scholarly journals Molecular dynamics simulations of Factor Xa: Insight into conformational transition of its binding subsites

Biopolymers ◽  
2008 ◽  
Vol 89 (12) ◽  
pp. 1104-1113 ◽  
Author(s):  
Narender Singh ◽  
James M. Briggs
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Transition ◽  
Factor Xa ◽  
Dynamics Simulations ◽  
Binding Subsites ◽  
Insight Into

scholarly journals Insight into the origin of SARS-CoV-2 through structural analysis of receptor recognition: a molecular simulation study

RSC Advances ◽  
2021 ◽  
Vol 11 (15) ◽  
pp. 8718-8729
Author(s):  
Jixue Sun ◽  
Meijiang Liu ◽  
Na Yang
Keyword(s):  
Molecular Dynamics ◽  
Structural Analysis ◽  
Molecular Dynamics Simulations ◽  
Molecular Simulation ◽  
Simulation Study ◽  
Receptor Recognition ◽  
Dynamics Simulations ◽  
Insight Into

The origin of SARS-CoV-2 through structural analysis of receptor recognition was investigated by molecular dynamics simulations.

Atomistic Simulation of Volumetric Properties of Epoxy Networks: Effect of Monomer Length

Soft Matter ◽  
2021 ◽  
Author(s):  
Ketan S. Khare ◽  
Cameron F Abrams
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Atomistic Simulation ◽  
Volumetric Properties ◽  
Epoxy Networks ◽  
Design Requirements ◽  
Dynamics Simulations ◽  
Insight Into

Properties of epoxy thermosets can be varied broadly to suit design requirements by altering the chemistry of the component agents. Atomistically-detailed molecular dynamics simulations are well-suited for molecular insight into...

UNDERSTANDING DIFFERENT LCST LEVELS OF POLY(N-ALKYLACRYLAMIDE)S BY MOLECULAR DYNAMICS SIMULATIONS AND QUANTUM MECHANICS CALCULATIONS

2011 ◽  
Vol 10 (03) ◽  
pp. 359-370 ◽  
Author(s):  
JUAN PANG ◽  
HU YANG ◽  
JING MA ◽  
RONGSHI CHENG
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Aqueous Solutions ◽  
Molecular Dynamics Simulations ◽  
Steric Effect ◽  
Conformational Transition ◽  
Methyl Group ◽  
Branched Chain ◽  
Dynamics Simulations ◽  
Different Levels

Poly(N-alkylacrylamide) is a group of thermo-sensitive polymers that include poly (N-isopropylacrylamide), poly(N-n-propylacrylamide), poly(N-isopropylmethacryl-amide), and so on. The polymers exhibit different levels of lower critical solution temperatures (LCST) in aqueous solutions. In this article, their monomers and oligomers with 10 repeating units are selected, respectively, to demonstrate the cause of different LCST levels of the polymers in aqueous solutions using molecular dynamics simulations and quantum mechanics calculations. The monomers have functional groups of different steric volume that greatly affect the conformational transition of chains and LCST levels of the polymers. A branched chain of N-propyl group in N-isopropylacrylamide and an additional methyl group at α-carbon in N-isopropylmethacrylamide both increase the steric effect, making it more difficult for monomers to draw closer and resulting in higher LCST levels of the polymers. In addition, the simulated results from their corresponding oligomers exhibit the similar trend to those from the monomers.

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