Tomás Kubar

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We present a new computational strategy to evaluate the charge-transfer (CT) parameters for hole transfer in DNA. On the basis of a fragment-orbital approach, site energies and coupling integrals for a coarse-grained tight-binding description of the electronic structure of DNA are rapidly calculated using the approximative density functional method(More)
We present a hybrid method based on a combination of classical molecular dynamics simulations, quantum-chemical calculations, and a model Hamiltonian approach to describe charge transport through biomolecular wires with variable lengths in presence of a solvent. The core of our approach consists in a mapping of the biomolecular electronic structure, as(More)
We investigate in detail the charge transport characteristics of DNA wires with various sequences and lengths in the presence of solvent. Our approach combines large-scale quantum/classical molecular dynamics (MD) simulations with transport calculations based on Landauer theory. The quantum mechanical transmission function of the wire is calculated along MD(More)
The electrical conduction properties of G4-DNA are investigated using a hybrid approach, which combines electronic structure calculations, molecular dynamics (MD) simulations, and the formulation of an effective tight-binding model Hamiltonian. Charge transport is studied by computing transmission functions along the MD trajectories. Though G4-DNA is(More)
The approximate density-functional tight-binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle-mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make(More)
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