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
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Force Field ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Constant Ph ◽  
Constant Ph Molecular Dynamics ◽  
Simulation Scheme

scholarly journals Molecular dynamics simulation of imidazolium CnMIM-BF4 ionic liquids using a coarse grained force-field

2020 ◽  
Vol 22 (3) ◽  
pp. 1682-1692 ◽  
Author(s):  
Oscar Y. Fajardo ◽  
Silvia Di Lecce ◽  
Fernando Bresme
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulation ◽  
Force Field ◽  
Interfacial Properties ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Structure Dynamics

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

scholarly journals Coarse-grained molecular dynamics study of the self-assembly of polyphilic bolaamphiphiles using the SAFT-γ Mie force field

2021 ◽  
Author(s):  
Maziar Fayaz-Torshizi ◽  
Erich A. Müller
Keyword(s):  
Molecular Dynamics ◽  
Liquid Crystals ◽  
Molecular Dynamics Simulation ◽  
Force Field ◽  
Self Assembly ◽  
The Self ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Molecular Models ◽  
Coarse Grained Molecular Dynamics

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

scholarly journals Human IgG1 Fc pH-dependent optimization from a constant pH molecular dynamics simulation analysis

RSC Advances ◽  
2020 ◽  
Vol 10 (22) ◽  
pp. 13066-13075
Author(s):  
Yee Ying Lim ◽  
Theam Soon Lim ◽  
Yee Siew Choong
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
In Silico ◽  
Simulation Analysis ◽  
Dynamics Simulation ◽  
Constant Ph ◽  
Human Igg1 ◽  
Ph Dependent ◽  
Constant Ph Molecular Dynamics

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

scholarly journals pKa Determination of Histidine Residues in α-Conotoxin MII Peptides by 1H NMR and Constant pH Molecular Dynamics Simulation

2013 ◽  
Vol 117 (9) ◽  
pp. 2653-2661 ◽  
Author(s):  
Owen M. McDougal ◽  
David M. Granum ◽  
Mark Swartz ◽  
Conrad Rohleder ◽  
C. Mark Maupin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
1H Nmr ◽  
Dynamics Simulation ◽  
Histidine Residues ◽  
Constant Ph ◽  
Pka Determination ◽  
Constant Ph 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 Molecular Dynamics Simulation of Silicon Dioxide Etching by Hydrogen Fluoride Using the Reactive Force Field

ACS Omega ◽  
2021 ◽  
Author(s):  
Dong Hyun Kim ◽  
Seung Jae Kwak ◽  
Jae Hun Jeong ◽  
Suyoung Yoo ◽  
Sang Ki Nam ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Silicon Dioxide ◽  
Force Field ◽  
Hydrogen Fluoride ◽  
Dynamics Simulation ◽  
Reactive Force ◽  
Reactive Force Field

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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