Numerous pigment protein complexes exist in natural systems to harvest light energy such as photosystem II and Nanosalina xenorhodopsin. However, the mechanisms of these lipid embedded photo-active complexes have yet to be fully understood. Photosystem II is of interest due to being a compact complex which can perform the three initial key steps of photosynthesis: absorb light, transfer the excitation from the antennae to reaction center, and perform efficient charge separation. Despite considerable theoretical and experimental effort the exact mechanism of this process remains uncertain. Nanosalina xenorhodopsin is a more recently discovered inwards proton pump with minimal studies into the inwards proton pumping mechanism. Nanosalina xenorhodopsin is of interest as it contrasts with other known and well studied rhodopsins which serve as outwards proton pumps, moving H+ ions out of a cell.
In this work, we use the Hamiltonian ensemble method to construct the first fully ab initio computational models of these systems which will be used to determine the mechanisms of these systems. To construct these models we first investigated the effect of the modeled surrounding membrane and simulated temperature. The effect of the extended modeled environment on calculated results is often overlooked but important for the construction of an accurate ab initio model.
Our models showed that both membrane composition and temperature result in significant changes in the behavior of the extended membrane system, relative excitation energies of chromophores, and energy dynamics of a pigment protein complex. The absolute excitation energies of chromophores, absorption spectra, and linear dichroism spectra were comparatively insensitive to changes in the modeled environment. With the effect of the environment established, we present a preliminary method to extend our photosystem II model to include charge transfer states, and a preliminary model of Nanosalina xenorhodopsin which can determine the photocycle states through validation of calculated spectra against experimental results.
| Identifer | oai:union.ndltd.org:bu.edu/oai:open.bu.edu:2144/49077 |
| Date | 16 July 2024 |
| Creators | Hino, Alexander T. |
| Contributors | Coker, David F. |
| Source Sets | Boston University |
| Language | en_US |
| Detected Language | English |
| Type | Thesis/Dissertation |
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