scholarly journals Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics

2004 ◽  
Vol 58 (2) ◽  
pp. 459-471 ◽  
Author(s):  
Giacomo M.S. De Mori ◽  
Giorgio Colombo ◽  
Cristian Micheletti
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Coarse Grained ◽  
Villin Headpiece ◽  
Folding Dynamics

scholarly journals Simulations of the 2D self-assembly of tripod-shaped building blocks

2020 ◽  
Vol 11 ◽  
pp. 884-890
Author(s):  
Łukasz Baran ◽  
Wojciech Rżysko ◽  
Edyta Słyk
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Diffraction Pattern ◽  
Triangular Lattice ◽  
Self Assembly ◽  
Building Blocks ◽  
Coarse Grained ◽  
Coarse Grained Model

We introduce a molecular dynamics (MD) coarse-grained model for the description of tripod building blocks. This model has been used by us already for linear, V-shape, and tetratopic molecules. We wanted to further extend its possibilities to trifunctional molecules to prove its versatility. For the chosen systems we have also compared the MD results with Monte Carlo results on a triangular lattice. We have shown that the constraints present in the latter method can enforce the formation of completely different structures, not reproducible with off-lattice simulations. In addition to that, we have characterized the obtained structures regarding various parameters such as theoretical diffraction pattern and average association number.

Dynamics and reaction kinetics of coarse-grained bulk vitrimers: a molecular dynamics study

2019 ◽  
Vol 21 (24) ◽  
pp. 13258-13267 ◽  
Author(s):  
Jian-Bo Wu ◽  
Shu-Jia Li ◽  
Hong Liu ◽  
Hu-Jun Qian ◽  
Zhong-Yuan Lu
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Reaction Kinetics ◽  
Dynamic Behavior ◽  
Coarse Grained ◽  
Exchange Reactions ◽  
Dynamics Model ◽  
System P ◽  
Intrinsic Mechanism ◽  
Kinetics Of

We used the hybrid molecular dynamics–Monte Carlo (MD–MC) algorithm to establish a molecular dynamics model that can accurately reflect bond exchange reactions, and reveal the intrinsic mechanism of the dynamic behavior of the vitrimer system.

Multiscale modelling of charge transport in P3HT:DIPBI bulk heterojunction organic solar cells

2021 ◽  
Author(s):  
Tobias Koch ◽  
Jim-Martin Bachmann ◽  
Tobias Lettmann ◽  
Nikos Doltsinis
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Solar Cell ◽  
Charge Transport ◽  
Organic Solar Cells ◽  
Bulk Heterojunction ◽  
Kinetic Monte Carlo ◽  
Coarse Grained ◽  
Bulk Heterojunction Solar Cell ◽  
Kinetic Monte Carlo Simulations

Charge transport properties of a P3HT:DIPBI bulk heterojunction solar cell are modelled by kinetic Monte Carlo simulations based on a morphology obtained from coarse grained molecular dynamics. Different methods for...

Distinguishing the influence of structural and energetic disorder on electron transport in fullerene multi-adducts

2015 ◽  
Vol 2 (1) ◽  
pp. 113-119 ◽  
Author(s):  
Florian Steiner ◽  
Samuel Foster ◽  
Arthur Losquin ◽  
John Labram ◽  
Thomas D. Anthopoulos ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Electron Transport ◽  
Kinetic Monte Carlo ◽  
Structural Disorder ◽  
Coarse Grained ◽  
Monte Carlo Modeling ◽  
Energetic Disorder ◽  
Coarse Grained Molecular Dynamics

A combination of coarse-grained molecular dynamics and kinetic Monte-Carlo modeling shows that electron transport in fullerene multi-adducts is limited by energetic disorder due to different isomers rather than by structural disorder.

MOLECULAR DYNAMICS SIMULATIONS OF HELIX BUNDLE PROTEINS USING UNRES FORCE FIELD AND ALL-ATOM FORCE FIELD

2012 ◽  
Vol 11 (06) ◽  
pp. 1201-1215 ◽  
Author(s):  
KAIFU GAO ◽  
MINGHUI YANG
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Protein A ◽  
Md Simulations ◽  
Time Frame ◽  
Coarse Grained ◽  
Staphylococcal Protein A ◽  
Villin Headpiece ◽  
Helix Bundle ◽  
Dynamics Simulations

We have investigated the folding of two helix-bundle proteins, 36-residue Villin headpiece and 56-residue E-domain of Staphylococcal protein A, by combining molecular dynamics (MD) simulations with Coarse-Grained United-Residue (UNRES) Force Field and all-atom force field. Starting from extended structures, each of the proteins was folded to a stable structure within a short time frame using the UNRES model. However, the secondary structures of helices were not well formed. Further refinement using MD simulations with the all-atom force field was able to fold the protein structure into the native-like state with the smallest main-chain root-mean-square deviation of around 3 Å. Detailed analysis of the folding trajectories was presented and the performance of GPU-based MD simulations was also discussed.

A coarse-grained molecular dynamics – reactive Monte Carlo approach to simulate hyperbranched polycondensation

RSC Advances ◽  
2014 ◽  
Vol 4 (100) ◽  
pp. 56625-56636 ◽  
Author(s):  
Zidan Zhang ◽  
Long Wang ◽  
Zilu Wang ◽  
Xuehao He ◽  
Yu Chen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Coarse Grained ◽  
Monte Carlo Approach ◽  
Coarse Grained Molecular Dynamics
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