Diffusion in multicomponent aqueous alcoholic mixtures

AbstractThe Fick diffusion coefficient matrix of the highly associating quaternary mixture water + methanol + ethanol + 2-propanol as well as its ternary and binary subsystems is analyzed with molecular dynamics simulation techniques. Three of the ternary subsystems are studied in this sense for the first time. The predictive capability of the employed force fields, which were sampled with the Green–Kubo formalism and Kirkwood–Buff integration, is confirmed by comparison with experimental literature data on vapor-liquid equilibrium, shear viscosity and Fick diffusion coefficient, wherever possible. A thorough analysis of the finite size effects on the simulative calculation of diffusion coefficients of multicomponent systems is carried out. Moreover, the dependence of the Fick diffusion coefficient matrix on the velocity reference frame and component order is analyzed. Their influence is found to be less significant for the main matrix elements, reaching a maximum variation of 19%. The large differences found for the cross elements upon variation of the reference frame hinder a straightforward interpretation of the Fick diffusion coefficient matrix with respect to the presence of diffusive coupling effects.

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Molecular Dynamics Simulation of Irradiation Damage in bcc Iron

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.179-180.513 ◽

2011 ◽

Vol 179-180 ◽

pp. 513-518 ◽

Cited By ~ 1

Author(s):

Jian Wei Wang ◽

Xin Chun Shang ◽

Guo Cai Lv

Keyword(s):

Molecular Dynamics ◽

Equilibrium Position ◽

Dynamics Simulation ◽

Irradiation Damage ◽

Displacement Cascades ◽

Simulation Techniques ◽

Bcc Iron ◽

High Degree ◽

Eam Potential ◽

First Time

Computer simulation techniques in atom scale have now become so powerful that phenomena associated with irradiation damage effects in metals can be modelled with a high degree of realism. As a powerful tool, molecular dynamics (MD) is applied to study the displacement cascades initiated by the neutrons when they interact with matter. There exist a lot of inter-atomic potentials dedicated to bcc Fe and we choose the EAM potential. At first time PKAs (Primary knock-on atoms) knocked on a atom and send a part of energy to it what result displacement cascades. After about several ps, a lot of atoms are knocked to leave the equilibrium position and became self- interstitial atoms (SIAs). A lot of equilibrium position became vacancies. Some SIAs and vacancies form dumb-bells structure. Several vacancies or SIAs assembled the clusters. In other papers we haven’t found about the SIAs and vacancies can be assembled the SFT-like clusters in bcc Fe. In our study, we occasionally find SIAs can assemble to form the cluster in bcc Fe but need a higher energy. In our study, we choose the temperature from 100K to 600K, the energy from 100eV to 20keV. The particles scale is about 300 thousands. In a series of experimentation we find that as the temperature increase as the number of the SIAs and vacancies increase too. By the same token, as the energy increase we will find the same result.

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Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

ASME/JSME 2011 8th Thermal Engineering Joint Conference ◽

10.1115/ajtec2011-44457 ◽

2011 ◽

Author(s):

Toshihiro Kaneko ◽

Kenji Yasuoka ◽

Ayori Mitsutake ◽

Xiao Cheng Zeng

Keyword(s):

Molecular Dynamics ◽

Heat Capacity ◽

Transition Temperature ◽

Peak Position ◽

Temperature Curve ◽

Dynamics Simulation ◽

Lennard Jones ◽

Dynamics Simulations ◽

First Time ◽

Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

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Modeling and Molecular Dynamics of the 3D Structure of the HPV16 E7 Protein and Its Variants

International Journal of Molecular Sciences ◽

10.3390/ijms22031400 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1400

Author(s):

Ciresthel Bello-Rios ◽

Sarita Montaño ◽

Olga Lilia Garibay-Cerdenares ◽

Lilian Esmeralda Araujo-Arcos ◽

Marco Antonio Leyva-Vázquez ◽

...

Keyword(s):

Molecular Dynamics ◽

3D Structure ◽

Epidemiological Studies ◽

Dynamics Simulation ◽

Structural Refinement ◽

Oncogenic Potential ◽

Structural Differences ◽

Reference Protein ◽

E6 And E7 ◽

First Time

The oncogenic potential of high-risk human papillomavirus (HPV) is predicated on the production of the E6 and E7 oncoproteins, which are responsible for disrupting the control of the cell cycle. Epidemiological studies have proposed that the presence of the N29S and H51N variants of the HPV16 E7 protein is significantly associated with cervical cancer. It has been suggested that changes in the amino acid sequence of E7 variants may affect the oncoprotein 3D structure; however, this remains uncertain. An analysis of the structural differences of the HPV16 E7 protein and its variants (N29S and H51N) was performed through homology modeling and structural refinement by molecular dynamics simulation. We propose, for the first time, a 3D structure of the E7 reference protein and two of Its variants (N29S and H51N), and conclude that the mutations induced by the variants in N29S and H51N have a significant influence on the 3D structure of the E7 protein of HPV16, which could be related to the oncogenic capacity of this protein.

