Page - 98 - in Charge Transport in DNA - Insights from Simulations

AParametrizedModel toSimulateCT inDNA Figure7.5: Transmission function calculatedwith the Landauer–Büttikermodel. Av- eraged transmission function for aMDsimulation of 20ns of a sequence of three adenines (red) and for themodeledCTparameters (black) 7.4 ChargeTransferExtensions Inorder tosimulatechargetransferwithnon-adiabaticmulti-scaleschemes, certain additions to theCTmodelHamiltoniandescribed so far arenecessary. TheEnvironmentalEffect Until now, the Hamiltonian was created for "neutral" systems, unaffected by a charge residing in the system. The introduction of a charge has several effects on the systemand thereforeon theCTHamiltonian. Previous work showed that the charge (hole) is stabilized by the polarization of the surroundingwatermolecules. This canbedescribedas apolaron [96–99]. The stabilizationcanbeseen in the lowered IPof thenucleobases carryingacharge. To quantify thedecrease of IP of a chargednucleobase, simulationswith a stationary charge (hole) introduced into the systemwereperformed. ApolyA sequencewas equilibratedwitha charge residing completely localizedononenucleobase. Then, anMDsimulation of 1nswasperformed, and theHamiltonianwas calculated in every time step. During this simulation, the chargewas restricted to resideonone nucleobase and did not transfer. The resulting IP time series were recorded for everynucleobase, andmeanvalueswere calculated. Thesemeanvalues showthat 98