Physical properties of polymer confined in cylindrical pore as model bacterial chromosome

Abstract

\textit{Escherichia coli} is a rod-shaped bacterium of which structure is relatively simple, and is usually found in the large intestine. A ring-shaped chromosome of \textit{E. coli} is strongly confined in a small cell, and does not have a sophisticated structure like an eukaryotic cell. This system can be described by the ring-shaped polymer confined in a cylinder. The mechanical properties of the chromosome of \textit{E. coli} have been reported in many studies. Recently, some attempts are made by researchers to explain living phenomena in \textit{E. coli} by the thermodynamic forces caused by the polymer nature of DNA as well as the functions of proteins. This thesis is devoted to understanding the living phenomena in the \textit{E. coli} chromosome as a ring polymer confined in a cylinder.

In the first part of this thesis, we investigated the dynamics of a ring chain confined in a cylindrical pore using molecular dynamics simulations. Although the dynamics of the linear chain under confinements is well understood, it is not certain whether the dyanmics of the linear chain can be applied to the ring chain. In our study, we found that the topological constraints of the ring polymer do not influence on the qualitative dynamics where the ring chain is confined in a narrow cylindrical pore, and the ring chain and the linear chain follow the same interpretation of the chain conformations in cylindrical confinements. Furthermore, we proposed the picture that the ring chain confined in a narrow cylindrical pore can be considered as two independent linear subchains, and these two subchains act as confinements to each other in the athermal condition by occupying the half of the volume of the cylinder divided along the long axis of the cylinder. The rescaled results by this picture are in quantitative agreement with the results of the linear chain, which means that the dynamics of the ring chain under such confinements directly corresponds to the linear chain.

The...