Atlas of Bacterial and Archaeal Cell Structure

Atlas of Bacterial and Archaeal Cell Structure

Atlas of Bacterial and Archaeal Cell Structure

This thesis focuses on the management of protons and electrons in the formation of X−H bonds. In our pursuit of better understanding this process, we have been particularly interested in the nitrogen fixation reaction (N2-to-NH3) because of the high number of protons and electrons involved in this conversion (6) and the significant difficulty of functionalizing N2. The first chapter introduces the important themes of this thesis: (i) multiple bonding, (ii) proton-coupled electron transfer, (iii) overpotential...

Global warming and the related problem of water scarcity are predicted to cause widespread environmental, humanitarian, and economic challenges. New technologies may be able to reduce greenhouse gas emissions enough to prevent many of the worst consequences of climate change However, in order to be competitive in the market, new, low emissions technologies much be affordable. In this thesis I present work on building a technology to lower the cost of decentralized, electrochemical wastewater treatment...

Part 1: Broadband observations of comets P/Stephan-Oterma (1980g), Bowell (1980b) and Panther (1980u) in the visual (0.5 ≾ λ(µm) ≾ 0.9) and infrared (1.2 ≾ λ(µm) ≾ 20) wavelength regions are reported together with measurements in the 1.5 to 2.4 µm wavelength range having 5% spectral resolution. The visual data indicate the existence of solid grains in extended halos around the nuclei of the three comets. The visual photometric profiles of comets P/Stephan-Oterma and Panther...

This repository contains a video recorded by a Dalsa Falcon VGA 300 camera recording at 250 FPS. Playback is at 10 FPS, a factor of 25 slow-down.

Protein-bound iron sulfur clusters are critical in cells and allow proteins to carry out many essential functions as electron carriers, catalysts for challenging organic reactions, and sensors of cellular environments. A wide range of protein families are known to coordinate iron sulfur clusters, and a growing category includes proteins involved in maintenance of the genome. Within the last three decades, iron sulfur clusters have been demonstrated to be important for enzymes that function in DNA...

The Hecke orbit conjecture plays an important role in understanding the geometric structure of Shimura varieties. First postulated by Chai and Oort in 1995, the Hecke orbit conjecture predicts that prime-to-p Hecke correspondences on mod p reductions of Shimura varieties characterize the foliation structure formed by Oort's central leaves. In other words, every prime-to-p Hecke orbit is Zariski dense in the central leaf containing it. Roughly speaking, a central leaf is the locus in a...

Biomass burning is a significant source of atmospheric particulate matter less than 2.5 micrometers in diameter (PM2.5) and encompasses a variety of activities, fuels, and emissions profiles. A significant portion of the world population relies on solid biofuels for cooking and other household activities. Residential use of solid biofuels can have negative impacts on human health, particularly in southeast Asia, and contribute to ambient air quality. In addition, wildfires are of increasing concern as climate...

This thesis concerns three key aspects of reduced-order modeling for turbulent shear flows. They are linear mechanisms, nonlinear interactions, and data-driven techniques. Each aspect is explored by way of example through analysis of three different problems relevant to the broad area of turbulent channel flow. First, linear analyses are used to both describe and better understand the dominant flow structures in elastoinertial turbulence of dilute polymer solutions. It is demonstrated that the most-amplified mode predicted...

Efficient unassisted solar fuel generation, a pathway to storable renewable energy in the form of chemical bonds, requires optimization of a photoelectrochemical device based on photonic design and interface study. We first focused on enhancing absorption via nanophotonic design of light absorbers. Near-unity, broadband absorption in sparse InP nanowire arrays with multi-radii and tapered nanowire array designs are simulated and experimentally demonstrated. Later, a few strategies are introduced to achieved high solar-to-fuel efficiency. Optically, photoelectrochemical...

