Simulation of polymeric systems

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Computer simulation has become a popular approach for the study of complex physical systems. A simulation is an artificial experiment conducted on a computer using a simple model of a system which can be used to test both the interpretation of an experiment and the approximations used in an analytical theory. There are many different kinds of standard simulation techniques, including "molecular dynamics'' and "Monte Carlo'' methods. In addition to these methods, I will test and use other, recently developed, considerably more efficient methods which are designed to model properly dynamical behaviour of large molecules in fluids. I use computer simulation methods to study the physical behaviour of polymers. A polymer is any long, flexible molecule that looks like a chain composed of a large number of links called monomers. An important example of a polymer in nature is a protein molecule, which is composed of amino acid monomers.  A protein undergoes a complicated "folding" process to form a compact cluster such that it can fulfill its biological function. I am interested in elucidating the generic physical behaviour of simple model polymers, including structural properties and dynamical processes, in order to provide insight into the folding process. I will address the following questions. (i) How do the interaction forces between the polymer and the solvent molecules (the solvent is the fluid in which the polymer is immersed, e.g., water), the structure of the polymer molecule itself, the confinement of the polymer between hard surfaces, and the sequencing of monomers of different types along the polymer affect the collapse and freezing temperatures of the polymer? (ii) How does solvent flow ("hydrodynamics") affect the motion of polymers at fixed temperature and the dynamical pathway as a polymer collapses and folds as the temperature is lowered?