Conformational Behavior and Self-Assembly of Disjoint Semi-Flexible Ring Polymers Adsorbed on Solid Substrates

Soft Matter ◽  
2021 ◽  
Author(s):  
Yu Zhu ◽  
Sunil P. B. Kumar ◽  
Mohamed Laradji
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
Spatial Organization ◽  
Coarse Grained ◽  
Conformational Behavior ◽  
Solid Substrates ◽  
Ring Polymers ◽  
Dynamics Simulations ◽  
Flexible Ring

The conformational behavior and spatial organization of self-avoiding semi-flexible ring polymers that are fully adsorbed on solid substrates are investigated via systematic coarse-grained molecular dynamics simulations. Our results show that...

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 Effects of Topological Constraints on Penetration Structures of Semi-Flexible Ring Polymers

Polymers ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 2659
Author(s):  
Fuchen Guo ◽  
Ke Li ◽  
Jiaxin Wu ◽  
Linli He ◽  
Linxi Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Effective Potential ◽  
Topological Constraints ◽  
Chain Stiffness ◽  
Ring Polymers ◽  
Dynamics Simulations ◽  
Flexible Ring ◽  
Peak Value ◽  
Improved Algorithm

The effects of topological constraints on penetration structures of semi-flexible ring polymers in a melt are investigated using molecular dynamics simulations, considering simultaneously the effects of the chain stiffness. Three topology types of rings are considered: 01-knot (the unknotted), 31-knot and 61-knot ring polymers, respectively. With the improved algorithm to detect and quantify the inter-ring penetration (or inter-ring threading), the degree of ring threading does not increase monotonously with the chain stiffness, existing a peak value at the intermediate stiffness. It indicates that rings interpenetrate most at intermediate stiffness where there is a balance between coil expansion (favoring penetrations) and stiffness (inhibiting penetrations). Meanwhile, the inter-ring penetration would be suppressed with the knot complexity of the rings. The analysis of effective potential between the rings provides a better understanding for this non-monotonous behavior in inter-ring penetration.

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.

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 Coarse-Grained Molecular Dynamics Simulations of the Self-Assembly of Amphiphilic Dendrimers as Gene Carriers

2015 ◽  
Vol 108 (2) ◽  
pp. 172a
Author(s):  
Valeria Marquez-Miranda ◽  
Iingrid Araya ◽  
Maria Belen Camarada ◽  
Lars Ratjen ◽  
Maria Carolina Otero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Coarse Grained ◽  
Gene Carriers ◽  
Amphiphilic Dendrimers ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics
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