Numerical study on electrophoretical stretching dynamics of DNA in microcontraction

Brownian dynamics simulations are used to characterize the electrophoretical stretching process of long T4 DNA in microchannels. When DNA is forced to move through the microchannels, the pure elongational flow generated by electric field gradients in hyperbolic contraction will unravel the molecules of DNA. The effects of hydrodynamic interactions, the strain rate, the Brownian fluctuation, and the initial states of molecules on the stretching dynamics are analyzed in this paper. The computational results show us the weak dependence of polymer dynamics on hydrodynamic interactions in microcontractions. In the case of low Deborah number, the stretching process of a molecule depends on the Brownian fluctuation. However, in the case of high Deborah number, the individualistic stretching behavior can be traced to variations in the starting conformation.