Figure 1
Wormlike chains are simple homopolymers with an intrinsic resistance to bending. Confined wormlike chains to cylinders or spheres may be significantly bent, and the interplay of these two length scales dictate the conformations of the polymer. This picture is further complicated by additional forces, such as an externally applied tension.

Biophysics is an extremely broad field, combining physical modeling and computer simulation to better understand and describe important biological systems. These systems can range from macroscopic scales (e.g. flocking and self-organization) to microscopic (e.g. protein folding or neuronal interactions). Biophysical modeling is of fundamental importance in a number of fields, with applications in chemistry, bioengineering, and drug design. Our group is interested in biophysics in a number of aspects:

The statistics and dynamics of confined biomolecules

The physics of biological systems is dictated not only by the properties of the biomolecules, but also by the environment in which it is found. In many biologically relevant conditions, including viral encapsulation and the structure of DNA in the cell, the effects of confinement can significantly change the statistics and dynamical properties of the molecule, by requiring elongated, bent, or other conformations that are not typically seen in bulk behavior. We are working on a number of confinement-related projects relevant for the description of DNA-nuclosome binding and next-generation sequencing techniques that exploit the elongation of DNA in micro- or nano-channels.

Analytical models for interacting and multistate systems

Much of the complexity of biological systems arises from the complex inter- or intra-molecular interactions along the backbone of a molecule. These can give rise to multi-state protein or RNA structures, with multiple intermediate states potentially traversed while the system attempts to find its native structure. Interactions between molecules can likewise have profound effects on the structure and dynamics of the system at large. We are interested in a number of simple polymer models to describe the dynamics of systems with multiple interacting sites, ranging from the dynamics of bundles of wormlike chains to Generalized Rouse Models of multi-state polymers with tunable interaction strengths. Understanding the dynamics of these simple, analytically tractable systems is useful in developing a better understanding of a variety of biological systems.

Bundles of polymers can have very different behavior depending on their microscopic properties. The top shows a simulation of a bundle of wormlike chains, with rigid cross-links and an extensible backbone. Despite each polymer having a strong resistance to bending, the coupling between individual chain bending and bundle-wide shearing produce strong, persistent bending. This waves are not seen in the bottom simulation, showing the dynamics of flexible, inextensible chains. The figure shows the mean end-to-end distance of the bundles, indicating the scale of the fluctuations of each.