Two-level system with a thermally fluctuating transfer matrix element: Application to the problem of DNA charge transfer

Charge transfer along the base-pair stack in DNA is modeled in terms of thermally-assisted tunneling between adjacent base pairs. Central to our approach is the notion that tunneling between fluctuating pairs is rate-limited by the requirement of their optimal alignment. We focus on this aspect of the process by modeling two adjacent base pairs in terms of a classical damped oscillator subject to thermal fluctuations as described by a Fokker-Planck equation. We find that the process is characterized by two time scales, a result that is in accord with experimental findings.Comment: original file is revtex4, 10 pages, three eps figure

Molecular Modeling of Nucleic Acid Structure: Setup and Analysis

The last in a set of units by these authors, this unit addresses some important remaining questions about molecular modeling of nucleic acids. It describes how to choose an appropriate molecular mechanics force field; how to set up and equilibrate the system for accurate simulation of a nucleic acid in an explicit solvent by molecular dynamics or Monte Carlo simulation; and how to analyze molecular dynamics trajectories.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153007/1/cpnc0710.pd

Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation

This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all‐atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152997/1/cpnc0709.pd