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Molecular dynamics simulation data of self-diffusion coefficient for Lennard–Jones chain fluids

Fluid Phase Equilibria ◽

10.1016/j.fluid.2004.04.007 ◽

2004 ◽

Vol 221 (1-2) ◽

pp. 25-33 ◽

Cited By ~ 17

Author(s):

R.A. Reis ◽

F.C. Silva ◽

R. Nobrega ◽

J.Vladimir Oliveira ◽

F.W. Tavares

Keyword(s):

Molecular Dynamics ◽

Diffusion Coefficient ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Simulation Data ◽

Self Diffusion ◽

Lennard Jones ◽

Chain Fluids ◽

Self Diffusion Coefficient

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Finite-size effects on the molecular dynamics simulation of fast-ion conductors: A case study of lithium garnet oxide Li7La3Zr2O12

Solid State Ionics ◽

10.1016/j.ssi.2016.03.002 ◽

2016 ◽

Vol 289 ◽

pp. 143-149 ◽

Cited By ~ 20

Author(s):

Matthew J. Klenk ◽

Wei Lai

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Size Effects ◽

Finite Size ◽

Dynamics Simulation ◽

Finite Size Effects ◽

Lithium Garnet ◽

Fast Ion Conductors ◽

Fast Ion

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Correction for finite-size effects in molecular dynamics simulation of liquid alloys

Journal of Non-Crystalline Solids ◽

10.1016/s0022-3093(99)00263-x ◽

1999 ◽

Vol 250-252 ◽

pp. 354-359 ◽

Cited By ~ 4

Author(s):

A. Baumketner ◽

Ya. Chushak

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Size Effects ◽

Finite Size ◽

Dynamics Simulation ◽

Liquid Alloys ◽

Finite Size Effects

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A dissipative particle dynamics simulation study on phase diagrams for the self-assembly of amphiphilic hyperbranched multiarm copolymers in various solvents

Soft Matter ◽

10.1039/c7sm01170a ◽

2017 ◽

Vol 13 (36) ◽

pp. 6178-6188 ◽

Cited By ~ 20

Author(s):

Haina Tan ◽

Chunyang Yu ◽

Zhongyuan Lu ◽

Yongfeng Zhou ◽

Deyue Yan

Keyword(s):

Phase Diagrams ◽

Simulation Study ◽

Self Assembly ◽

Dissipative Particle Dynamics ◽

Particle Dynamics ◽

The Self ◽

Dynamics Simulation ◽

Dynamics Simulations ◽

First Time ◽

Dissipative Particle Dynamics Simulation

This work discloses for the first time the self-assembly phase diagrams of amphiphilic hyperbranched multiarm copolymers in various solvents by dissipative particle dynamics simulations.

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Momentum Removal to Obtain the Position-Dependent Diffusion Constant in Constrained Molecular Dynamics Simulation

10.26434/chemrxiv.14776965 ◽

2021 ◽

Author(s):

Kazushi Fujimoto ◽

Tetsuro Nagai ◽

Tsuyoshi Yamaguchi

Keyword(s):

Molecular Dynamics ◽

Diffusion Coefficient ◽

Mass Velocity ◽

Center Of Mass ◽

Heterogeneous Systems ◽

Diffusion Constant ◽

Dynamics Simulation ◽

Coulombic Interaction ◽

Ewald Method ◽

Theoretical Predictions

<div>The position-dependent diffusion coefficient along with free energy profile are important parameters needed to study mass transport in heterogeneous systems such as biological and polymer membranes, and molecular dynamics (MD) calculation is a popular tool to obtain them. Among many methodologies, the Marrink-Berendsen (MB) method is often employed to calculate the position-dependent diffusion coefficient, in which the autocorrelation function of the force on a fixed molecule is related to the friction on the molecule. However, the diffusion coefficient is shown to be affected by the period of the removal of the center-of-mass velocity, which is necessary when performing MD calculations using the Ewald method for Coulombic interaction. We have clarified theoretically in this study how this operation affects the diffusion coefficient calculated by the MB method, and the theoretical predictions are proven by MD calculations. Therefore, we succeeded in providing guidance on how to select an appropriate the period of the removal of the center-of-mass velocity in estimating the position-dependent diffusion coefficient by the MB method. This guideline is applicable also to the Woolf-Roux method.</div>

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Molecular Dynamics Simulation Study of the Effect of Ni, Fe, Cu on Cryolite Molten Salt System 78% Na3AlF6-9.5%AlF3-5.0%CaF2-7.5%-Al2O3

Materials Science Forum ◽

10.4028/www.scientific.net/msf.1026.39 ◽

2021 ◽

Vol 1026 ◽

pp. 39-48

Author(s):

Han Bing He ◽

Yu Si Wang ◽

Ze Xiang Luo ◽

Jing Zeng

Keyword(s):

Molecular Dynamics ◽

Diffusion Coefficient ◽

Molten Salt ◽

Diffusion Mechanism ◽

Research Work ◽

Dynamics Simulation ◽

Salt System ◽

Electrolyte System ◽

Aluminum Composite ◽

Molten Salt System

The effect of different additives Ni, Fe, Cu on the structure and properties of electrolyte system 78% Na3AlF6- -9.5%AlF3-5.0%CaF2-7.5%Al2O3 at 1200K and 1.01Mpa was studied by molecular dynamics method. The radial distribution function, coordination number, diffusion coefficient, conductivity, and viscosity of the system were discussed in detail. The results demonstrated that the order of the self-diffusion coefficient of ions in the electrolyte system is: Na+ > F- > O2- > Ca2+ >Al3+. The addition of Ni and Fe connected the free aluminum composite ion groups in the system through fluorine bridges, which enhanced the interaction between Al3+ and Al3+. The addition of Cu weakened the interaction between Al3 + and Al3+ and the F-. The interaction between Al3+ and Na+, [AlF7]4- ionic groups might appeared in the melt system. After adding NiO, Fe2O3, and Cu, the electrical conductivity of the system increased, and the viscosity decreased. The research work revealed the influence of Ni, Fe, Cu on the ion existence form, mobility, inter-ion interaction and diffusion mechanism of cryolite molten salt system, which has important guiding significance for aluminum electrolysis production.

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