Theoretical Studies On The Dynamic Aspects Of Macromolec

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Dramatic advances have been made in the last few years in our ability to study the behavior of single macromolecules. These new experiments require sopisticated applications of cutting-edge technologies. Moreover they require the development of new theoretical approaches to interpret them so as to extract the maximum possible but no more!) microscopic information. This has recently become the main focus of our research.In this reporting period, eight papers papers dealing with the following topics appeared in print: (1) Enhancement of association rates by nonspecific binding to DNA and cell membranes (2) Ensemble of transition states for two state protein folding from the eigenvectors of rate matrices and (3) The theory of photon statistics in single molecule Forster resonance energy transfer (4)The existance of a one-dimensional reaction coordinate for complex diffusive activated processes such as protein folding.(5) A new analytic expression for the time dependent rate coefficient of diffusion influenced reactions in the presence of interaction potentials that will greatly facilitate the analysis of experimental data. (6) The protocal of extracting equilibrium free energy surfaces from single molecule force spectroscopy (i.e., from experiments in which molecules are manipulated by atomic force microscopes and laser tweezers). (7) The information content of two state single molecule trajectories (e.g the ionic current turns on and off because of opening and closing of membrane channels) and (8) How to analyze time-resolved photon trajectories emitted by fluorescent single-molecules to learn about the nature of conformational changes associated with the quenching of fluorophores. The first three papers were briefly described in my previous report. The next two deal with fundamental issues in chemical reaction dynamics. The last three are devoted to developping the theory required to analyze single-molecule force and fluorescence spectroscopic experiments.