Changes in the end-to-end distance distribution in an oligonucleotide following hybridization

1994 ◽  
Author(s):  
Lawrence J. Parkhurst ◽  
Kay M. Parkhurst
Keyword(s):  
Distance Distribution ◽  
End Distance ◽  
End To End

END-TO-END DISTANCE DISTRIBUTION OF FORCE STRETCHED CHAINS RECONSTRUCTION BY MAXIMUM-ENTROPY METHOD

2004 ◽  
Vol 18 (17n19) ◽  
pp. 2365-2375
Author(s):  
LURU DAI ◽  
FEI LIU ◽  
ZHONG-CAN OU-YANG
Keyword(s):  
Secondary Structure ◽  
Maximum Entropy ◽  
Single Molecule ◽  
Maximum Entropy Method ◽  
Entropy Method ◽  
Distance Distribution ◽  
Extension Force ◽  
End Distance ◽  
Force Curves ◽  
End To End

Using the maximum-entropy method, the end-to-end distance distribution of the force stretched chain is calculated from the moments of the distribution, which can be obtained from the extension-force curves recorded in single-molecule experiments. If one knows force expansion of the extension through the (n-1)th power of force, it is enough information to calculate the n moments of the distribution. The method is examined with force stretched chain models, Gaussian chain and excluded-volume chain on two-dimension lattice. The method reconstructs all distributions precisely. The method also is applied to force stretched complex chain molecules: the hairpin and secondary structure conformations. We find that the distributions of homogeneous chains of two conformations are very different: there are two independent peaks in hairpin distribution; while only one peak is observed in the distribution of secondary structure conformations. Our discussion also shows that the end-to-end distance distribution may discover more critical physical information than the simpler extension-force curves can give.

Influence of long-range interactions on the end-to-end distance distribution and cyclization probability of short chains

1991 ◽  
Vol 24 (18) ◽  
pp. 5167-5170 ◽  
Author(s):  
Ana M. Rubio ◽  
Juan J. Freire ◽  
Arturo Horta ◽  
Ines Fernandez de Pierola
Keyword(s):  
Long Range ◽  
Distance Distribution ◽  
Long Range Interactions ◽  
End Distance ◽  
End To End

End-to-end Distance Distribution in Fluorescent Derivatives of Bradykinin in Interaction with Lipid Vesicles

2012 ◽  
Vol 22 (4) ◽  
pp. 1151-1158 ◽  
Author(s):  
L. R. Montaldi ◽  
M. Berardi ◽  
E. S. Souza ◽  
L. Juliano ◽  
A. S. Ito
Keyword(s):  
Lipid Vesicles ◽  
Distance Distribution ◽  
End Distance ◽  
End To End ◽  
Derivatives Of ◽  
Fluorescent Derivatives

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.

Sign in / Sign up

Export Citation Format

Share Document