scholarly journals Entropy-Induced Separation of Binary Semiflexible Ring Polymer Mixtures in Spherical Confinement

Polymers ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1992 ◽  
Author(s):  
Xiaolin Zhou ◽  
Fuchen Guo ◽  
Ke Li ◽  
Linli He ◽  
Linxi Zhang
Keyword(s):  
Coarse Grained ◽  
Number Density ◽  
Polymer Mixtures ◽  
Bending Energy ◽  
Volume Depletion ◽  
Small Ratio ◽  
The Matrix ◽  
Ring Polymers ◽  
Ring Polymer ◽  
Dynamics Simulations

Coarse-grained molecular dynamics simulations are used to investigate the conformations of binary semiflexible ring polymers (SRPs) of two different lengths confined in a hard sphere. Segregated structures of SRPs in binary mixtures are strongly dependent upon the number density of system (ρ), the bending energy of long SRPs (Kb, long), and the chain length ratio of long to short SRPs (α). With a low ρ or a weak Kb, long at a small ratio α, long SRPs are immersed randomly in the matrix of short SRPs. As ρ and bending energy of long SRPs (Kb, long) are increased up to a certain value for a large ratio α, a nearly complete segregation between long and short SRPs is observed, which can be further characterized by the ratio of tangential and radial components of long SRPs velocity. These explicit segregated structures of the two components in spherical confinement are induced by a delicate competition between the entropic excluded volume (depletion) effects and bending contributions.

scholarly journals Reaction–diffusion basis of retroviral infectivity

2016 ◽  
Vol 374 (2080) ◽  
pp. 20160148 ◽  
Author(s):  
S. Kashif Sadiq
Keyword(s):  
Chemical Reactions ◽  
Membrane Surface ◽  
Reaction Diffusion ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Multiscale Approach ◽  
The Matrix ◽  
Membrane Bound ◽  
Spatio Temporal ◽  
Dynamics Simulations

Retrovirus particle (virion) infectivity requires diffusion and clustering of multiple transmembrane envelope proteins (Env 3 ) on the virion exterior, yet is triggered by protease-dependent degradation of a partially occluding, membrane-bound Gag polyprotein lattice on the virion interior. The physical mechanism underlying such coupling is unclear and only indirectly accessible via experiment. Modelling stands to provide insight but the required spatio-temporal range far exceeds current accessibility by all-atom or even coarse-grained molecular dynamics simulations. Nor do such approaches account for chemical reactions, while conversely, reaction kinetics approaches handle neither diffusion nor clustering. Here, a recently developed multiscale approach is considered that applies an ultra-coarse-graining scheme to treat entire proteins at near-single particle resolution, but which also couples chemical reactions with diffusion and interactions. A model is developed of Env 3 molecules embedded in a truncated Gag lattice composed of membrane-bound matrix proteins linked to capsid subunits, with freely diffusing protease molecules. Simulations suggest that in the presence of Gag but in the absence of lateral lattice-forming interactions, Env 3 diffuses comparably to Gag-absent Env 3 . Initial immobility of Env 3 is conferred through lateral caging by matrix trimers vertically coupled to the underlying hexameric capsid layer. Gag cleavage by protease vertically decouples the matrix and capsid layers, induces both matrix and Env 3 diffusion, and permits Env 3 clustering. Spreading across the entire membrane surface reduces crowding, in turn, enhancing the effect and promoting infectivity. This article is part of the themed issue ‘Multiscale modelling at the physics–chemistry–biology interface’.

scholarly journals Friction between ring polymer brushes

Soft Matter ◽  
2015 ◽  
Vol 11 (16) ◽  
pp. 3139-3148 ◽  
Author(s):  
Aykut Erbaş ◽  
Jarosław Paturej
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Polymer Brushes ◽  
Polymer Brush ◽  
Linear Polymer ◽  
Coarse Grained ◽  
Ring Polymer ◽  
Dynamics Simulations ◽  
Scaling Arguments ◽  
Coarse Grained Molecular Dynamics

Friction between ring polymer brush bilayers sliding past each other is studied using extensive coarse-grained molecular dynamics simulations and scaling arguments, and the results are compared to the friction between bilayers of linear polymer brushes.

Intrinsic structure and dynamics of monolayer ring polymer melts

Soft Matter ◽  
2021 ◽  
Author(s):  
Jinseong Kim ◽  
Jun Mo Kim ◽  
Chunggi Baig
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Two Dimensional ◽  
Intrinsic Structure ◽  
Dynamical Characteristics ◽  
Structure And Dynamics ◽  
Ring Polymers ◽  
Ring Polymer ◽  
Dynamics Simulations ◽  
Flexible Ring

We present the general structural and dynamical characteristics of flexible ring polymers in narrowly confined two-dimensional (2D) melt systems using atomistic molecular dynamics simulations. The results are further analyzed via...

Collective Motion of Cells Modeled as Ring Polymers

Soft Matter ◽  
2022 ◽  
Author(s):  
Haosheng Wen ◽  
Yu Zhu ◽  
Chenhui Peng ◽  
Sunil P. B. Kumar ◽  
Mohamed Laradji
Keyword(s):  
Collective Behavior ◽  
Collective Motion ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Ring Polymers ◽  
Ring Polymer ◽  
Flexible Ring

In this article, we use a coarse-grained model of disjoint semi-flexible ring polymers to investigate computationally the spatiotemporal collective behavior of cell colonies. A ring polymer in this model is...

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...

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

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...

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