Phonon dispersion curves and atomic mean square displacement for several fcc and bcc materials

The atomic mean square displacement (MSD) and the phonon dispersion curves (PDC's) of a number of face-centred cubic (fcc) and body-centred cubic (bcc) materials have been calclllated from the quasiharmonic (QH) theory, the lowest order (A2 ) perturbation theory (PT) and a recently proposed Green's function (GF) method by Shukla and Hiibschle. The latter method includes certain anharmonic effects to all orders of anharmonicity. In order to determine the effect of the range of the interatomic interaction upon the anharmonic contributions to the MSD we have carried out our calculations for a Lennard-Jones (L-J) solid in the nearest-neighbour (NN) and next-nearest neighbour (NNN) approximations. These results can be presented in dimensionless units but if the NN and NNN results are to be compared with each other they must be converted to that of a real solid. When this is done for Xe, the QH MSD for the NN and NNN approximations are found to differ from each other by about 2%. For the A2 and GF results this difference amounts to 8% and 7% respectively. For the NN case we have also compared our PT results, which have been calculated exactly, with PT results calculated using a frequency-shift approximation. We conclude that this frequency-shift approximation is a poor approximation. We have calculated the MSD of five alkali metals, five bcc transition metals and seven fcc transition metals. The model potentials we have used include the Morse, modified Morse, and Rydberg potentials. In general the results obtained from the Green's function method are in the best agreement with experiment. However, this improvement is mostly qualitative and the values of MSD calculated from the Green's function method are not in much better agreement with the experimental data than those calculated from the QH theory. We have calculated the phonon dispersion curves (PDC's) of Na and Cu, using the 4 parameter modified Morse potential. In the case of Na, our results for the PDC's are in poor agreement with experiment. In the case of eu, the agreement between the tlleory and experiment is much better and in addition the results for the PDC's calclliated from the GF method are in better agreement with experiment that those obtained from the QH theory.

Optimizing Computational Frameworks to Study the Influence of the Protein Environment on the Individual Site Energies of Chromophores in Photosystem II of Photosynthesis

Photosynthesis is a process in which electromagnetic radiation is converted into chemical energy. Photosystems capture photons with chromophores and transfer their energy to reaction centers using chromophores as a medium. In the reaction center, the excitation energy is used to perform chemical reactions. Knowledge of chromophore site energies is crucial to the understanding of excitation energy transfer pathways in photosystems and the ability to compute the site energies in a fast and accurate manner is mandatory for investigating how protein dynamics ef-fect the site energies and ultimately energy pathways with time. In this work we developed two software frameworks designed to optimize the calculations of chro-mophore site energies within a protein environment. The first is for performing quantum mechanical energy optimizations on molecules and the second is for com-puting site energies of chromophores in a fast and accurate manner using the polar-izability embedding method. The two frameworks allow for the fast and accurate calculation of chromophore site energies within proteins, ultimately allowing for the effect of protein dynamics on energy pathways to be studied. We use these frame-works to compute the site energies of the eight chromophores in the reaction center of photosystem II (PSII) using a 1.9 Å resolution x-ray structure of photosystem II. We compare our results to conflicting experimental data obtained from both isolat-ed intact PSII core preparations and the minimal reaction center preparation of PSII, and find our work more supportive of the former.