Persistence Length, End-to-End Distance, and Structure of Coarse-Grained Polymers

2018 ◽  
Vol 14 (4) ◽  
pp. 2219-2229 ◽  
Author(s):  
K. Michael Salerno ◽  
Noam Bernstein
Keyword(s):  
Persistence Length ◽  
Coarse Grained ◽  
End Distance ◽  
End To End

scholarly journals Development of Coarse-Grained Models for Poly(4-vinylphenol) and Poly(2-vinylpyridine): Polymer Chemistries with Hydrogen Bonding

Polymers ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 2764
Author(s):  
Utkarsh Kapoor ◽  
Arjita Kulshreshtha ◽  
Arthi Jayaraman
Keyword(s):  
Hydrogen Bonding ◽  
Bond Angle ◽  
Persistence Length ◽  
Distance Distribution ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Implicit Solvent ◽  
End Distance ◽  
End To End ◽  
Chain Lengths

In this paper, we identify the modifications needed in a recently developed generic coarse-grained (CG) model that captured directional interactions in polymers to specifically represent two exemplary hydrogen bonding polymer chemistries—poly(4-vinylphenol) and poly(2-vinylpyridine). We use atomistically observed monomer-level structures (e.g., bond, angle and torsion distribution) and chain structures (e.g., end-to-end distance distribution and persistence length) of poly(4-vinylphenol) and poly(2-vinylpyridine) in an explicitly represented good solvent (tetrahydrofuran) to identify the appropriate modifications in the generic CG model in implicit solvent. For both chemistries, the modified CG model is developed based on atomistic simulations of a single 24-mer chain. This modified CG model is then used to simulate longer (36-mer) and shorter (18-mer and 12-mer) chain lengths and compared against the corresponding atomistic simulation results. We find that with one to two simple modifications (e.g., incorporating intra-chain attraction, torsional constraint) to the generic CG model, we are able to reproduce atomistically observed bond, angle and torsion distributions, persistence length, and end-to-end distance distribution for chain lengths ranging from 12 to 36 monomers. We also show that this modified CG model, meant to reproduce atomistic structure, does not reproduce atomistically observed chain relaxation and hydrogen bond dynamics, as expected. Simulations with the modified CG model have significantly faster chain relaxation than atomistic simulations and slower decorrelation of formed hydrogen bonds than in atomistic simulations, with no apparent dependence on chain length.

scholarly journals Semiflexible Polymer Enclosed in a 3D Compact Domain

2021 ◽  
Vol 9 ◽  
Author(s):  
Pavel Castro-Villarreal ◽  
J. E. Ramírez
Keyword(s):  
Persistence Length ◽  
Compact Domain ◽  
Mean Square ◽  
Shape Transition ◽  
Conformational States ◽  
Semiflexible Polymer ◽  
End Distance ◽  
The Mean ◽  
End To End ◽  
Polymer Shape

The conformational states of a semiflexible polymer enclosed in a volume V:=ℓ3 are studied as stochastic realizations of paths using the stochastic curvature approach developed in [Rev. E 100, 012503 (2019)], in the regime whenever 3ℓ/ℓp>1, where ℓp is the persistence length. The cases of a semiflexible polymer enclosed in a cube and sphere are considered. In these cases, we explore the Spakowitz–Wang–type polymer shape transition, where the critical persistence length distinguishes between an oscillating and a monotonic phase at the level of the mean-square end-to-end distance. This shape transition provides evidence of a universal signature of the behavior of a semiflexible polymer confined in a compact domain.

scholarly journals Phosphorylation Increases Persistence Length and End-to-End Distance of a Segment of Tau Protein

2016 ◽  
Vol 110 (2) ◽  
pp. 362-371 ◽  
Author(s):  
Alexander F. Chin ◽  
Dmitri Toptygin ◽  
W. Austin Elam ◽  
Travis P. Schrank ◽  
Vincent J. Hilser
Keyword(s):  
Tau Protein ◽  
Persistence Length ◽  
End Distance ◽  
End To End

Self‐avoiding walks with span limitations. I. The mean square end‐to‐end distance

1980 ◽  
Vol 72 (4) ◽  
pp. 2702-2707 ◽  
Author(s):  
Ronnie Barr ◽  
Chava Brender ◽  
Melvin Lax
Keyword(s):  
Mean Square ◽  
End Distance ◽  
The Mean ◽  
End To End ◽  
Self Avoiding Walks

scholarly journals Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA

2018 ◽  
Author(s):  
Debayan Chakraborty ◽  
Naoto Hori ◽  
D. Thirumalai
Keyword(s):  
Electrostatic Interactions ◽  
Persistence Length ◽  
Data Bank ◽  
Coarse Grained ◽  
Force Extension ◽  
Sequence Dependence ◽  
Coarse Grained Model ◽  
Interaction Sites ◽  
Double Stranded Dna ◽  
Centers Of Mass

AbstractWe develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes base-stacking, hydrogen bond, and electrostatic interactions as well as bond-stretching and bond angle potentials that account for the polymeric nature of DNA. The choices of force constants for stretching and the bending potentials were guided by a Boltzmann inversion procedure using a large representative set of DNA structures extracted from the Protein Data Bank. Some of the parameters in the stacking interactions were calculated using a learning procedure, which ensured that the experimentally measured melting temperatures of dimers are faithfully reproduced. Without any further adjustments, the calculations based on the TIS model reproduces the experimentally measured salt and sequence dependence of the size of single stranded DNA (ssDNA), as well as the persistence lengths of poly(dA) and poly(dT) chains. Interestingly, upon application of mechanical force the extension of poly(dA) exhibits a plateau, which we trace to the formation of stacked helical domains. In contrast, the force-extension curve (FEC) of poly(dT) is entropic in origin, and could be described by a standard polymer model. We also show that the persistence length of double stranded DNA, formed from two complementary ssDNAs with one hundred and thirty base pairs, is consistent with the prediction based on the worm-like chain. The persistence length, which decreases with increasing salt concentration, is in accord with the Odijk-Skolnick-Fixman theory intended for stiff polyelectrolyte chains near the rod limit. The range of applications, which did not require adjusting any parameter after the initial construction based solely on PDB structures and melting profiles of dimers, attests to the transferability and robustness of the TIS model for ssDNA and dsDNA.

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