An Elemental Mercury Diffusion Coefficient for Natural Waters Determined by Molecular Dynamics Simulation

2009 ◽  
Vol 43 (9) ◽  
pp. 3183-3186 ◽  
Author(s):  
Joachim Kuss ◽  
Jörg Holzmann ◽  
Ralf Ludwig
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Molecular Dynamics Simulation ◽  
Natural Waters ◽  
Elemental Mercury ◽  
Dynamics Simulation

scholarly journals Construction of the Small Intestine Epithelial Cell Model Based on Molecular Dynamics Simulation and Preliminary Exploration of Drug Intestinal Absorption Prediction

2021 ◽  
Author(s):  
Yanshuang Shi ◽  
Menke Sheng ◽  
Qingsong Qu ◽  
Yuyao Liao ◽  
Lijng Lv ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Molecular Dynamics Simulation ◽  
Epithelial Cell ◽  
Cell Membrane ◽  
Intestinal Epithelial Cell ◽  
Dynamics Simulation ◽  
Intestinal Epithelial ◽  
Free Diffusion ◽  
Small Intestinal

Abstract In this study, molecular dynamics simulation was applied to the construction of small intestinal epithelial cell membrane and prediction of drug absorption. First, we constructed a system of a small intestinal epithelial cell membrane that was close to the real proportion and investigated the effects of temperature, water layer thickness, and ionic strength on membrane properties to optimize environmental parameters. Next, three drugs with different absorptivity, including Ephedrine (EPH), Quercetin (QUE), and Baicalin (BAI), were selected as model drugs to study the ability of drugs through the membrane by the free diffusion and umbrella sampling simulation, and the drug permeation ability was characterized by the free diffusion coefficient D and free energy barrier (△G) in the processes. The results showed that the free diffusion coefficient D’ and △G’ orders of the three drugs were consistent with the classical experimental absorption order, indicating that these two parameters could be used to jointly characterize the membrane permeability of the drugs.

scholarly journals Diffusion of Water and Diatomic Oxygen in Poly(3-hexylthiophene) Melt: A Molecular Dynamics Simulation Study

2012 ◽  
Vol 11 (1 and 2) ◽  
Author(s):  
Julia Deitz ◽  
Yeneneh Yimer ◽  
Mesfin Tsige
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Fick’S Law ◽  
Fick's Law ◽  
Diffusion Behavior

Diffusion behavior of water, diatomic oxygen, and a mixture of both into a poly(3-hexylthiophene)[P3HT] melt were investigated using Molecular Dynamics Simulation. Once simulations were complete, the data was analyzed to determine the diffusion coefficient of those molecules in P3HT using Fick’s law. The diffusion coefficient values were then plotted as a function of concentration and temperature to determine if trends existed. For both water and oxygen, no dependence was observed of the diffusion coefficient on concentration and temperature for the ranges studied. However, a variation in the diffusion coefficient on concentration was observed due to the expected inhomogeneity of the P3HT melt. In the presence of O2, the diffusion of H2O decreased significantly by a factor between four and five, while in the presence of H2O, the diffusion of O2 slightly decreased.

scholarly journals Structural Analyses of [Li Salt+Triglyme)] and Ionic Transport in Li-Air Battery Using Molecular Dynamics Simulation

2020 ◽  
Vol 27 (1) ◽  
pp. 13-22
Author(s):  
Md Khorshed Alam ◽  
Wataru Yamamoto ◽  
Hiromitsu Takaba
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Molecular Dynamics Simulation ◽  
Force Fields ◽  
Ionic Transport ◽  
Dynamics Simulation ◽  
Self Diffusion ◽  
Air Battery ◽  
Self Diffusion Coefficient

In this work, molecular dynamics (MD) study of triglyme (G3) solution containing lithium bis (trifluoro methyl sulfonyl) amide (Li[TFSA]) were investigated using classical atomistic force fields. G3 is a typical solvent used in non-aqueous Li-air battery. It shows here coordination of Li+ with G3 and [TFSA]- does not significantly change with increasing the concentration of G3 but self-diffusion coefficient of all the ions increases with increasing G3 concentration. The density of [Li(G3)[TFSA] complex decreases with increasing G3 concentration which lead to accelerate diffusivity of ions. Bangladesh Journal of Physics, 27(1), 13-22, June 2020

scholarly journals Modeling of Ferrous Metal Diffusion in Liquid Lead Using Molecular Dynamics Simulation

2019 ◽  
Vol 2 (1) ◽  
pp. 45
Author(s):  
Ahmad Anwar Nuris
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Molecular Dynamics Simulation ◽  
Ferrous Metal ◽  
Dynamics Simulation ◽  
Liquid Lead ◽  
Material System ◽  
Material Models ◽  
Volume Number ◽  
Metal Diffusion

Modeling of Iron metal diffusion in liquid lead using molecular dynamics simulation has been done. Molecular dynamics simulations are used to predict the value of physical quantities that we want to know based on the designed material model and on the input simulation data. In this research, effect of different geometry of material models was observed to know the diffusion coefficient. The material system was iron (Fe) in liquid lead (Pb). The material models is designed using Packmol software to get the initial configuration of atom's arrangement by inputting the material's characteristics such as mass, density, volume, number of atoms. This work examines the diffusion coefficient of iron in molten lead metal with the geometric shape of the simulation system in the form of iron in molten metal for various simulation models of boxes in a box, balls in a box and balls in balls. To design simulated geometric shapes we use the Packmol program. To calculate the diffusion coefficient we use the molecular dynamics simulation method. To find out which geometry is suitable, we compare the diffusion coefficient of the simulation results with existing references. The diffusion coefficient value of the spherical iron (Fe) system in the spherical liquid lead (Pb) has the best value compared to the other two forms with an accuracy rate of 99.94% because it is influenced by the even distribution of atoms in each part.

Formaldehyde diffusion within crystalline and amorphous cellulose at different temperatures and electric fields: A molecular dynamics study

2017 ◽  
Vol 28 (2) ◽  
pp. 175-185 ◽  
Author(s):  
Bo Xu ◽  
Zhenqian Chen
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Molecular Dynamics Simulation ◽  
Electric Field ◽  
Electric Fields ◽  
Amorphous Region ◽  
Dynamics Simulation ◽  
Amorphous Cellulose ◽  
Different Temperatures ◽  
The Relationship

To provide a microcosmic theoretical support for the reduction of formaldehyde in building material, the diffusion process was investigated by molecular dynamics simulation. In addition, the diffusion model of formaldehyde molecules in crystalline and amorphous cellulose was built, and diffusion coefficients at different temperatures and electric fields were studied. The simulation temperature was from 293 to 393 K and electric field was from 0 to 400 kV/m. Diffusion coefficient increased with greater temperature and electric field both in crystalline and amorphous region. However, the diffusion coefficient in amorphous region could be ignored for it was two orders of magnitude lower than diffusion coefficient in crystalline region. The relationship between diffusion coefficient and temperature, and the relationship between diffusion coefficient and electric field were obtained by simulation, verified by the experiment. Temperature was shown to have a significant contribution to formaldehyde diffusion than electric field. Compared with experimental studies, the molecular dynamics simulation could only analyse the diffusion coefficient qualitatively because of the difference between micro-scale and macro-scale.

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