scholarly journals 2P046 Screening for Mechanical Communication in Proteins by Coarse-Grained Molecular Dynamics(01B. Protein: Structure & Function,Poster)

2013 ◽  
Vol 53 (supplement1-2) ◽  
pp. S166
Author(s):  
Yuichi Togashi
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Structure Function ◽  
Coarse Grained ◽  
Coarse Grained Molecular Dynamics

Investigation of the Microscopic Viscoelastic Property for Cross-linked Polymer Network by Molecular Dynamics Simulation

2011 ◽  
Vol 39 (1) ◽  
pp. 44-58 ◽  
Author(s):  
Y. Masumoto ◽  
Y. Iida
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Analytical Method ◽  
Viscoelastic Properties ◽  
Polymer Network ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
The Cross ◽  
Microscopic Dynamic ◽  
Coarse Grained Molecular Dynamics

Abstract The purpose of this work is to develop a new analytical method for simulating the microscopic mechanical property of the cross-linked polymer system using the coarse-grained molecular dynamics simulation. This new analytical method will be utilized for the molecular designing of the tire rubber compound to improve the tire performances such as rolling resistance and wet traction. First, we evaluate the microscopic dynamic viscoelastic properties of the cross-linked polymer using coarse-grained molecular dynamics simulation. This simulation has been conducted by the coarse-grained molecular dynamics program in the OCTA) (http://octa.jp/). To simplify the problem, we employ the bead-spring model, in which a sequence of beads connected by springs denotes a polymer chain. The linear polymer chains that are cross-linked by the cross-linking agents express the three-dimensional cross-linked polymer network. In order to obtain the microscopic dynamic viscoelastic properties, oscillatory deformation is applied to the simulation cell. By applying the time-temperature reduction law to this simulation result, we can evaluate the dynamic viscoelastic properties in the wide deformational frequency range including the rubbery state. Then, the stress is separated into the nonbonding stress and the bonding stress. We confirm that the contribution of the nonbonding stress is larger at lower temperatures. On the other hand, the contribution of the bonding stress is larger at higher temperatures. Finally, analyzing a change of microscopic structure in dynamic oscillatory deformation, we determine that the temperature/frequency dependence of bond stress response to a dynamic oscillatory deformation depends on the temperature dependence of the average bond length in the equilibrium structure and the temperature/frequency dependence of bond orientation. We show that our simulation is a useful tool for studying the microscopic properties of a cross-linked polymer.

Coarse-grained simulation of the self-assembly of lipid vesicles concomitantly with novel block copolymers with multiple tails

Soft Matter ◽  
2021 ◽  
Author(s):  
Alexander Kantardjiev
Keyword(s):  
Molecular Dynamics ◽  
Block Copolymers ◽  
Self Assembly ◽  
Lipid Vesicles ◽  
The Self ◽  
Coarse Grained ◽  
Copolymer Concentration ◽  
Copolymer Structure ◽  
Coarse Grained Molecular Dynamics

We carried out a series of coarse-grained molecular dynamics liposome-copolymer simulations with varying extent of copolymer concentration in an attempt to understand the effect of copolymer structure and concentration on vesicle self-assembly and stability.

Sliding Dynamics of Ring on Polymer in Rotaxane: A Coarse-Grained Molecular Dynamics Simulation Study

2019 ◽  
Vol 52 (10) ◽  
pp. 3787-3793 ◽  
Author(s):  
Yusuke Yasuda ◽  
Masatoshi Toda ◽  
Koichi Mayumi ◽  
Hideaki Yokoyama ◽  
Hiroshi Morita ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Sliding Dynamics ◽  
Coarse Grained Molecular Dynamics
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