Quantifying large-scale dynamics of complex molecular assemblies

Proper biological function is often governed by the dynamics of large-scale molecular rearrangements. While incredible progress has been made in terms of structural techniques and single-molecule methods, establishing a precise physical-chemical understanding of the dynamics requires the use of theoretical models. To this end, we develop and apply a range of models that allow for the simulation of large-scale (10-300Å) rearrangements in biomolecular systems. In this talk, I will focus on how we have used all-atom structure-based "SMOG" models to quantify the dynamics of collective rearrangements that involve tens of thousands of atoms. By customizing these models for each system, we are able to uncover precise relationships between the various components of complex molecular assemblies. To illustrate the philosophy behind these models, as well as their utility, I will describe applications where the predicted dynamics have been subsequently corroborated by independent experimental measurements.