scholarly journals Fick Diffusion Coefficients via Molecular Dynamics: An Alternative Approach in the Fourier Domain

2020 ◽  
Author(s):  
Thiago José Pinheiro dos Santos ◽  
Frederico W. Tavares ◽  
Charlles Abreu
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
High Pressures ◽  
Finite Size ◽  
Correlation Method ◽  
Finite Size Effect ◽  
New Approach ◽  
Molecular Systems ◽  
Alternative Approach ◽  
Wide Range

Mutual diffusion coefficient data are required for several systems of scientific and engineering interest to properly describe mass transport phenomena over a wide range of pressures, temperatures, and compositions. In this work, we calculated Fick diffusion coefficients for some CO2+n-alkane mixtures at high pressures using a new method, which we derived by introducing modifications to the Fourier Correlation Method (FCM) originally proposed by Nichols and Wheeler [I&EC Research, 54, 12156–12164 (2015)]. The modified FCM (mFCM) results were validated through comparisons with experimental data and with Fick coefficients calculated by employing well-established Molecular Dynamics methodologies. The new approach has some interesting advantages, such as providing Fick coefficients for molecular systems directly through a single equilibrium calculation, in contrast to traditional methods in which an extra calculation is needed to obtain the so-called thermodynamic factor. It is shown that the new approach considerably reduces the finite-size effect of the simulation box on the calculated diffusion coefficients, which are thus obtained in the thermodynamic limit.<br>

scholarly journals Fick Diffusion Coefficients via Molecular Dynamics: An Alternative Approach in the Fourier Domain

2020 ◽  
Author(s):  
Thiago José Pinheiro dos Santos ◽  
Frederico W. Tavares ◽  
Charlles Abreu
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
High Pressures ◽  
Finite Size ◽  
Correlation Method ◽  
Finite Size Effect ◽  
New Approach ◽  
Molecular Systems ◽  
Alternative Approach ◽  
Wide Range

Mutual diffusion coefficient data are required for several systems of scientific and engineering interest to properly describe mass transport phenomena over a wide range of pressures, temperatures, and compositions. In this work, we calculated Fick diffusion coefficients for some CO2+n-alkane mixtures at high pressures using a new method, which we derived by introducing modifications to the Fourier Correlation Method (FCM) originally proposed by Nichols and Wheeler [I&EC Research, 54, 12156–12164 (2015)]. The modified FCM (mFCM) results were validated through comparisons with experimental data and with Fick coefficients calculated by employing well-established Molecular Dynamics methodologies. The new approach has some interesting advantages, such as providing Fick coefficients for molecular systems directly through a single equilibrium calculation, in contrast to traditional methods in which an extra calculation is needed to obtain the so-called thermodynamic factor. It is shown that the new approach considerably reduces the finite-size effect of the simulation box on the calculated diffusion coefficients, which are thus obtained in the thermodynamic limit.<br>

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

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 ◽  
Dynamics Simulations

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.

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

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 ◽  
Dynamics Simulations

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.

scholarly journals Finite-size effects of diffusion coefficients computed from molecular dynamics: a review of what we have learned so far

2020 ◽  
pp. 1-15 ◽  
Author(s):  
Alper T. Celebi ◽  
Seyed Hossein Jamali ◽  
André Bardow ◽  
Thijs J. H. Vlugt ◽  
Othonas A. Moultos
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Size Effects ◽  
Finite Size ◽  
Finite Size Effects

scholarly journals Equilibrium Molecular Dynamics Study of Lattice Thermal Conductivity/Conductance of Au-SAM-Au Junctions

2009 ◽  
Vol 132 (3) ◽  
Author(s):  
Tengfei Luo ◽  
John R. Lloyd
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Thermal Energy ◽  
Energy Transport ◽  
Thermal Conductance ◽  
Finite Size ◽  
Thickness Effect ◽  
Finite Size Effect ◽  
Substrate Thickness ◽  
Thermal Energy Transport

In this paper, equilibrium molecular dynamics simulations were performed on Au-SAM (self-assembly monolayer)-Au junctions. The SAM consisted of alkanedithiol (–S–(CH2)n–S–) molecules. The out-of-plane (z-direction) thermal conductance and in-plane (x- and y-direction) thermal conductivities were calculated. The simulation finite size effect, gold substrate thickness effect, temperature effect, normal pressure effect, molecule chain length effect, and molecule coverage effect on thermal conductivity/conductance were studied. Vibration power spectra of gold atoms in the substrate and sulfur atoms in the SAM were calculated, and vibration coupling of these two parts was analyzed. The calculated thermal conductance values of Au-SAM-Au junctions are in the range of experimental data on metal-nonmetal junctions. The temperature dependence of thermal conductance has a similar trend to experimental observations. It is concluded that the Au-SAM interface resistance dominates thermal energy transport across the junction, while the substrate is the dominant media in which in-plane thermal energy transport happens.

