(179b) Bead-Rod Simulation of DNA Dynamics in Converging/Diverging Micro/Nanofluidics

The dynamics of single DNA molecules in the confined geometry has attracted a lot of attention due to the importance of the biomedical applications of DNA molecules such as the gene mapping and gene delivery. In the electrophoretic driven converging/diverging micro/nano-channel, the electric field gradient can be locally enhanced compared with the conventional entropy trapping channel. It has been observed in the experiments that the DNA molecules are gradually stretched in the converging microchannel (size of the small end is 20 microns) and coil back quickly after getting into the diverging channel. The bead-rod chain model has been used to simulate the dynamics of DNA molecules in converging/diverging microchannel and the qualitative results have been achieved by picking the DNA molecules with similar initial configuration as those in the experiments. With the size of the small end of the converging/diverging channel goes down to 200 nm (nearly three times of the DNA persistence length), the interactions (repulsive force) between the beads and wall affect the dynamics of single DNA molecules. We use the truncated Lennard-Jones and hard core repulsive potentials to get the excluded volume force between the beads and wall to carry out the bead-rod chain Brownian dynamics simulation in the nanoscale and the results are compared with those without considering the repulsive forces.