Direct prediction of HP sequences of compact polymer chains from elastic force

In this paper, a new method is proposed to predict HP sequences of compact polymer chains from elastic force based on the PERM (pruned-enriched-Rosenbluth method) simulation. Two different HP sequences are selected here, and we let them pass through a nanopore after acting of elastic force, which only allow single but not double strands to pass. Some thermodynamics properties of compact polymer chains are investigated during the translocation process, such as average Helmholtz free energy 〈A〉, average energy per bond 〈U〉, and average contact energy per bond 〈Uc〉. We find that the curves of them change non-monotonously with different steps, which inversely can be used to distinguish H and P accurately. The most important parameter of them is elastic force f because it can be measured directly using single-molecule force spectroscopy (SMFS) in experiment. Through recording and comparing force-extension curves, we can determine the HP sequences accurately. This method is also applied to determine DNA sequence directly, and to study the contact interactions in proteins and the protein folding.