Dynamical Simulations On The Translocation Of Polymer Chains Through Nanopores

The translocation process of polymer chains through nanopores is a basic but very important process in living organisms.It is also a common phenomenon in biological systems,such as the translocation of RNA from nuclear pores and viruses,DNA inj ected into the host cell,and protein transported across the membrane.The translocation of polymer chains has broad application prospects and research value in biology,life sciences,physics,chemistry and other disciplines,such as genetic testing,gene therapy,drug delivery,etc.Controlling the DNA translocation speed,which can improve the precision and accuracy of DNA detection,is a important research topic in the polymer translocation.In this article,starting from controlling the translocation speed of the polymer chain,two simulation methods are used to study the polymer chain translocation process under the action of constant tension/constant speed and the factors affecting the DNA translocation speed.The results of the paper are summarized as follows:(1)Pulling translocation of polymer chains through a nanopore.We use the Langevin dynamics method to simulate the translocation process of droplet-shaped polymer chains through a nanopore under a pulling force at the head of polymer.Due to the intra-polymer attraction of the polymer chain,the polymer chains are a compacted globule state before being pulled.We studied the scale relation between the translocation time ? of the polymer chain and the pulling force F,and the scale relation between the translocation time ? of the polymer chain and the chain length N and the driving speed v.When the intra-polymer interaction of the polymer chain is weak or the pulling force is large,the scale relation between the displacement time ? of the polymer chain and the pulling force F is ??F-?,where the scale index is ?=0.88.We found that,when pulling force is large enough,the scale relation ? is almost independent of the chain length but only related to the interaction within the chain.When the chain length N of the polymer chain is small or the intra-polymer interaction is weak,the scale relation between the translocation time and the chain length is ?? N?,where the scale index ?=1.6,and the translocation time is independent of the interaction strength in the chain.When the chain length is large enough,? is affected by the intra-polymer interaction,and different interactions result in different translocation exponent ?.When the driving speed or the intra-polymer interaction is large,we obtain the scale relation between the translocation time ? and the driving speed v as ??v-?,where ?=0.92.In the case of constant driving speed,when the chain length N is large enough,the scale relation between the translocation time ? and the chain length N is ??N1.24,and it is independent of the driving speed.Therefore,we can control the translocation time and translocation speed of the polymer chain by changing the pulling force,driving speed,chain length,interaction and other conditions of the polymer chain.The simulation results provide a better solution for more accurate DNA detection.(2)Factors affecting the translocation speed of single-stranded DNA through carbon nanotubes.We used the method of all-atom molecular dynamics simulation to investigate the effects of the Bzim-modified 5hmC,the applied bias electric field strength E,and the temperature T on the translocation speed of single-stranded DNA.In the simulation,we applied a localized bias electric field to the system.Although the size of the Bzim-modified 5hmC is larger than the general base,our results show that the number of ions when the DNA sequence containing 5hmC passes through the carbon nanotube is greater than DNA that does not contain 5hmC but has the same other bases.This result is consistent with the previous experimental results and simulation results.Our further analysis found that there is an attraction between the Bzim-modified 5hmC and the inner wall of the carbon nanotube.The attraction makes the 5hmC attracted to the inner wall of the carbon nanotube,which causes the DNA fragments near the 5hmC closer to the inner wall of the carbon nanotube.As a result,the ion blocked effect in the DNA carbon nanotubes is reduced,leaving space for more ions to pass through the carbon nanotubes.However,the attraction between Bzim-modified 5hmC and the inner wall of the carbon nanotube hinders DNA translocation and increase the translocation time.We also studied the influence of the electric field intensity E on the DNA translocation time ?.We found that the greater the electric field strength E,the smaller the DNA translocation time ?.At the same time,we also found that when the electric field strength is small,the scale exponent of the translocation time ? and the electric field strength E is small due to the attraction interaction of Bzim-modified 5hmC.When the electric field strength is large,the electric field force dominates and the scale exponent becomes larger.Finally,we found that the higher the temperature T,the shorter the DNA translocation time.