Quantum diffusion in polaron model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers

Abstract

We numerically investigate quantum diffusion of an electron in a model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with fluctuation of the parameters due to the impact of colored noise. The randomness is introduced by fluctuations of distance between two consecutive bases along the stacked base pairs. We demonstrate that in the model the decay time of the correlation can control the spread of the electronic wavepacket. Furthermore it is shown that in a motional narrowing regime the averaging over fluctuation causes ballistic propagation of the wavepacket, and in the adiabatic regime the electronic states are affected by localization.

Electronic couplings and on-site energies for hole transfer in DNA: Systematic quantum mechanical/molecular dynamic study

“…The effects of DNA conformational dynamics on the efficiency of HT have also been considered from different points of view. [10][11][12][13][14][15][16][17][18][19][20] The obtained results suggest that the electronic couplings found for idealized B-DNA ͑Refs. 21-23͒ may substantially differ from the corresponding values averaged over thermally accessible DNA configurations, and therefore, a combined quantum mechanical/ molecular dynamic ͑QM/MD͒ approach should be used to obtain more accurate estimates of the electronic couplings.…”

Charge migration through DNA molecules in the presence of mismatches

“…Many efforts [19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35] have been performed to analyze charge propagation through DNA oligomers from both the theoretical and the experimental points of view. Although for hole transfer in solutions there seems to be some agreement that the hole motion takes place in an incoherent manner, the microscopic charge transport mechanisms for DNA contacted by electrodes still seem to remain elusive, since a purely incoherent hopping mechanism does not seem to be able to yield electrical currents in the order of nanoampere as observed in some experiments.…”

Modeling Charge Transport and Dynamics in Biomolecular Systems

“…Unfortunately, systematic investigations (within a given experimental setup) on base sequence, length, and the temperature dependence of charge transport are still missing, so that the theoretical analysis of possible charge transport pathways faces big challenges [40]. Initial modeling of charge transport was mainly based on effective Hamiltonians with fixed electronic parameters and describing e.g hole transport through the highest occupied molecular orbitals (HOMO) of the bases [41][42][43][44][45][46][47] (see also [48,49] for recent reviews). Model Hamiltonians clearly offer the possibility to explore different charge transport scenarios in a relatively flexible way, but they also contain usually many parameters which are difficult to estimate.…”

“…Indeed, strong conformational dynamics and a related spectrum of different time scales seem to be ubiquitous for biomolecules, as shown e.g., in the modulation of the kinetics of electron transfer during the early stages of the photosynthetic reaction cycle [73], by the analysis of dispersed kinetics [74,75], or by fluorescense correlation spectroscopy [76]. The treatment of dynamical effects in DNA transport calculations has been, however, addressed only recently either in the frame of pure model Hamiltonians [47,[77][78][79][80] or by including information from first principle calculations and molecular dynamics (MD) simulations [67,69,[81][82][83][84].…”