Nonequilibrium Dynamics in Biomolecules

Nguyen Hoang Phuong, Institut für Physikalische und Theoretische Chemie; Universität Frankfurt

Femtosecond experiments on photoswitchable peptides provide a new and promising way to study the folding and unfolding of biomolecules in real time and unprecedented detail. To obtain an appropriate theoretical description of these experiments, we suggest to extend well-established molecular dynamics simulation techniques to the description of photoinduced conformational dynamics in peptides. The goal is to perform true nonequilibrium molecular dynamics simulations in which the laser-induced initial state of the molecule is represented by a suitable semiclassical phase-space distribution, from which initial conditions of nonequilibrium trajectories are sampled. Performing a time-dependent ensemble average over these trajectories, the observables of interest are calculated, including the time-dependent transfer of vibrational energy as well as the photoinduced conformational rearrangements of the peptide. The results are directly compared to experiments.