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BP: Fachverband Biologische Physik

BP 14: Posters: Protein Structure and dynamics

BP 14.19: Poster

Tuesday, April 1, 2014, 09:30–12:30, P1

Using Molecular Dynamics Simulation to Obtain Protein Pigment Interaction in Photosynthetic Pigment Protein Complex — •Xiaoqing Wang, Sebastian Wuester, and Alexander Eisfeld — Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187 Dresden, Germany

Protein pigment interaction is very important on the electronic excitation energy transfer and spectral properties in photosynthetic pigment-protein complex. However, investigating the interaction from full quantum mechanics is out of reach because of the large number of protein atoms and the complicated arrangement of pigment molecules. In our work classical molecular dynamics simulation is used to simulate the dynamics of pigment-protein complex on the ground state. The local excitation energies and transition dipole-dipole couplings which used to build the Hamiltonian of the complex are extracted from the structure information of the molecular dynamics trajectories. In order to investigate the protein pigment coupling interaction the spectral density is calculated. Since the excitation energy is calculated by electrostatic energy shift caused by the atomic charge of protein environment we can investigate the influence of various parts of the protein. The method also might help to understand the effects on the molecular dynamics parameters.