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photosynthesis involves the harvesting of light energy from the sun by the antenna (made
of pigments) of the PSII trans-membrane complex. The harvested excitation energy is
transferred from the antenna complex to the reaction center of the PSII, which leads to a
light-driven charge separation event, from water to plastoquinone. This phenomenal
process has been producing the oxygen that maintains the oxygenic environment of our
planet for the past 2.5 billion years.
The oxygen molecule formation involves the light-driven extraction of 4 electrons
and protons from two water molecules through a multistep reaction, in which the Oxygen
Evolving Center (OEC) of PSII cycles through 5 different oxidation states, S0 to S4.
Unraveling the water-splitting mechanism remains as a grant challenge in the field of
photosynthesis research. This requires the development of an entirely new capability, the
ability to produce molecular movies. This dissertation advances a novel technique, Serial
Femtosecond X-ray crystallography (SFX), into a new realm whereby such time-resolved
molecular movies may be attained. The ultimate goal is to make a “molecular movie” that
reveals the dynamics of the water splitting mechanism using time-resolved SFX (TRSFX)
experiments and the uniquely enabling features of X-ray Free-Electron Laser
(XFEL) for the study of biological processes.
This thesis presents the development of SFX techniques, including development of
new methods to analyze millions of diffraction patterns (~100 terabytes of data per XFEL
experiment) with the goal of solving the X-ray structures in different transition states.
ii
The research comprises significant advancements to XFEL software packages (e.g.,
Cheetah and CrystFEL). Initially these programs could evaluate only 8-10% of all the
data acquired successfully. This research demonstrates that with manual optimizations,
the evaluation success rate was enhanced to 40-50%. These improvements have enabled
TR-SFX, for the first time, to examine the double excited state (S3) of PSII at 5.5-Å. This
breakthrough demonstrated the first indication of conformational changes between the
ground (S1) and the double-excited (S3) states, a result fully consistent with theoretical
predictions.
The power of the TR-SFX technique was further demonstrated with proof-of principle
experiments on Photoactive Yellow Protein (PYP) micro-crystals that high
temporal (10-ns) and spatial (1.5-Å) resolution structures could be achieved.
In summary, this dissertation research heralds the development of the TR-SFX
technique, protocols, and associated data analysis methods that will usher into practice a
new era in structural biology for the recording of ‘molecular movies’ of any biomolecular
process.
(XFEL) allows it to outrun radiation damage in coherent diffractive imaging since elastic scattering terminates before photoelectron cascades commences. This “diffract-before-destroy” feature of XFEL opened up new opportunities for biological macromolecule imaging and structure studies by breaking the limit to spatial resolution imposed by the maximum dose that is allowed before radiation damage. However, data collection in serial femto-second crystallography (SFX) using XFEL is affected by a bunch of stochastic factors, which pose great challenges to the data analysis in SFX. These stochastic factors include crystal size, shape, random orientation, X-ray photon flux, position and energy spectrum. Monte-Carlo integration proves effective and successful in extracting the structure factors by merging all diffraction patterns given that the data set is sufficiently large to average out all stochastic factors. However, this approach typically requires hundreds of thousands of patterns collected from experiments. This dissertation explores both experimental and algorithmic methods to eliminate or reduce the effect of stochastic factors in data acquisition and analysis. Coherent convergent X-ray beam diffraction (CCB) is discussed for possibilities of obtaining single-shot angular-integrated rocking curves. It is also shown the interference between Bragg disks helps ab-initio phasing. Two-color diffraction scheme is proposed for time-resolved studies and general data collection strategies are discussed based on error metrics. A new auto-indexing algorithm for sparse patterns is developed and demonstrated for both simulated and experimental data. Statistics show that indexing rate is increased by 3 times for I3C data set collected from beam time LJ69 at Linac coherent light source (LCLS). Finally, dynamical inversion from electron diffraction is explored as an alternative approach for structure determination.
