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Physical Review E
Article
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Physical Review E
Article . 2004 . Peer-reviewed
License: APS Licenses for Journal Article Re-use
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Conformation of local denaturation in double-stranded DNA

Authors: Jae-Hyung Jeon; Wokyung Sung;

Conformation of local denaturation in double-stranded DNA

Abstract

Double-stranded DNA (dsDNA) undergoes a denaturing transition above which the strands unbind completely. At temperatures (including the physiological temperature) below the transition the base pairs tend to unbind locally, giving way to loops, i.e., locally denatured states. In the flexible-chain model, the imaginary time Schrödinger equation describes the interstrand distance distribution of dsDNA with the time variable replaced by the sequence number. We transform the equation to the Fokker-Planck equation (FPE), which provides a convenient and powerful analytical method and, via the equivalent Langevin equation, a simulation scheme. The temperature-dependent potential that emerges in the FPE manifests how the DNA conformation changes dramatically near the transition temperature. We present several simulation plots along with analytical results illustrating the order parameter (concentration of bound base pairs), base pair distance correlation function, and loop size distribution at different temperatures.

Keywords

Models, Molecular, Stochastic Processes, Temperature, DNA, Nucleic Acid Denaturation, Energy Transfer, Models, Chemical, Nonlinear Dynamics, Nucleic Acid Conformation, Computer Simulation, Base Pairing

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    citations
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    16
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    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
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    influence
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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
16
Average
Top 10%
Top 10%
hybrid
Related to Research communities
Energy Research