Multi-scale simulations of biophysics problems, with emphasis on Importance Sampling
The behavior of biophysical systems often is quite different when investigated on different length scales and a complete description of such a system typically requires different approaches for these different length scales. At atomic and mesoscopic scales, a considerable number of degrees of freedom are involved. The associated free energy profiles are relatively rugged with energy barriersor kinetic bottlenecks preventing efficient sampling when doing numerical simulations. To alleviate this problem, a variety of sampling strategies have been developed.
In this thesis, I will start with a general background of multi-scale modeling of biophysical systems, and review the different sampling strategies that are being used when doing simulations. Next, I will talk about three of my projects. The first two involve protein binding problems at both the microscopic and mesoscopic levels. The third one is thediffusion-driven phase separation problem inside a cross-linked network of semiflexible polymers. I will use these three projects to illustrate how one can apply multi-scale descriptions and sampling techniques to biophysical systems in and out of equilibrium.