pH-dependent self-assembly of EAK16 peptides in the presence of a hydrophobic surface: Coarse-grained molecular dynamics simulation

Soft Matter ◽  
2014 ◽  
Vol 10 (24) ◽  
pp. 4248 ◽  
Author(s):  
Soheila Emamyari ◽  
Hossein Fazli
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Self Assembly ◽  
Hydrophobic Surface ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Ph Dependent ◽  
Coarse Grained Molecular Dynamics

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 Coarse-grained molecular dynamics simulation of the interface behaviour and self-assembly of CTAB cationic surfactants

2018 ◽  
Vol 20 (41) ◽  
pp. 26422-26430 ◽  
Author(s):  
Sílvia Illa-Tuset ◽  
David C. Malaspina ◽  
Jordi Faraudo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Self Assembly ◽  
Cationic Surfactants ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Interface Behaviour ◽  
Coarse Grained Molecular Dynamics

We study surfactant molecules at interfaces, micelles and their self-assembly with different models (all atomic and coarse grained).

scholarly journals A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water

2014 ◽  
Vol 2014 ◽  
pp. 1-6 ◽  
Author(s):  
Dwi Hudiyanti ◽  
Muhammad Radifar ◽  
Tri Joko Raharjo ◽  
Narsito Narsito ◽  
Sri Noegrohati
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Self Assembly ◽  
The Self ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Energy Profile ◽  
Assembly Process ◽  
Planar Bilayer ◽  
Coarse Grained Molecular Dynamics

The energy profile of self-assembly process of DLPE, DLPS, DOPE, DOPS, DLiPE, and DLiPS in water was investigated by a coarse-grained molecular dynamics simulation using NAMD package. The self-assembly process was initiated from random configurations. The simulation was carried out for 160 ns. This study presented proof that there were three major self-assembled arrangements which became visible for a certain duration when the simulation took place, that is, liposome, deformed liposome, and planar bilayer. The energy profile that shows plateau at the time of these structures emerge confirmed their stability therein. Our findings have highlighted the idea that liposomes and deformed liposomes are metastable phases which eventually will turn into planar bilayer, the stable one.

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.

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