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Description
Time-resolved serial femtosecond crystallography is an emerging method that allows for structural discovery to be performed on biomacromolecules during their dynamic trajectory through a reaction pathway after activation. This is performed by triggering a reaction on an ensemble of molecules in nano- or microcrystals and then using femtosecond X-ray laser pulses produced by an X-ray free electron laser to collect near-instantaneous data on the crystal. A full data set can be collected by merging a sufficient number of these patterns together and multiple data sets can be collected at different points along the reaction pathway by manipulating the delay time between reaction initiation and the probing X-rays. In this way, these ‘snapshot’ structures can be viewed in series to make a molecular movie, allowing for atomic visualization of a molecule in action and, thereby, a structural basis for the mechanism and function of a given biomacromolecule.
This dissertation presents results towards this end, including the successful implementations of the first diffusive mixing chemoactivated reactions and ultrafast dynamics in the femtosecond regime. The primary focus is on photosynthetic membrane proteins and enzymatic drug targets, in pursuit of strategies for sustainable energy and medical advancement by gaining understanding of the structure-function relationships evolved in nature. In particular, photosystem I, photosystem II, the complex of photosystem I and ferredoxin, and 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase are reported on, from purification and isolation, to crystallogenesis, to experimental design and data collection and subsequent interpretation of results and novel insights gained.
This dissertation presents results towards this end, including the successful implementations of the first diffusive mixing chemoactivated reactions and ultrafast dynamics in the femtosecond regime. The primary focus is on photosynthetic membrane proteins and enzymatic drug targets, in pursuit of strategies for sustainable energy and medical advancement by gaining understanding of the structure-function relationships evolved in nature. In particular, photosystem I, photosystem II, the complex of photosystem I and ferredoxin, and 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase are reported on, from purification and isolation, to crystallogenesis, to experimental design and data collection and subsequent interpretation of results and novel insights gained.
ContributorsCoe, Jesse (Author) / Fromme, Petra (Thesis advisor) / Sayres, Scott (Thesis advisor) / Mujica, Vladimiro (Committee member) / Redding, Kevin (Committee member) / Arizona State University (Publisher)
Created2018
Description
In the developing field of nonlinear plasmonics, it is important to understand the nonlinear responses of the metallic nanostructures. In the present thesis, rigorous electrodynamical simulations based on the fully vectorial three-dimensional nonlinear hydrodynamic Drude model describing metal coupled to Maxwell's equations are performed to investigate linear and nonlinear responses of the plasmonic materials and their coupling with quantum emitters.The first part of this thesis is devoted to analyzing properties of the localized surface plasmon resonances of metallic nanostructures and their nonlinear optical responses. The behavior of the second harmonic is investigated as a function of various physical parameters at different plasmonic interfaces, revealing highly complex dynamics. By collaborating with several research teams, simulations are proven to be in close agreement with experiments, both quantitative and qualitative.
The second part of the thesis explores the strong coupling regime and its influence on the second harmonic generation. Considering plasmonic systems of molecules and periodic nanohole arrays on equal footing in the nonlinear regime is done for the first time. The results obtained are supported by a simple analytical model.
ContributorsDrobnyh, Elena (Author) / Sukharev, Maxim (Thesis advisor) / Schmidt, Kevin (Committee member) / Goodnick, Stephen (Committee member) / Mujica, Vladimiro (Committee member) / Arizona State University (Publisher)
Created2022