Show simple item record

dc.contributor.authorCheesman, Andrew
dc.date.accessioned2016-03-09T20:45:43Z
dc.date.available2016-03-09T20:45:43Z
dc.identifier.urihttp://hdl.handle.net/10464/8683
dc.description.abstractPhotosynthesis 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.en_US
dc.language.isoengen_US
dc.publisherBrock Universityen_US
dc.subjectPhotosynthesisen_US
dc.subjectQuantum Mechanicsen_US
dc.subjectCalculationsen_US
dc.subjectEnergy levelsen_US
dc.subjectChromophoreen_US
dc.titleOptimizing Computational Frameworks to Study the Influence of the Protein Environment on the Individual Site Energies of Chromophores in Photosystem II of Photosynthesisen_US
dc.typeElectronic Thesis or Dissertationen_US
dc.degree.nameM.Sc. Physicsen_US
dc.degree.levelMastersen_US
dc.contributor.departmentDepartment of Physicsen_US
dc.degree.disciplineFaculty of Mathematics and Scienceen_US


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record