OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field

2019 ◽  
Vol 15 (6) ◽  
pp. 3875-3888 ◽  
Author(s):  
Fernando Luís Barroso da Silva ◽  
Fabio Sterpone ◽  
Philippe Derreumaux
2020 ◽  
Vol 22 (3) ◽  
pp. 1682-1692 ◽  
Author(s):  
Oscar Y. Fajardo ◽  
Silvia Di Lecce ◽  
Fernando Bresme

A Coarse Grained (CG) model to investigate the structure, dynamics and interfacial properties of the [C2–8MIM][BF4] family of ionic liquids is proposed.


Author(s):  
Maziar Fayaz-Torshizi ◽  
Erich A. Müller

A methodology is outlined to parametrize coarse grained molecular models for the molecular dynamics simulation of liquid crystals.


RSC Advances ◽  
2020 ◽  
Vol 10 (22) ◽  
pp. 13066-13075
Author(s):  
Yee Ying Lim ◽  
Theam Soon Lim ◽  
Yee Siew Choong

An in silico IgG-Fc variant with better affinity at pH 6.0 but retained the dissociation at pH 7.5 was designed.


2011 ◽  
Vol 39 (1) ◽  
pp. 44-58 ◽  
Author(s):  
Y. Masumoto ◽  
Y. Iida

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.


2019 ◽  
Vol 52 (10) ◽  
pp. 3787-3793 ◽  
Author(s):  
Yusuke Yasuda ◽  
Masatoshi Toda ◽  
Koichi Mayumi ◽  
Hideaki Yokoyama ◽  
Hiroshi Morita ◽  
...  

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