Monte Carlo study of polymer translocation through a hole

In this work we studied a simplified model of a polypeptide chain. The model chain was embedded to a [3 1 0] lattice. It was represented as a sequence of united atoms located at the positions of alpha carbons. The force field used consisted of the long-range contact potential between united atoms with the excluded volume and with a local preference of forming α-helical states. The chain was built of hydrophilic and hydrophobic segments forming helical septets –HHPPHPP–. The properties of model chains were determined using the Monte Carlo simulation method based on a Metropolis-like algorithm. During the simulations the translocation of the chain through a hole in an impenetrable wall was observed. The influence of the chain length, the temperature differences on both side of the wall and the size of the hole on the chain properties were investigated.