Molecular Dynamics Simulation For The DNA Molecular Electrophoresis Sieving In Micro-nanometer Channel

In this paper, we combine the advantages of the coarse-grained dynamic method and dissipative particle dynamics method and We apply the coarse-grained hybrid molecular dynamics(CGH-MD) to simulate migration of coarse-grained DNA in a micro-nanometer cable channel. After we research the changes of the coarse-grained DNA conformation in the micro-nanometer channel, the migration rate of DNA beads and the free energy barrier that DNA beads must overcome between the interface of micrometer-channel and nanometer-channel, We confirm that in the entropic trapping micro-nanometer channel,the long chain DNA molecules migrate more faster than short chain DNA molecules. Furthermore, we also studied several reasons which cause this phenomenon, including the DNA beads size, the electric field strength between both end of the channel and the electroosmotic flow of the wall and so on. The different migration status of DNA molecules in micro-nanometer channel which we research has guided the fabrication and optimization of facilities. What we research in this paper is the foundation of biological molecular sieving and purification technology.