Page - 39 - in Charge Transport in DNA - Insights from Simulations

CHAPTER3 SimulationSetup In thischapter, thedevelopedsimulationsetupwillbedescribedshortly. Thiswork dealswith the simulation of the structure and the charge transport characteristics of DNA. Therefore, an introduction into themolecular structure of DNAwill be given. Then, the studied DNA species and their designation in this work will be introduced. The simulation setup of theMMcalculations is then described in detail to give insight into the specific challenges of the simulation ofDNAunder experimental conditions. The first subject here is the simulation of DNA under mechanicalstress, like it iscausedbypullingapart theattachedelectrodes intheCT experiments. Further on, simulationsofDNAstrandswith reducedwater amount are performed. In the end, in this chapter the complete framework of force-field basedmolecular dynamics simulations forDNAunder experimental conditions is presented. 3.1 TheDNAMolecule ADNAstrand is composed ofmonomeric nucleotideswhich build up to a linear chain like polymer. One of these monomers is composed of a phosphate group and a five-carbon sugar, which build the so called backbone, and a nucleobase. 39