3 research outputs found
Advancing hierarchical equations of motion for efficient evaluation of coherent two-dimensional spectroscopy
To advance hierarchial equations of motion as a standard theory for quantum
dissipative dynamics, we put forward a mixed Heisenberg--Schrodinger scheme
with block-matrix implementation on efficient evaluation of nonlinear optical
response function. The new approach is also integrated with optimized
hierarchical theory and numerical filtering algorithm. Different configurations
of coherent two-dimensional spectroscopy of model excitonic dimer systems are
investigated, with focus on the effects of intermolecular transfer coupling and
bi-exciton interaction
Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre
One longstanding puzzle concerning photosystem II, a core component of photosynthesis, is that only one of the two symmetric branches in its reaction centre is active in electron transfer. To investigate the effect of the photosystem II environment on the preferential selection of the energy transfer pathway (a prerequisite for electron transfer), we have constructed an exciton model via extensive molecular dynamics simulations and quantum mechanics/molecular mechanics calculations based on a recent X-ray structure. Our results suggest that it is essential to take into account an ensemble of protein conformations to accurately compute the site energies. We identify the cofactor CLA606 of active chain as the most probable site for the energy excitation. We further pinpoint a number of charged protein residues that collectively lower the CLA606 site energy. Our work provides insights into the understanding of molecular mechanisms of the core machinery of the green-plant photosynthesis. © 2014 Macmillan Publishers Limited. All rights reserved