There is a lot of variation in health outcomes when it comes to individual states in America. Some states, such as Hawaii, have the life expectancy equivalent to that of developed countries, whereas states like Mississippi have the life expectancy equivalent to that of third world countries. This raised the questions of which states are doing well in health and why, and if their health has to do with their performance in the primary, secondary, tertiary, and/or quaternary prevention levels. The purpose of this research was to investigate if there is a correlation between performance in any of the prevention levels and the overall health status of a state, and if there is, which prevention level would be most beneficial for states to prioritize. The hypothesis of this research was: states that prioritized primary and secondary levels of prevention would have better health than states that prioritized tertiary and quaternary levels of prevention, since basic health measures contribute more to health outcomes than advanced medicine. To investigate this question, indicators were chosen to derive the ranking of each state in health and each of the four prevention levels. Six states were then chosen to represent the high, average, and low health statuses respectively. The six states were ranked for all indicators, and the data was analyzed and compared to determine a potential relationship between the prevention level rankings and the overarching health ranking. It was found that there is a correlation between performance in the primary and secondary prevention levels and a state’s overall health status, whereas there was no such correlation for the tertiary and quaternary levels. A model for health was proposed for states looking to improve their health status, which was to invest in primary prevention, followed by secondary, tertiary, then quaternary prevention and only moving to the next prevention level once the previous level reached a satisfactory threshold.
This project will be a tribute to my experiences as a person, a chef, and as an ASU student. During my time spent here at ASU I have met a diverse group of people that I call my friends. Every time we would spend time together, I would learn about their lives and the experiences they are going through at this university. Everyone I met had a different background, story, and experience. Some of these memorable nights would be spent at my place. Depending on the circumstance, I would cook for my friends, and every time I did, they were amazed by my craft. Growing up, my mother was always working in the realm of fundraising. Through her jobs, we both had the opportunity to meet and work with some of the best chefs the Phoenix valley had to offer. Chefs like Robert Irvine, Mario Batali, Beau MacMillan, Christopher Gross, Michael DiMaria, Eddie Matney, and more. As a child and teenager, my fascination with cooking and food stood out to these figures and many taught me various skills and techniques in the kitchen. I learned to do everything from properly julian tangerines to preparing beef tartar. I even developed from making lemonade on my own when I was two years old to working in a four star restaurant as a line chef at the age of 15. These memories I will be forever grateful for. Through these skills, I have impressed my friends with delicious meals at night. And as we matured through college both in age and living situations, many of my friends have asked to learn from me. The change from freshman dorms to our own houses and townhomes have offered an endless opportunity of options for meals. But, everyone has a different background and skill set when it comes to cooking. A few of my friends have never picked up a knife before and have claimed to “burn water in the microwave.” Others tend to challenge me in preparing meals in their own homes and together we have our own “cookoffs.” From person to person, and living quarter to living quarter, there are many challenges to cooking. This is why I have decided to take the knowledge from my Industrial Engineering classes, my personal cooking skills, and data collected from the student body to create a cookbook for the average ASU student. I plan to include recipes and techniques in the form of Standard Operating Procedures to ensure that the instructions are as easy to follow as they can be. The recipes and techniques I plan to include will encompass data I have collected from the student body. The data will focus around a few key components of any chef and kitchen: tools and appliances available, personal cooking skills, and personal cooking experience. To take on such a challenge, I plan to complete this thesis/creative project in a few direct steps. First and foremost, complete this prospectus (already completed), next, secure funding from ASU for a survey completion incentive. For this survey, I will need a minimum of $250 to distribute between 5 winners. The monetary incentive is to ensure that more than 30 pieces of data (survey responses) are collected from each grade level of students. Next I will send a survey that asks about the aforementioned topics. After the survey is complete, I will collect the data, analyze it, and hone in on the most important and available tools. Finally, I will write stories surrounding my chosen recipes and create said recipes.
COVID-19 has proved that our society can be adaptable in the most unexpected situations. Chaos and fear struck the nation causing people to react in a variety of ways in an attempt to protect their own self interests. The retail space has had to adjust in large scales, making the shopping experience safer both for the customer and the employees. I was able to experience this first hand at Target, working there many years previous to and during the pandemic, getting to see the shift in consumer patterns. I noticed customers would purchase more products in one department, then the next month it would shift to another department. This paper will analyze those shifts in sales trends both departmentaly and within shopping methods at Target to help identify the largest changes and the possible reasons behind these.