High-Temperature and High-Pressure Pyrolysis of Hexadecane: Molecular Dynamic Simulation Based on Reactive Force Field (ReaxFF)

2017 ◽  
Vol 121 (10) ◽  
pp. 2069-2078 ◽  
Author(s):  
Zhuojun Chen ◽  
Weizhen Sun ◽  
Ling Zhao
Keyword(s):  
High Pressure ◽  
High Temperature ◽  
Force Field ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Reactive Force ◽  
Reactive Force Field ◽  
Simulation Based

scholarly journals Discovery of Potential Anti-Ischemic Stroke Agents Through Inhibiting Sulfonylurea Receptor 1 (SUR1): A Pharmacophore-based Screening, Docking, and Molecular Dynamic Simulation

2021 ◽  
Vol 12 (5) ◽  
pp. 6915-6932
Keyword(s):  
Ischemic Stroke ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Sulfonylurea Receptor ◽  
Brain Membrane ◽  
Simulation Based ◽  
Intact Brain ◽  
Docking Energy

Stroke is the leading cause of disability and death worldwide. Inhibition of sulfonylurea 1 receptor (SUR1) using glibenclamide previously has been studied in CNS ischemic tissues and faster recovery from stroke injury in different animal models of stroke. Unfortunately, glibenclamide cannot enter the brain through an intact brain membrane (BBB) due to its ionization at physiological pH. Therefore, it was hypothesized that compounds with structural properties similar to glibenclamide but with the ability to penetrate through BBB would be superior to glibenclamide in ischemic stroke. Docking energy and interactions of glibenclamide with SUR1 active site were assessed using AutoDock Vina. NCI databases search engines with limitations for penetration to CNS were used to find the best compounds with desired properties. Then two selected compounds were assessed with dynamic molecular studies. Two compounds called CID-415537 and CID-419074 with docking energies of -10.3 kcal/mol and -11 kcal/mol were identified. CID-415537 was selected as the best compound due to its proper interactions with SUR1 amino acids and stability in molecular dynamic simulation. Based on this study, compound CID-415537 would be a good candidate for a SUR1 inhibitor in ischemic stroke. However, further in vivo investigations are required to confirm these findings.

Molecular Dynamic Simulation of Oxaliplatin Diffusion in Poly(lactic acid-co -glycolic acid). Part A: Parameterization and Validation of the Force-Field CVFF

2015 ◽  
Vol 25 (1) ◽  
pp. 45-62 ◽  
Author(s):  
Jurgen Lange ◽  
Fernando Gomes de Souza ◽  
Marcio Nele ◽  
Frederico Wanderley Tavares ◽  
Iuri Soter Viana Segtovich ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Force Field ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Glycolic Acid ◽  
Poly Lactic Acid

scholarly journals Elastic properties of cement phases using molecular dynamic simulation

2021 ◽  
Author(s):  
Mohamed Arar
Keyword(s):  
Force Field ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Elastic Properties ◽  
Dynamic Simulation ◽  
Young Modulus ◽  
Hydration Products ◽  
Dynamic Simulations ◽  
Packing Factor ◽  
Shed Light

The goal of this thesis is to shed light on the elastic properties, especially the Young modulus, of clinker phases and hydration products of cement paste through molecular dynamic simulation by COMPASS force field. The parameters that can affect the elastic properties of cement phases were also targeted, with special attention paid to analog C-S-H minerals, in which the Tobermorite family and Jennite were simulated to render their structures representative of C-S-H structure. The molecular dynamic simulations of this study show that CO force field can be applicable for most clinker phases and hydration products. Jennite, with its porosity and finite silicate chain accounted for, can be considered the closer and representative structure of C-S-H. In addition, this study confirms the important effect of C/S ratio, packing factor and chain length on elastic properties of C-S-H.

scholarly journals Elastic properties of cement phases using molecular dynamic simulation

2021 ◽  
Author(s):  
Mohamed Arar
Keyword(s):  
Force Field ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Elastic Properties ◽  
Dynamic Simulation ◽  
Young Modulus ◽  
Hydration Products ◽  
Dynamic Simulations ◽  
Packing Factor ◽  
Shed Light

The goal of this thesis is to shed light on the elastic properties, especially the Young modulus, of clinker phases and hydration products of cement paste through molecular dynamic simulation by COMPASS force field. The parameters that can affect the elastic properties of cement phases were also targeted, with special attention paid to analog C-S-H minerals, in which the Tobermorite family and Jennite were simulated to render their structures representative of C-S-H structure. The molecular dynamic simulations of this study show that CO force field can be applicable for most clinker phases and hydration products. Jennite, with its porosity and finite silicate chain accounted for, can be considered the closer and representative structure of C-S-H. In addition, this study confirms the important effect of C/S ratio, packing factor and chain length on elastic properties of C-S-H.

Molecular Dynamic Simulation of Escape of Hydrogen Atoms from (5, 5) Carbon Nanotubes

2008 ◽  
Vol 24 (2) ◽  
pp. 173-177 ◽  
Author(s):  
C. S. Wang ◽  
J. S. Chen ◽  
Y. C. Wang ◽  
J. Lee ◽  
Y. P. Chyou
Keyword(s):  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Energy Gap ◽  
Hydrogen Atoms ◽  
Carbon Tube ◽  
Hole Area ◽  
Simulation Based ◽  
Mass And Heat Transfer ◽  
Atom Release

ABSTRACTIn this article the mass and heat transfer between fluid molecule and carbon tube is studied via molecular dynamic simulation based on Lennard-Jones Potentia and Bernner-Tersoff Potential model. Some valve holes are formed by removing different numbers of molecules from flank of (5, 5) armchair carbon tube (the hole area = 17.3 ∼ 116.9Å2). The results indicate that only diffusion behavior is not able to describe the phenomena, otherwise the atom release rate and valve hole size are interdependent. Meanwhile the variation of potential energy barrier, work function, energy gap arose from different valve geometrical size are observed. These variations can influence the dynamic behavior such as flow rate and velocity by molecule penetration.

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