Quantification of sampling uncertainty for molecular dynamics simulation: Time-dependent diffusion coefficient in simple fluids

2015 ◽  
Vol 302 ◽  
pp. 485-508 ◽  
Author(s):  
Changho Kim ◽  
Oleg Borodin ◽  
George Em Karniadakis
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Molecular Dynamics Simulation ◽  
Time Dependent ◽  
Dynamics Simulation ◽  
Sampling Uncertainty ◽  
Simple Fluids ◽  
Simulation Time

Nano-Indentation Simulation Study Based on Parallel Computing

2012 ◽  
Vol 500 ◽  
pp. 696-701
Author(s):  
Ying Zhu ◽  
Sen Song ◽  
Ling Ling Xie ◽  
Shun He Qi ◽  
Qian Qian Liu
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computing ◽  
Molecular Dynamics Simulation ◽  
Large Scale ◽  
Dynamics Simulation ◽  
Parallel Computer ◽  
Nano Indentation ◽  
Simulation Results ◽  
The Impact ◽  
Simulation Time

This method of parallel computing into nanoindentation molecular dynamics simulation (MDS), the author uses a nine-node parallel computer and takes the single crystal aluminum as the experimental example, to implement the large-scale process simulation of nanoindentation. Compared the simulation results with experimental results is to verify the reliability of the simulation. The method improves the computational efficiency and shortens the simulation time and the expansion of scale simulation can significantly reduce the impact of boundary conditions, effectively improve the accuracy of the molecular dynamics simulation of nanoindentation.

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.

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