Structural fluctuations and quantum transport through DNA molecular wires: a combined molecular dynamics and model Hamiltonian approach

TL;DR

This study combines molecular dynamics and quantum modeling to explore how structural fluctuations in DNA influence charge transport, revealing that solvent interactions can enhance conduction by modulating electronic properties.

Contribution

It introduces a hybrid computational approach integrating molecular dynamics with a model Hamiltonian to analyze DNA charge transport considering structural fluctuations.

Findings

Solvent fluctuations can enhance charge transport in DNA.

Structural vibrations influence electronic parameters significantly.

The hybrid method efficiently captures dynamic effects on DNA conductivity.

Abstract

Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure calculations and classical molecular dynamics simulations with a model Hamiltonian approach. Based on a fragment orbital description, the DNA electronic structure can be coarse-grained in a very efficient way. The influence of dynamical fluctuations arising either from the solvent fluctuations or from base-pair vibrational modes can be taken into account in a straightforward way through time series of the effective DNA electronic parameters, evaluated at snapshots along the MD trajectory. We show that charge transport can be promoted through the coupling to solvent fluctuations, which gate the onsite energies along the DNA wire.