Author(s):

Yunqi Shao ◽

Keisuke Shigenobu ◽

Masayoshi Watanabe ◽

Chao Zhang

Keyword(s):

Molecular Dynamics ◽

Periodic Boundary ◽

Cross Correlation ◽

Finite Size ◽

Finite Size Effect ◽

Einstein Relation ◽

Experimental Measurements ◽

<div><div><div><p>Deviations from the Nernst-Einstein rela- tion are commonly attributed to ion-ion (cross)correlation and ion-pairing. Despite the fact that these deviations can be quantified by either experimental measurements or molecular dynamics simulations, there is no rule of thumb to tell the extent of deviations. Here, we show that deviations from the Nernst-Einstein relation scale linearly with the inverse viscosity by exploring the finite-size effect in periodic boundary conditions. This conclusion is in accord with published experimental results of ionic liquids.</p></div></div></div>

Computer-Generated Structural Models for a-Si:H

MRS Proceedings ◽

10.1557/proc-141-71 ◽

1988 ◽

Vol 141 ◽

Author(s):

Laurent J. Lewis ◽

Normand Mousseau ◽

FranÇois Drolet

Keyword(s):

Molecular Dynamics ◽

Boundary Conditions ◽

Amorphous Silicon ◽

Periodic Boundary ◽

Hydrogenated Amorphous Silicon ◽

Structural Models ◽

Dynamics Simulations ◽

Hydrogenated Amorphous ◽

Good Agreement

AbstractA new algorithm for generating fully-coordinated hydrogenated amorphous silicon models with periodic boundary conditions is presented. The hydrogen is incorporated into an a-Si matrix by a bond-switching process similar to that proposed by Wooten, Winer, and Weaire, making sure that four-fold coordination is preserved and that no rings with less than 5 members are created. After each addition of hydrogen, the structure is fully relaxed. The models so obtained, to be used as input to molecular dynamics simulations, are found to be in good agreement with experiment. A model with 12 at.% H is discussed in detail.

Self-Diffusion Coefficients of Methane/n-Hexane Mixtures at High Pressures: An Evaluation of the Finite-Size Effect and a Comparison of Force Fields

10.26434/chemrxiv.9593585.v1 ◽

2019 ◽

Author(s):

Thiago José Pinheiro dos Santos ◽

Charlles Abreu ◽

Bruno Horta ◽

Frederico W. Tavares

Keyword(s):

Molecular Dynamics ◽

Diffusion Coefficients ◽

High Pressures ◽

Force Fields ◽

Transport Coefficients ◽

Finite Size ◽

Finite Size Effect ◽

Self Diffusion ◽

Analytical Correction ◽

Mass transport coefficients play an important role in process design and in compositional grading of oil reservoirs. As experimental measurements of these properties can be costly and hazardous, Molecular Dynamics simulations emerge as an alternative approach. In this work, we used Molecular Dynamics to calculate the self-diffusion coefficients of methane/n-hexane mixtures at different conditions, in both liquid and supercritical phases. We evaluated how the finite box size and the choice of the force field affect the calculated properties at high pressures. Results show a strong dependency between self-diffusion and the simulation box size. The Yeh-Hummer analytical correction [J. Phys. Chem. B, 108, 15873 (2004)] can attenuate this effect, but sometimes makes the results depart from experimental data due to issues concerning the force fields. We have also found that different all-atom and united-atom models can produce biased results due to caging effects and to different dihedral configurations of the n-alkane.

Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.7b10830 ◽

2018 ◽

Vol 122 (9) ◽

pp. 2495-2503 ◽

Cited By ~ 6

Author(s):

Kota Kasahara ◽

Shun Sakuraba ◽

Ikuo Fukuda

Keyword(s):

Molecular Dynamics ◽

Boundary Conditions ◽

Molecular Dynamics Simulations ◽

Periodic Boundary ◽

Peptide Conformation ◽

Enhanced Sampling ◽

Self-Diffusion Coefficients of Methane/n-Hexane Mixtures at High Pressures: An Evaluation of the Finite-Size Effect and a Comparison of Force Fields

10.26434/chemrxiv.9593585 ◽

2019 ◽

Author(s):

Thiago José Pinheiro dos Santos ◽

Charlles Abreu ◽

Bruno Horta ◽

Frederico W. Tavares

Keyword(s):

Molecular Dynamics ◽

Diffusion Coefficients ◽

High Pressures ◽

Force Fields ◽

Transport Coefficients ◽

Finite Size ◽

Finite Size Effect ◽

Self Diffusion ◽

Analytical Correction ◽

Mass transport coefficients play an important role in process design and in compositional grading of oil reservoirs. As experimental measurements of these properties can be costly and hazardous, Molecular Dynamics simulations emerge as an alternative approach. In this work, we used Molecular Dynamics to calculate the self-diffusion coefficients of methane/n-hexane mixtures at different conditions, in both liquid and supercritical phases. We evaluated how the finite box size and the choice of the force field affect the calculated properties at high pressures. Results show a strong dependency between self-diffusion and the simulation box size. The Yeh-Hummer analytical correction [J. Phys. Chem. B, 108, 15873 (2004)] can attenuate this effect, but sometimes makes the results depart from experimental data due to issues concerning the force fields. We have also found that different all-atom and united-atom models can produce biased results due to caging effects and to different dihedral configurations of the n-alkane.

Lattice induced crystallization of nanodroplets: the role of finite-size effects and substrate properties in controlling polymorphism

Nanoscale ◽

10.1039/c7nr08705e ◽

2018 ◽

Vol 10 (10) ◽

pp. 4921-4926 ◽

Cited By ~ 5

Author(s):

Julien Lam ◽

James F. Lutsko

Keyword(s):

Molecular Dynamics ◽

Size Effects ◽

Finite Size ◽

Solid Substrate ◽

General Phenomenon ◽

Finite Size Effects ◽

Substrate Properties ◽

Dynamics Simulations ◽

Induced Crystallization

Freezing a nanodroplet deposited on a solid substrate leads to the formation of crystalline structures. We study the inherent mechanisms underlying this general phenomenon by means of molecular dynamics simulations.

Molecular Dynamics Simulations of Interaction between the Mixture of Glycerol and 1,6-Hexanediol and Silicon Dioxide Surface

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.291-294.716 ◽

2013 ◽

Vol 291-294 ◽

pp. 716-721

Author(s):

Zhan Xiu Chen ◽

Guan Yi Chen ◽

Wei Juan Lan

Keyword(s):

Molecular Dynamics ◽

Distribution Function ◽

Silicon Dioxide ◽

Periodic Boundary ◽

Self Diffusion ◽

Amorphous Silicon Dioxide ◽

Method Of Molecular Dynamics ◽

Dynamics Simulations ◽

Self Diffusion Coefficient

The interaction between amorphous silicon dioxide (SiO2) with surface (100) and mixture of glycerol and 1,6-hexanediol was simulated with periodic boundary conditions using the method of molecular dynamics. The properties of silicon dioxide depend on polarity of the groups of the surface. The simulation was respectively calculated that silicon dioxide surface with all silanol groups (Si-OH bonds) or all Si-O bonds interacts with hydroxyl of mixture of glycerol and 1,6-hexanediol in the paper. The results show that the peak of radial distribution function of hydroxyl of mixture on silicon dioxide surface with Si-O bonds is higher than that of the hydroxyl of the mixture on the surface with Si-OH bonds. And self-diffusion coefficient of hydroxyl of the mixture on the surface with the Si-O bonds was smaller than that of hydroxyl of the mixture on the surface with the Si-OH bonds. Interaction energy of silicon dioxide surface with Si-O bonds and the mixture is stronger than that of silicon dioxide surface with Si-O bonds and the mixture at different temperature respectively.