Elastic behavior of compact polymer chain transporting through an infinite adsorption channel

The elastic behavior of a single compact chain transporting through an infinite adsorption channel is investigated using the pruned-enriched-Rosenbluth method (PERM). In our model, single compact chain is fixed with one of its first monomer at a position in an infinite adsorption channel, is then pulled slowly along the direction of z-axis. We first calculate the chain size and shape of compact chains transporting through an infinite channel, such as mean-square end-to-end distance per bond 〈R2〉/N, mean-square radii of gyration per bond 〈S2〉/N, 〈S2〉xy/N and 〈S2〉z/N, and shape factor 〈δ〉 for the changes in the size and shape of compact chains during the translocation process. If there are strong adsorption interactions between the monomers and the channel, some special behaviors for the size and shape of compact chains are obtained during the process. On the other hand, some thermodynamics properties are also investigated, such as average energy bond, average Helmholtz free energy per bond, elastic force per bond f and energy contribution to elastic force per bond fE. During the translocation process, elastic force f is less than zero, and has some plateaus in some special regions for strong adsorption interaction, which may explain how the adsorption interaction drives chains through narrow channels or pores in many biological systems because f<0 means that the translocation process need no external force on the chains. These investigations can provide some insights into the mechanics of proteins infiltrating through membrane. In the meantime, by recording and comparing these force-extension curves, we may also investigate the complex interactions between biopolymers (such as protein, RNA, and DNA) and the membranes, and determine indirectly the complicated structure of the channel.