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.

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...

scholarly journals From the Potential of the Mean Force to a Quasiparticle’s Effective Potential in Narrow Ion Channels

2019 ◽  
Vol 18 (02) ◽  
pp. 1940006 ◽  
Author(s):  
M. L. Barabash ◽  
W. A. T. Gibby ◽  
C. Guardiani ◽  
D. G. Luchinsky ◽  
P. V. E. McClintock
Keyword(s):  
Molecular Dynamics ◽  
Ion Channels ◽  
Molecular Dynamics Simulations ◽  
Strong Interaction ◽  
Effective Potential ◽  
Current Voltage ◽  
Ionic Motion ◽  
The Mean ◽  
Highly Correlated ◽  
Dynamics Simulations

We consider the selective permeation of ions through narrow water-filled channels in the presence of strong interaction between the ions. These interactions lead to highly correlated ionic motion, which can conveniently be described via the concept of a quasiparticle. Here, we connect the quasiparticle’s effective potential and the multi-ion potential of the mean force, found through molecular dynamics simulations, and we validate the method on an analytical toy model of the KcsA channel. Possible future applications of the method to the connection between molecular dynamical calculations and the experimentally measured current-voltage and current-concentration characteristics of the channel are discussed.

scholarly journals “On-the-fly” coupled cluster path-integral molecular dynamics: impact of nuclear quantum effects on the protonated water dimer

2015 ◽  
Vol 17 (22) ◽  
pp. 14355-14359 ◽  
Author(s):  
Thomas Spura ◽  
Hossam Elgabarty ◽  
Thomas D. Kühne
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Path Integral ◽  
Effective Potential ◽  
Water Dimer ◽  
Coupled Cluster ◽  
Single Well ◽  
Cluster Path ◽  
Dynamics Simulations ◽  
Nuclear Quantum Effects

“On-the-fly” coupled cluster-based path-integral molecular dynamics simulations predict that the effective potential of the protonated water–dimer has a single-well only.

scholarly journals Effects of precursor topology and synthesis under crowding conditions on the structure of single-chain polymer nanoparticles

Soft Matter ◽  
2017 ◽  
Vol 13 (37) ◽  
pp. 6430-6438 ◽  
Author(s):  
Maud Formanek ◽  
Angel J. Moreno
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Polymer Nanoparticles ◽  
Cross Linking ◽  
Single Chain ◽  
Chain Polymer ◽  
Ring Polymers ◽  
Concentrated Solution ◽  
Dynamics Simulations

By means of molecular dynamics simulations, we investigate the formation of single-chain nanoparticles through intramolecular cross-linking of linear and ring polymers, in the presence of their precursors acting as purely steric crowders in concentrated solution.

Molecular-Dynamics Simulations of Magnetic Structures in Metallic Systems

2001 ◽  
Vol 677 ◽  
Author(s):  
Ralf Meyer ◽  
Laurent J. Lewis
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Rotational Symmetry ◽  
Tight Binding ◽  
Exchange Interactions ◽  
Magnetic Structures ◽  
Simulated System ◽  
Dynamics Simulations ◽  
Metallic Systems ◽  
Improved Algorithm

ABSTRACTRecently a method has been proposed which allows the calculation of complex magnetic structures from a simple d-band tight-binding Hamiltonian including Coulomb and exchange interactions with the help of a molecular-dynamics simulations. In this article an improved version of this ap- proach is suggested which retains the rotational symmetry of the simulated system. The improved algorithm is applied to systems with electron numbers in the range 7 ≤nd ≤ 8.

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