Page - 54 - in Charge Transport in DNA - Insights from Simulations

DNAUnderExperimentalConditions Figure4.5: The Watson–Crick hydrogen-bonding pattern in the A9 oligomer during stretching. Redcolordenotes anexistinghydrogenbondat the correspond- ing magnitude of force. Note the temporary break of hydrogen bonds in several base pairs during the overstretching transition at170pN. Figure4.6: Profiles of distance vs external force for the stretching ofA9 with different loading rates. 200 pN, the formation of the ladder is observed at 150 pN at the smaller load- ing rates. Even more markedly, the separation of strands follows at quite large force of 750 and 700 pN at the larger loading rates of 50 and 10 pN/ns, respec- tively, but alreadyat270pNat the slowest loading rateof2pN/ns. This facthints at the non-equilibrium character of the process being simulated. The question of irreversibility was addressed inmore detail bymeans of removal of the external force, and theobservationsarepresented in thenext section. Thedependenceof the lengthontheexternal force,orsimulationtimeisessentially identicalwith all theDNAspecies studied. See figure 4.7 for the extension–force profilesobtainedat10pN/ns. The end-to-end distance is expressed as a relative value with respect to the av- erage length in the free simulation performed before. In a first interval after the 54