Page - 89 - in Charge Transport in DNA - Insights from Simulations

CHAPTER7 AParametrizedModel toSimulateCT inDNA In this chapter, aparametrizedmodel for the charge transfer inDNAispresented. Asshowninthepreviouschapters, theCTinDNAissensitive toseveralquantities: theelectronic couplings (EC), the ionizationpotentials (IP) and the influenceof the environment. In the shownQM/MMsetup, theseparameters are obtainedwith a combinationof classicalMDsimulationsandQCcalculations. Bothof these canbe very timeconsuming,particularlywhen it comes to largesystemsizesorextended periodsof time. The idea of the parametrized approach is tomodel these parameterswithout the need of MM or QC calculations. To do so, data acquired from QM/MM simu- lations are analyzed extensively in order tomodel the CT quantitieswith simple algorithms. As a first step, the EC and IP are parametrized and an appropriate Hamiltonian ismodeled, which already can be used in charge transport calcula- tions in theLandauer–Büttikerpicture. Thenext step is to include theenvironmen- tal effects in themodel approach. Here, the charge is introduced into the CT model, and the resulting polaron is modeled. Relaxationeffects of the environment are taken intoaccount inaddition. Finally, first test calculations of the charge transfer in theDNAsequenceGAGare performed. 89