Simulation techniques for predicting the nonlinear response of biomolecules to sequences of infrared and visible pulses, and connecting them to various secondary structure motifs, structure fluctuations and dynamical processes, will be developed. These multidimensional signals, which provide femtosecond snapshots of dynamical events, will be calculated and analyzed, using multipoint correlation functions obtained from ab initio density functional and MD codes. Large scale simulations of vibrational signatures of fluctuations of the environment (backbone conformations, side chains and solvent) will be performed, using an electrostatic map obtained from electronic structure calculations of individual chromophores subjected to a nonuniform electric field. Specific infrared signatures of protein folding pathways, triggered by temperature jump, photoisomerization of an embedded switch, and by optically induced dipoles will be simulated. Coherent time resolved spectroscopic probes of chirality which use novel light polarization configurations will be studied. Design strategies for pulse sequences in coherent.vibrational and electronic spectroscopies, drawing upon the analogy with NMR, will be developed. Coherent control algorithms and sensitivity analysis will be used to tailor pulse shapes to specific secondary structural motifs in globular proteins, disentangle complex spectra and relate them to specific structural and dynamical processes. Two dimensional vibrational spectra of the amide I band will be used to distinguish between parallel and anti-parallel beta sheet structures of Amyloid Fibrils. Other applications will be made to DNA base pairs and photosynthetic aggregates. Specific signatures of hydrogen bonding between amino acid residues, and with water in multidimentional infrared signals, will be predicted.
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