Page - 103 - in Charge Transport in DNA - Insights from Simulations

7.6Conclusion Toaccess theCTcharacteristics in this sequence, threeparameterswere calculated: the rate of transfer, thedelocalizationof thehole and theoccupationof thebridge (A). The rate of transfer is calculated by counting the transfers fromone guanine to another in a period of 1 ns. Counted are only those transfers, which are not followed by a back transferwithin 20ps. The delocalization of the hole Srec over nucleobaseswithoccupations |ai|2 is calculatedby taking the inverseof the sumof squaredoccupations. Srec=1/∑(|ai|2)2 Andfinally, thepopulationof thebridge is evaluatedas ameanvalueof theoccu- pationof theadeninenucleobase. Table7.6: Comparison of the parametrized CT model with QM/MM simulations of charge transfer in the sequenceGAGwith themean-field theory Parameter DNACTmodel QM/MMsimulation rateof transfer (perns) 2.8±1.1 4.3±2.1 delocalizationof thehole 1.31±0.03 1.40±0.34 populationof thebridge 0.047±0.003 0.062±0.064 Table7.6 shows theobtainedparameters and thevaluesbyT.Kubarˇ ([73], Table4) are shownasa reference. Comparisonof thesevalues shows that theparametrized CTmodel is able to reproduce the results ofQM/MMsimulationsof charge trans- fer with the mean-field method in the sequence GAG accurately. All important characteristics are reproducedquantitatively. While fullMD simulations involving theQM/MMscheme need about 2 days to complete oneof these simulations, theparametrizedCTmodel needs about 5min for a simulationof the same length (1ns). 7.6 Conclusion In this chapter, the newlydevelopedparametrizedmodel for theCT inDNAwas described. Therelevantparameters for theCTwerefitted to results fromQM/MM 103