The proposed research program will focus on the development of new computational algorithms for the microscopic simulation of complex biological molecules and their probing using coherent optical spectroscopies. Multiple-pulse techniques have the capacity to prepare electronic and vibrational degrees of freedom in nonequilibrium states and monitor their subsequent evolution, yielding femtosecond snapshots of dynamical events; energy transfer pathways, charge transfer, photoisomerization, and structural fluctuations. A molecular dynamics code which interfaces time-dependent quantum chemistry packages (density functional and the time dependent Hartree Fock) with semiclassical molecular dynamics algorithms for multipoint correlation functions will be developed. Multidimensional techniques should reveal the multitude of coherence sizes of photosynthetic complexes with specific spectroscopic signatures. Systems to be studied: LH2 of purple bacteria, the FMO complex, LHCII, CP29, and the Chlorosome. Nonlocal information on electron and energy transfer pathways, solvation dynamics, and vibrational relaxation will be extracted from fluorescence, pump probe, and three-pulse techniques. The application of these measurements towards refining the structure of photosynthetic antennae will be explored. Vibrational spectra of the amide I band and of OH hydrogen-bonded networks will be simulated. The structure and fluctuations of a small cyclic 10 residue polypeptide (Antamanide) and a globular 76-residue protein (Ubiquitin will be studied, focusing on Hydrogen bonding and Phenylalanine side chain dynamics in Antamanide and backbone and Glutamine sidechain dynamics in Ubiquitin. Protein folding in beta-peptides and its real-time probing by nonlinear spectroscopies will be investigated. An new spectroscopic algorithm for simulating excited-state photodynamics and relating it to protein-pigment interactions will be developed. Applications will be made to energy transfer processes in photodynamic therapy.
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