Conformational states of HAMP domains interacting with sensory rhodopsin membrane systems: an integrated all-atom and coarse-grained molecular dynamics simulation approach

2017 ◽  
Vol 13 (1) ◽  
pp. 193-207 ◽  
Author(s):  
Bikash Ranjan Sahoo ◽  
Toshimichi Fujiwara
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Structural Basis ◽  
Simulation Approach ◽  
Membrane Systems ◽  
Sensory Rhodopsin ◽  
Helix Bundle ◽  
Natronomonas Pharaonis

The mechanistic and structural basis of srII–htrII signaling mediated by a HAMP four-helix bundle inNatronomonas pharaonis.

scholarly journals Self-Assembly Behavior of Amphiphilic Janus Dendrimers in Water: A Combined Experimental and Coarse-Grained Molecular Dynamics Simulation Approach

Molecules ◽  
2018 ◽  
Vol 23 (4) ◽  
pp. 969 ◽  
Author(s):  
Mariana Elizondo-García ◽  
Valeria Márquez-Miranda ◽  
Ingrid Araya-Durán ◽  
Jesús Valencia-Gallegos ◽  
Fernando González-Nilo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Self Assembly ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Simulation Approach ◽  
Assembly Behavior ◽  
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.

scholarly journals Distribution and Transport of CO2 in Hydrated Hyperbranched Poly(ethylenimine) Membranes: A Molecular Dynamics Simulation Approach

ACS Omega ◽  
2021 ◽  
Vol 6 (4) ◽  
pp. 3390-3398
Author(s):  
Kyung Il Kim ◽  
Robin Lawler ◽  
Hyun June Moon ◽  
Pavithra Narayanan ◽  
Miles A. Sakwa-Novak ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Simulation Approach ◽  
Hyperbranched Poly

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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