Using Molecular Dynamics Simulations To Understand Pattern Formation In Polymers

We use Molecular Dynamics simulations to study single chain polymer dynamics and collapse to imitate the early stages of protein folding, as well as polymer brush collapse, to understand the physics and morphology of collapsing polymer brushes. Simulations of this nature can help us understand complex phenomena such as glass transition, molecular crowding and complex higher order organisation. As an example, we demonstrate a study of the physical origin of the polymer glass transition from the point of view of marginal rigidity, which is achieved above a certain number of intermolecular contacts. We find that when the average number of contacts per monomer (covalent and non-covalent) exceeds the critical value z∗=4, the system becomes solid and the dynamics arrested - a state that we declare the glass. We also look at polymer brushes and describe spinodal decomposition-like processes that take place upon brush collapse. It is often impossible to simulate large systems without a certain level of sophisticated coarse graining. We introduce a possible model for studying higher order organisation of chromatin, a biological complex of DNA and histone proteins within the nucleus of a cell. Chromatin organisation is a fascinating topic that resembles protein folding, however, it is much more complex due to multiple levels at which chromatin folding and dynamics have to be understood. Using a simplified force field, we also study helical structures formed by peptoids, small peptidomimetic molecules that are of importance to the pharmacological industry.