Abstract
Charge transport through a short DNA oligomer (Dickerson dodecamer (DD)) in the 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 (MD) 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 the 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 on-site energies along the DNA wire.
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GENERAL SCIENTIFIC SUMMARY Introduction and background. Understanding charge migration mechanisms through biomolecular systems is a crucial issue from the biological point of view, but also has potential applications in molecular electronics. The huge structural complexity of biomolecules makes the theoretical study of such problems very challenging. In particular, the strong influence of conformational fluctuations on the charge migration process requires the use of non-conventional approaches, different from those known in solid state physics.
Main results. By using classical molecular dynamics coupled to electronic structure calculations, we are able to describe the temporal change of the electronic structure resulting from the coupling to structural fluctuations, and to discuss it in the case of a DNA oligomer (Dickerson dodecamer). We show that fluctuations can gate charge transport and counteract the intrinsic disordered potential profile related to the inhomogeneous base sequence.
Wider implications. Our methodology allows for a flexible coarse-graining of the electronic structure of complex systems, as well as for a straightforward inclusion of the influence of the conformational dynamics. This approach, coupled with appropriate model Hamiltonian formulations to treat charge transport, provides a very efficient platform for study of a variety of phenomena related to charge migration, not only in biomolecules but also in polymeric systems and in organic crystals. As such, it is expected to help develop new physical insights into charge motion in strongly structurally fluctuating systems.
Figure. Schematic representation of the coarse-graining of the DNA time-dependent electronic structure.