The self-assembly mechanism of tetra-peptides from the motif of β-amyloid peptides: a combined coarse-grained and all-atom molecular dynamics simulation

RSC Advances ◽  
2016 ◽  
Vol 6 (102) ◽  
pp. 100072-100078 ◽  
Author(s):  
Lijun Liang ◽  
Li-Wei Wang ◽  
Jia-Wei Shen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Self Assembly ◽  
The Self ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Aβ Peptides ◽  
Amyloid Peptides ◽  
Assembly Mechanism ◽  
Β Amyloid

Understanding the self-assembly mechanisms of tetra-peptides from Aβ-peptides into different nanostructures.

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 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.

Molecular insights into the self-assembly of short amphiphilic peptides FmDn and FmKn

RSC Advances ◽  
2014 ◽  
Vol 4 (105) ◽  
pp. 60741-60748 ◽  
Author(s):  
Naresh Thota ◽  
Yijia Ma ◽  
Jianwen Jiang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Self Assembly ◽  
The Self ◽  
Dynamics Simulation ◽  
Amphiphilic Peptides

Molecular dynamics simulation is reported for the self-assembly of short amphiphilic peptides FmDn and FmKn.

scholarly journals Supramolecular Nucleoside-Based Gel: Molecular Dynamics Simulation and Characterization of Its Nanoarchitecture and Self-Assembly Mechanism

Langmuir ◽  
2018 ◽  
Vol 34 (23) ◽  
pp. 6912-6921 ◽  
Author(s):  
Maria G. F. Angelerou ◽  
Pim W. J. M. Frederix ◽  
Matthew Wallace ◽  
Bin Yang ◽  
Alison Rodger ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Self Assembly ◽  
Dynamics Simulation ◽  
Assembly Mechanism
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