First-passage probability: a test for DNA Hamiltonian parameters

TL;DR

This paper introduces a method using first-passage probability to select appropriate parameters for a DNA Hamiltonian model, aiding in understanding DNA melting and base pair dynamics.

Contribution

It develops a novel approach linking first-passage probability with DNA model parameters, especially constraining the non-linear stacking parameter to about 1.

Findings

Non-linear stacking parameter should be approximately 1.

Relations established between fluctuation amplitude cutoff and model parameters.

Method applicable to compute lifetime of open base pairs in DNA.

Abstract

A method is proposed to select the suitable sets of potential parameters for a one-dimensional mesoscopic Hamiltonian model, first introduced to describe the DNA melting transition and later extended to investigate thermodynamic and dynamical properties of nucleic acids. The DNA base pair fluctuations are considered as time dependent trajectories whose initial condition sets the no crossing constraint enforced in the path integral for the first-passage probability. Performing the path integration at room temperature, relations are established between the cutoff on the amplitude of the base pair fluctuations and the model parameters. In particular, it is shown that the non-linear stacking parameter should be $\sim 1$. The formalism here developed may be applied to compute the lifetime of open base pairs in three-dimensional helical models for DNA molecules.