Confinement effects on conformational and dynamic properties of polymer

Abstract

Many biophysical processes, such as protein folding or segregation of bacterial chromosomes occurring {\it in vivo}, take place in geometrical confinement of the cell or of the organelle. In this case, protein or bacterial chromosomes can be thought as geometrically confined polymers, which is followed by the necessity of understanding the statics and dynamics of confined polymers. However, because it is rather difficult to study the confined polymers through an analytical method or experiment, instead, the scaling theory of de Gennes type or simulation method have been adopted in order to predict the behavior of the polymer. In particular, recent advances in computing power due to the rapid development of technology enable one to validate the scaling prediction or discover the new phenomena about polymer through simulation method. Therefore, this thesis examines how the conformational and dynamic properties of polymer changes due to the confinement effects, through the method of molecular dynamics simulations. With this, the spatial organization and the mechanism of segregation of bacterial chromosomes have been addressed. Furthermore, the structural and dynamic properties of the confined polymer at the atomic level was also studied in connection with the glass transition phenomenon.

First, we study the scaling prediction, especially on elasticity and relaxation of a linear chain confined in an open cylinder. Because the scaling theory has not been verified experimentally and not reconciled with numerical data, we validate this using molecular dynamics simulations. Of particular interest is the ``effective spring constant" given in the scaling form of $k_{eff}\sim D^{-\gamma}$, where D is the diameter of the cylindrical space. If the blob-scaling approach produces $\gamma = 1/3$, a series of numerical studies indicate unexpectedly large $\gamma \approx 0.9$. Through the simulations, we show that there exists a crossover from the formerly called unexpected to...