Molecular Dynamics Simulation Of DNA Molecules In Micro-nanometer Channel

Simulation of DNA electrophoresis facilitates the design of DNA separation devices. In this work, a coarse-grained hybrid molecular dynamics (CGH-MD) approach was used to simulate the electrophoresis process of DNA chain through a T micro-nanometer channel driven by an electric field. The mobility of different DNA chain in T micro-nanometer channel as a function of electric field was simulated. The free energy of different DNA chain length in the T micro-nanometer channel under the action of an electric field was calculated. The electrophoresis of different chain lengths (N=50, N=100, N=200, N=300) in the same average electric field was simulated. The mobility of DNA chain as a function of nanochannel length and depth was simulated respectively.The main analysis results are following:The mobility of long DNA chain is bigger than short DNA chain in the same average electric field, and the average mobility of DNA chain increased along with the increase of external electric field, and reached the saturation state finally. The DNA chain need to overcome the barrier to enter the thin channel, and short chain need overcome bigger barrier than long chain when enter the thin channel. It was also found that the electrophoresis process of DNA chain is characterized by three time scales:approach time Tapp, activation time tact, and across time tacross. The length of each time scale depends on the DNA chain length, the approach time τapp and activation time Tact decreased with the increase of the DNA chain length, but the across time Across nonlinear increased with the increase of DNA chain length. Besides, we found that the length and depth of nanochannel can produce an effect on the mobility of DNA chain. The migration rate of DNA fluctuated with the increase of the nanochannel length and depth, so the separation efficiency of different DNA chain length can be improved greatly if choose the appropriate T micro-nanometer channel size.The results of this paper have certain significance in the study of dynamics process of long DNA chains in micro-nanometer channel and can correctly explain Han et al’s experimental results.