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...

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.

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...

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...

Self-Similar Dynamics of a Flexible Ring Polymer in a Fixed Obstacle Environment: A Coarse-Grained Molecular Model

2009 ◽  
Vol 48 (21) ◽  
pp. 9514-9522
Author(s):  
Balaji V. S. Iyer ◽  
Ashish K. Lele ◽  
Vinay A. Juvekar ◽  
Raghunath A. Mashelkar
Keyword(s):  
Molecular Model ◽  
Coarse Grained ◽  
Ring Polymer ◽  
Self Similar ◽  
Flexible Ring

Insights Into Crowding Effects on Protein Stability From a Coarse-Grained Model

2009 ◽  
Vol 131 (7) ◽  
Author(s):  
Vincent K. Shen ◽  
Jason K. Cheung ◽  
Jeffrey R. Errington ◽  
Thomas M. Truskett
Keyword(s):  
Protein Stability ◽  
Coarse Grained ◽  
Protein Solutions ◽  
Native State ◽  
High Concentration ◽  
Coarse Grained Model ◽  
Excluded Volume Effects ◽  
Thermodynamic Phase ◽  
Broad Interest ◽  
Liquid Liquid Phase Separation

Proteins aggregate and precipitate from high concentration solutions in a wide variety of problems of natural and technological interest. Consequently, there is a broad interest in developing new ways to model the thermodynamic and kinetic aspects of protein stability in these crowded cellular or solution environments. We use a coarse-grained modeling approach to study the effects of different crowding agents on the conformational equilibria of proteins and the thermodynamic phase behavior of their solutions. At low to moderate protein concentrations, we find that crowding species can either stabilize or destabilize the native state, depending on the strength of their attractive interaction with the proteins. At high protein concentrations, crowders tend to stabilize the native state due to excluded volume effects, irrespective of the strength of the crowder-protein attraction. Crowding agents reduce the tendency of protein solutions to undergo a liquid-liquid phase separation driven by strong protein-protein attractions. The aforementioned equilibrium trends represent, to our knowledge, the first simulation predictions for how the properties of crowding species impact the global thermodynamic stability of proteins and their solutions.

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