Monte Carlo Simulation On The Translocation Of Polymer Through Channels

The translocation of polymer through nano-channels has been a hot topic in physics, chemistry, and biology, due to its universal existence in nature and its potential application in technology. Examples contain the transpot of RNA molecules, proteins, and DNA, etc, through nuclear pores, DNA seperation, gene sequencing, drug delivery, etc. Since the channel size is much smaller than the polymer size, there are remarkable interactions between polymer and channel during the translocation process, therefore the polymer-channel interaction turns out to be one of the important factors affecting the translocation. Many theoretical works and simulation works have studied the transaction of polymer through homogenous channel, where the polymer-channel interaction is uniform along the channel. However, the nano-channels in real systems may be made up by two or more components, so the polymer-channel interaction may vary along the channel, and this could remarkably affect the translocation process. Futhermore, though we have obtained a lot of information about the translocation of single polymer through nano-channel, the knowledge of the translocation of multi-polymer system is still rare. While, for real application, such as DNA seperation, the system contains many polymers with different kinds.In our study, we use Monte Carlo method to investigate the translocation of polymer through compound channels, and aim to reveal the influence of the property of the compound channel on the translocation dynamics. The compound channel is composed of two components along the channel, and the two compoents have different interactions with polymer. In addition, we use Monte Carlo method to study the translocation of a multi-polymer system containing two kinds of polymers through a homogenous channel, and try to separate the two kinds of polymers by changing the interactions between them and the channel. The main works and the corresponding conclusions are as follows:(1) Translocation of homogenous polymer through compound channel. The compound channel is composed of two parts:part a with length La and part (3 with length Lβ. The two parts have different polymer-channel interactions:a strong attractive interaction with strength  for part a and a variable interaction with strength εβ for part β. Results show that the translocation process is remarkably affected by both εβ and Lα, and the fastest translocation can be achieved with a proper choice of εβ and La. When εβ is large, the translocation is dominated by the last escaping process as it is difficult for the polymer chain to leave the channel. Whereas when Lα is small and εβ<<εα, the translocation is determined by the initial filling process. For this case, there is a free-energy well at the interface between the part a and the part β, which not only influences the filling dynamics but also affects the translocation probability.(2) Translocation of homogenous polymer through sandwich-like compound channels. The channel is composed of three parts:(ⅰ) part al with length Lα1 near the cis side, (ⅱ) part a2 with length Lα2 near the trans side, and (ⅲ) part β with length Lβ between part al and part a2. Part al and part a2 have a same strongly attractive polymer-channel interaction, while the part β has purely repulsive polymer-channel interaction. Results show that, the translocation is remarkably influenced by part β’s length (Lβ) and its position in the channel (Lα1). When Lβ is big and Lα1 is small, it is difficult for polymer to enter into the channel, and the translocation is controlled by the filling process. While when Lβ is small, it is difficult for polymer to escape from the channel, and the translocation is governed by the escaping process. For this case, the polymer can translocate through the channel quickly with a proper choice of Lα1. For the filling process, there is a free energy well at the interface between part α1 and part β, while for the escaping process, there is another free energy well near the exit of the channel. The translocation dynamics for the filling process and the escaping process is determined by the two wells, respectively.(3) Translocation of diblock copolymer (ANABNB) through compound channels. The compound channels composed of part a with length Lα near the cis side and part β with length Lβ near the trans side. The interaction between monomer A and channel a is strongly attractive, while all other interactions are purely repulsive. We study the translocation mode that the block A threads the channel ahead of the block B since it is the most probable translocation event. Simulation results show that the translocation process is remarkably dependent on La and there are two maxima of translocation time. The physical mechanisms are discussed from the free energy landscape of polymer translocation. The place of the first maximum, at which there is a deepest free energy well before the block A completely enters the channel, is independent of NA. The place of the second one is at NAbx with bx the mean bond length along the channel, resulted from the matching of block A with channel a. Results show that the translocation time of diblock copolymer can be tuned by using compound channels.(4) Separating different polymers using interacting channel. The multi-polymer system containing two kinds of polymers, polymer A and polymer B, which have different polymer-pore interactions. The probability of one kind of polymer first translocating through a nanopore is dependent on the polymer-pore interactions and the magnitude of driving force for monomers inside the nanopore. At weak driving, there are separation regions where one kind of polymer translocates through the pore always before another kind of polymer. A phase diagram containing separation regions and mixed region is presented. At last, the first-in first-out rule for the polymer translocation is investigated.