Complex Dynamics of Soft Matter

Complex Dynamics of Soft Matter

Proteins are molecular machines. No individual molecular machines work alone in cells. How are the subunits in each machine work together? How are they dynamically coupled together? Answering these questions has been limited to small proteins or truncated simplified molecular constructs, in the history of biophysical studies by both nulear magnetic resonance and molecular dynamics simulation. Single-molecule cryo-EM opens the possibility of observing biomolecules in their action in a physiological condition. The single-molecule images, although noisy, contain information that reflects spatial organization of atoms, as well as their position along the paths of conformational transitions. The challenge is how one may extract the dynamic information along with the atomic organization from the noisy projection images in a bulk. Theory regarding methods and procedures is incomplete and lacking. The current methods of studying complex dynamics are either through classification of datasets based on their difference of conformations, or time-dependent sample preparation, or combination of both. However, the limitation of current computational tools restricts the processing of big data on TB level, or over millions of molecular images. Large-scale classification of massive image data for thousands of conformations is practically prohibited using exiting tools. Scientists working at LCMMB are exploring advanced knowledge and tools in mathematics, physics and computer sciences to address these challenges in solving atomic-level dynamics of biomolecular complexes.