Page - 48 - in Charge Transport in DNA - Insights from Simulations

SimulationSetup Figure3.6: Studied microhydrated systems – A13 with varied number of water molecules. An additional constant external force was applied to the microhydrated DNA oligomers, emulating the experimental setupwhere the oligomer is held between two electrodes. A series of trial simulations with varied magnitude of the ex- ternal force was performed to estimate the force that would support a double- strandedstructureofDNA.This forcewasappliedasanharmonic constraintwith a force constant of 1000 kcal/(mol nm) between the O3’-atoms of the outermost nucleotides. Also studiedwere the systemsDry1 andDry2with a smaller numberof counteri- ons than required for neutralization. The clusterswere stripped randomlyof 1/4, 1/2, 3/4 aswell as off all ions, respectively. MD simulationswere performed for thesenegatively chargedsystemswith the samesetupasdescribedabove. ThesimulationsofmicrohydratedDNAwithanexternalpullingforceof increasing magnitudewereperformedinthesamefashionasthoseof thefullyhydratedDNA. Asingle loading rateof10pN/nswasappliedhere. 48