Figure 5.

Select terms of the coarse-grained Hamiltonian as a function of separation distance, averaged over all simulation runs. (a) Pairing energies between the first and second basepairs (solid red line and green dots, respectively). (b) Base-stacking energies between the first and second bases, and first and third bases on one of the two DNA strands (the curves for the second strand are similar). (c) Electrostatic interactions between the first basepair and different bases on the complementary DNA strands. To see this figure in color, go online.