Photosynthesis Fun

Hello from Dr. Sato’s physics lab! This summer we are using a variety of computer technology and software to gain insight on the molecular and quantum dynamics of photosynthesis. Our primary overarching goal is to understand the electronic landscape of the photosystem II reaction center (PSII RC), however, due to the size of the system in total, we are starting with a focus on a smaller, simpler component: the WSCP, or water-soluble chlorophyll proteins, in order to build our foundation on the quantum mechanical processes and chemical reactions of the photoreaction center in plants. While WSCPs are not directly involved in photosynthesis, they contribute to the protection and photostability of bound chlorophylls, meaning that they may play a role in preventing damage of the chlorophylls from light during photosynthesis and could aid in the stress response of the plant. This is super important as it could help us understand why plants are able to convert such strong rays of light into usable energy! Our project is motivated by previous work that found an asymmetrical charge transfer between the perfectly symmetrical RC branches. Therefore, by taking a look into the structure and energy states of the system, it is possible that we can understand why there is asymmetry during this stage of photosynthesis. If we are able to describe why and how this process functions, hopefully we will become closer to determining how to construct energy machines on a macroscopic level that mirrors the efficiency and cleanliness of photosynthetically produced energy. This is super important since our current best functioning solar panels are only about 20% efficient in comparison to the almost 100% efficiency of photosynthesis!

Henry’s work:

I have spent the summer working with a quantum chemistry program called ORCA to try and develop a method for predicting absorbance and fluorescence spectra of the chlorophyll included within the RC. We have decided to use a technique called time-dependent density functional theory, or TDDFT for short. Emma and I spent the first part of the summer working together to test different functionals to determine which predicted the most accurate results in the shortest amount of time. After this testing, we settled on the wB97X-D4 functional included with ORCA. Right now, I am applying this method to try and recreate experimental fluorescence spectra using ORCA.

Emma’s Work: Currently in lab my focus is on applying the computational software of NAMD and MOPAC on the entire WSCP to produce a visual simulation of the molecule solvated in water. By simulating this in a realistic environment we can see how it moves and changes over time. This provides information on the coordinates of the molecule at each stage of the simulation run and the partial charges of each atom at that time point as well. By using these information files, I can then use the computational power of MOPAC and ORCA software to calculate the ground state energies and excited state energies of the molecule at different points in time. From this data I then create absorption spectra using python scripts which will eventually be used to find the wavefunction and Hamiltonian of the molecule with the help of Dr. Sato.

An example of a python generated absorption spectrum using MOPAC data on the protein chain A and chlorophyll A core—a small part of the WSCP! 

A screenshot of the first frame of a VMD simulation of the WSCP in water. 

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