Improving the productivity of monodisperse polyhedral cages by the rational design of kinetic self-assembly pathways

2018 ◽  
Vol 20 (15) ◽  
pp. 10030-10037
Author(s):  
Xiangze Zeng ◽  
Zhan-Wei Li ◽  
Xiaoyan Zheng ◽  
Lizhe Zhu ◽  
Zhao-Yan Sun ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Self Assembly ◽  
Rational Design ◽  
Network Models ◽  
Coarse Grained ◽  
Patchy Particles ◽  
Dynamics Simulations ◽  
Assembly Pathways

By constructing kinetic network models from extensive coarse-grained molecular dynamics simulations, we elucidated the formation mechanism of the dodecahedral cage and further improved the productivity of the dodecahedral cage through the rational design of the patch arrangement of patchy particles.

scholarly journals Variation of Interaction Zone Size For The Target Design of 2D Supramolecular Networks

2021 ◽  
Author(s):  
Łukasz Piotr Baran ◽  
Wojciech Rżysko ◽  
Dariusz Tarasewicz
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Coarse Grained ◽  
Zone Size ◽  
Interaction Zone ◽  
Supramolecular Networks ◽  
Dynamics Simulations ◽  
Target Design

In this study we have performed extensive coarse-grained molecular dynamics simulations of the self-assembly of tetra-substituted molecules. We have found that such molecules are able to form a variety of...

scholarly journals Formation mechanism of bound rubber in elastomer nanocomposites: a molecular dynamics simulation study

RSC Advances ◽  
2018 ◽  
Vol 8 (23) ◽  
pp. 13008-13017 ◽  
Author(s):  
Jun Liu ◽  
Haixiao Wan ◽  
Huanhuan Zhou ◽  
Yancong Feng ◽  
Liqun Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Bound Rubber ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

The formation mechanism of the bound rubber in elastomer nanocomposites using the coarse-grained molecular-dynamics simulations.

Photoluminescent organic polymer nanofilms formed in water through a self-assembly formation mechanism

2019 ◽  
Vol 7 (11) ◽  
pp. 3286-3293 ◽  
Author(s):  
Baoxi Feng ◽  
Zhen Xu ◽  
Jiayu Wang ◽  
Fei Feng ◽  
Lin Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Real Time ◽  
Formation Mechanism ◽  
Self Assembly ◽  
Organic Polymer ◽  
Assembly Mechanism ◽  
Real Time Visualization ◽  
Dynamics Simulations

A self-assembly mechanism is demonstrated for the formation of polymer nanofilms based on real-time visualization and molecular dynamics simulations.

Self-assembly of amphiphilic polymers of varying architectures near attractive surfaces

Soft Matter ◽  
2020 ◽  
Vol 16 (3) ◽  
pp. 623-633 ◽  
Author(s):  
Michiel G. Wessels ◽  
Arthi Jayaraman
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
Amphiphilic Polymers ◽  
Coarse Grained ◽  
Polymer Architecture ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

We use coarse-grained molecular dynamics simulations to investigate the assembly of A–B amphiphilic polymers near/on surfaces as a function of polymer architecture and surface attraction to the solvophobic B-block in the polymer.

scholarly journals Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications

2019 ◽  
Vol 20 (15) ◽  
pp. 3774 ◽  
Author(s):  
Nidhi Singh ◽  
Wenjin Li
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
Structure Prediction ◽  
Biological Systems ◽  
Conformational Dynamics ◽  
Multiscale Simulation ◽  
Coarse Grained ◽  
Hierarchical Level ◽  
Dynamics Simulations

Molecular dynamics simulations have emerged as a powerful tool to study biological systems at varied length and timescales. The conventional all-atom molecular dynamics simulations are being used by the wider scientific community in routine to capture the conformational dynamics and local motions. In addition, recent developments in coarse-grained models have opened the way to study the macromolecular complexes for time scales up to milliseconds. In this review, we have discussed the principle, applicability and recent development in coarse-grained models for biological systems. The potential of coarse-grained simulation has been reviewed through state-of-the-art examples of protein folding and structure prediction, self-assembly of complexes, membrane systems and carbohydrates fiber models. The multiscale simulation approaches have also been discussed in the context of their emerging role in unravelling hierarchical level information of biosystems. We conclude this review with the future scope of coarse-grained simulations as a constantly evolving tool to capture the dynamics of biosystems.

scholarly journals Self-assembly of endohedral metallofullerenes: a decisive role of cooling gas and metal–carbon bonding

Nanoscale ◽  
2016 ◽  
Vol 8 (6) ◽  
pp. 3796-3808 ◽  
Author(s):  
Qingming Deng ◽  
Thomas Heine ◽  
Stephan Irle ◽  
Alexey A. Popov
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Self Assembly ◽  
Crucial Role ◽  
Decisive Role ◽  
Endohedral Metallofullerenes ◽  
Dynamics Simulations ◽  
Carbon Bonding

Molecular dynamics simulations of the endohedral metallofullerene formation reveal a crucial role of the cooling gas (He) and the strength of metal–carbon bonding in the formation mechanism.

scholarly journals Molecular Dynamics Simulations of a Catalytic Multivalent Peptide–Nanoparticle Complex

2021 ◽  
Vol 22 (7) ◽  
pp. 3624
Author(s):  
Sutapa Dutta ◽  
Stefano Corni ◽  
Giorgia Brancolini
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Self Assembly ◽  
Brownian Dynamics ◽  
Rational Design ◽  
Complex Structure ◽  
Gold Nanocluster ◽  
Field Development ◽  
Dynamics Simulations

Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide–nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure–function relationship, for technological and nanomedical applications.

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