Molecular Dynamics Simulaations Of Coarse-graining DNA Translocation Through A Nanopore

Contents of this paper are divided into two main parts, one partdiscusses several DNA’s coarse-grained models, the second is moleculardynamics simulations of translocation dsDNA through a nanopore. First,several studies have examined the DNA coarse-grained models, theappling condition of the Hamiltonian of each coarse-grained model ofDNA is discussed.Then the following results are obtained: thermalmelting property of dsDNA, especially in the dilute solution condition,was studied by using the Nucleotide’s3SPN model; the model ofanisotropic shapes of coarse-grained functional groups has advantages inthe simulation of conformational transition and helical twisting of non-BDNA; molecular renormalization coarse-graining method reduces theamount of free degrees in several folds and still retains some mechanicaland structural properties of DNA strands well.Second,using the moleculardynamics stimulation method researches the behavior of dsDNA translocation nanopore.Here mainly using FORTRAN programminglanguage simulates the system in the Linux environment.It has beendiscovered that the translocation time has relationship with pore radius,pore length, force through the pore, and the force difference between twosides of the nanopore.The force difference impacts the translocation timesignificantly,to some extent plays a decisive role in the translocationprocess.This result has some reference value on the study of rapidtranslocation.The studies of DNA coarse-graining and the behavior of DNAtranslocation through a nanopore in this paper have some reference valueon simulating DNA polymer,and promotes the understanding of thebehavior of DNA polymer translocation furthermore.