Single molecule conformational dynamics and mechanics: Theory, simulation, analysis and interpretation

Abstract : Recent advancement on single-molecule experiments has now made it possible to measure the kinetics, conformational dynamics and mechanical properties of a biomolecule (protein, nucleic acid etc.) with high precision and spectacular resolutions. In this talk I will introduce various theoretical and computational approaches to study such properties. In the first half of the talk, I will introduce a general theoretical framework that captures the conformational dynamics of a biomolecule through an intermediate. I will show that this theory not only captures non-trivial features in the key experimental observables, the mean unfolding rate, and the distribution of unfolding forces but also reveals the underlying physical and biological mechanism. In the second half of the talk, I will discuss how molecular dynamics simulations can be used to extract various bio-molecular properties through a systematic study of fluctuations at the atomic level. Using all atomistic molecular dynamics simulations I will illustrate how to calculate different elastic properties of various DNAs starting from short bare DNA to nucleosomal DNA.  I will demonstrate that macroscopic elastic theory is not adequate to calculate the elastic properties of various short DNAs. I believe that such realistic studies will certainly enrich the pool of techniques to interpret the experimental data as well as motivate to perform new experiments