Size Effect of Ion Translocation through Nanopore by Molecular Dynamics

2014 ◽  
Vol 692 ◽  
pp. 420-423 ◽  
Author(s):  
Itsuo Hanasaki ◽  
Yoshihiro Kuzuya ◽  
Satoyuki Kawano
Keyword(s):  
Molecular Dynamics ◽  
Size Effect ◽  
Cross Sections ◽  
Finite Size ◽  
Effective Size ◽  
Finite Size Effect ◽  
Channel Diameter ◽  
Sequencing Technologies ◽  
Ion Translocation ◽  
Pass Through

While the flow rates (in unit of particles/s) of the ions in aqueous solution depend on the cross sections of the channels they pass through, the flux (in unit of particles/(m2s)) is usually independent of them. However, if the diameter of the channel becomes extremely small and comparable to the effective size of the ions, there can be the dependence of the flux on the channel diameter. The finite size effect of solute ions through such small channel is relevant to the physical process of other nanofluidic technologies such as the DNA translocation through nanopore for the sequencing technologies. In this study, we examine the flow of K+ and Cl- ions in water through nanopores made of graphene structure by molecular dynamics method. The results show that there is a transition of zero to nonzero flux when the pore diameter is around the effective size of the ions. Furthermore, there is a dependence of the flux on the nanopore diameter around this regime.

scholarly journals Finite size effect on Dissociation and Diffusion of chiral partners in Nambu-Jona-Lasinio model

2021 ◽  
Author(s):  
Paramita Deb ◽  
Sabyasachi Ghosh ◽  
Jai Prakash ◽  
Santosh Kumar Das ◽  
Raghava Varma
Keyword(s):  
Size Effect ◽  
Chiral Symmetry ◽  
Diffusion Coefficients ◽  
Finite Size ◽  
Finite Size Effect ◽  
Detailed Structure ◽  
Different Temperatures ◽  
The Masses ◽  
Sigma Meson ◽  
And Diffusion

Abstract The masses of pion and sigma meson modes, along with their dissociation in the quark medium, provide detailed spectral structures of the chiral partners. One has seen collectivity in pA and pp systems both at LHC and RHIC. In this article, we study the restoration of chiral symmetry by investigating the finite size effect on the detailed structure of the chiral partners in the framework of the Nambu-Jona-Lasinio model. Their diffusions and conductions have been studied through this dissociation mechanism. It is found that the masses, widths, diffusion coefficients, conductivities of chiral partners merge at different temperatures in the restoration phase of chiral symmetry. However, merging points are shifted to lower temperatures when one introduces the finite size effect into the picture. The strengths of diffusions and conductions are also reduced once the finite size is introduced in the calculations.

scholarly journals High-Throughput Molecular Dynamics Simulations and Validation of Thermophysical Properties of Polymers

2020 ◽  
Author(s):  
Mohammad Atif Faiz Afzal ◽  
Andrea Browning ◽  
Alexander Goldberg ◽  
Mathew D. Halls ◽  
Jacob L. Gavartin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Specific Volume ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Molecular Systems ◽  
Branched Polyethylene ◽  
Wide Range ◽  
Experimental Values ◽  
Dynamics Simulations ◽  
Graphics Processing

Recent advances in graphics-processing-unit (GPU) hardware and improved efficiencies of atomistic simulation programs allow the screening of a large number of polymers to predict properties that require running and analyzing long Molecular Dynamics (MD) trajectories of large molecular systems. This paper outlines an efficient MD cooling simulation workflow based on GPU MD simulation and the refined Optimized Potentials for Liquids Simulation (OPLS) OPLS3e force field to calculate glass transition temperatures (T<sub>g</sub>) of 315 polymers for which experimental values were reported by Bicerano.<sup>1</sup> We observed good agreement of predicted T<sub>g</sub> values with experimental observation across a wide range of polymers, which confirms the clear utility of the described workflow. During the stepwise cooling simulation for the calculation of T<sub>g</sub>, a subset of polymers clearly showed an ordered structure developing as the temperature decreased. Such polymers have a point of discontinuity on the specific volume vs. temperature plot, which we associated with the melting temperature (T<sub>m</sub>). We demonstrate the distinction between crystallized and amorphous polymers by examining polyethylene. Linear polyethylene shows a discontinuity in the specific volume vs. temperature plot, but we do not observe the discontinuity for branched polyethylene simulations.

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