Page - 102 - in Charge Transport in DNA - Insights from Simulations

AParametrizedModel toSimulateCT inDNA Figure7.8: Graphical illustration of the energy landscape in theGAGsequence. Gua- nines have the lowest IP. Adeninewith higher IP acts as a barrier for the CT. Having set up the Hubbard matrix, it now has to be modified in terms of a self-interaction correction. All-DFT basedmethods suffer from the so-called self- interactionerror. Tocorrect thisbehavior, the second-order termshave tobescaled down. Therefore, theelementsof theHubbardmatrixarescaleddownwithafactor of0.2, the sameas in thepreviouswork [79]. Inner-SphereReorganizationEnergy So far, the inner-sphere reorganization energy is missing in the CT model. Al- though this is not connected to theHubbardmatrix at all, it easily can be intro- ducedby including it into it. Therefore, the inner-sphereRE,whichwasestimated tobe0.23 eV[79], is subtracted fromthediagonal elementsof theHubbardmatrix. 7.5 TestingwithChargeTransferMethods At thispoint, themodel is completeandshouldbeable todescribe charge transfer inDNA.To test this, hole transfer in the shortDNAsequenceGAGwassimulated 100 times for 1ns. This sequencewas chosen because of its special characteristics for charge transfer. The guanines have lower IP than the adenine in themiddle, therefore the adenine acts as a bridgewhichhas to be overcomewhenCT should occur. Figure7.8gives agraphical illustration. 102