Monte Carlo Simulations of the Equilibrium Properties of Semi-stiff Polymer Chains Efficient Sampling from Compact to Extended Structures

University dissertation from Uppsala : Acta Universitatis Upsaliensis

Abstract: Polymers is a class of molecules which can have many different structures due to a large number of degrees of freedom. Many biopolymers, e.g. DNA, but also synthetic macromolecules have special structural features due to their backbone stiffness. Since such structural properties are important for e.g. the biological function, a lot of effort has been put into the investigation of the configurational properties of semi-stiff molecules.A theoretical treatment of these systems is often accompanied by computer simulations. The main idea is to compare theoretically derived models with experimental results for real polymers. Using Monte Carlo simulations, I have investigated how this computational technique can build a bridge between theoretical models and experimentally observed phenomena. The effort was mainly directed to develop sampling techniques, for efficiently exploring the configurational space of semi-stiff chains in a wide range of structures. The work was concentrated on compact conformations, since they, as is well known from previous studies, are difficult to sample using conventional methods.In my studies I have shown that the simple and, at a first glance, time consuming method of bead-by-bead regrow as a way of changing the configuration of a semi-stiff chain gave very promising and encouraging results when combined with modern simulation techniques, like Entropic Sampling with the Wang-Landau algorithm. The resulting simulation package was also suitable for parallelization which resulted in a further speed-up of the calculations.In addition to the more elaborate sampling methods, I also investigated external conditions to induce compaction of a semi-stiff polymer. In the case of a polyampholyte the condensing agent could be a multivalent salt, creating effective attraction between the loops of the chain, while for neutral polymers, an external field and the geometry of the confining volume can induce a compaction.