There is a critical need for improved diagnostic tools to detect infectious diseases, especially in low-resource regions. A sample-to-answer point-of-care nucleic acid amplification test (NAAT) would be incredibly valuable for many different applications (e.g. COVID-19, Chlamydia/Gonorrhoeae, Influenza, Ebola, Zika/Chikungunya/Dengue, etc.). However, sample preparation (purification of pure nucleic acids) is a challenging bottleneck. In Chapter 2, commercial NA extraction methods were studied and improved. In Chapter 3, commercial stocks of SARS-CoV-2 RNA used in FDA emergency-use...

The "wires project" in the Gray group has been focused on characterizing short-lived intermediates of Fe heme enzyme catalytic cycles by designing and synthesizing photosensitizers (wires) that bind to the protein active site with high affinity. The heart of this thesis is on rhenium channel binding and ruthenium surface binding wires for inducible nitric oxide synthase (iNOS). Binding and inhibition studies were conducted, electron transfer (ET) kinetics were studied, and iNOS catalytic activity was assayed...

Recent shifts in the astrobiological community have prompted the development of methods for the direct search for extant life within our solar system. In order to look for life elsewhere in our solar system, it is important to also investigate the broad spectrum of extant life on Earth. Over millions of years of evolution, life has continually adapted such that an 'extreme' environment has become a relative term. What is considered extreme for one type...

In this thesis, I present a number of studies intended to improve our understanding of black holes using gravitational waves. Although black holes are relatively well understood from a theory perspective, many questions remain about the nature of the black holes in our Universe. According to general relativity, astrophysical black holes are fully described by just their mass and spin. Yet, relying on electromagnetic-based observatories alone, we still know very little about the distribution of...

My various projects in graduate school have centered around a common theme: harnessing relatively well-understood phases of matter and combining them to create exotic physics. They also involve Majoranas, or more accurately, defects that bind Majorana zero modes and are the centerpiece for topological quantum computation. We exploit and enrich this Majorana zero mode by employing topological superconductors, time crystals, and quantum dots and combining them together. Our first project involved joining Majorana nanowires and...

This thesis offers a contribution to the study of Social Learning and Networks. It studies information aggregation and its effect on individual's actions (Chapter 2, 3) and social network (Chapter 4). Chapter 2, co-authored with Omer Tamuz and Wade Hann-Caruthers, studies how quickly does the public belief converge to its true value when agents are able to observe actions of their predecessors. In the classical herding literature, agents receive a private signal regarding a binary...

There are no updates for this release; it is a release to get a DOI from [CaltechDATA](https://data.caltech.edu).

A number of efforts to determine function from sequence of RNA and DNA have been made with varying success. Here we study the determination of function from sequence of DNA and RNA through their secondary structure kinetics, specifically the series of transitions between secondary structures. This series of transitions or microscopic structure can be described by a system of ordinary differential equations that can be approximating using balanced truncation to determine the macroscopic structure. By...

Recent research on bilayer two-dimensional electron gasses (2DEG) indicates the possibility of excitonic superfluidity, though experiments have measured small dissipation due to motion of unpaired vortices. In regular superconductors, carriers flow without dissipation beacuse vortices are "pinned" by impurities. This research investigates the effects of C and Si dopants within the quantum well of a single quantum well 2DEG. These dopants are candidates for improving vortex pinning in bilayer 2DEG systems. Four C-doped samples, with...

This dissertation focuses on fundamental research in two areas of magnetism, the technologically advanced field of magnetic resonance imaging (MRI) and the nascent discipline of molecular magnetic materials. Contrast agents for MRI based on the gadolinium(III) ion were designed and studied to gain insight into the parameters that may be modulated to control contrast agent efficacy. Two parameters in particular, the inner-sphere coordination environment and the electronic relaxation of the gadolinium(III) ion, were examined. Investigations...

Low interfacial electron-hole recombination rates are essential for low-noise electronic devices and high-efficiency solar energy converters. This recombination rate is dependent on both the surface electrical trap state density, NT,s, and the surface concentrations of electrons, ns, and holes, ps. A reduction in NT,s is often accomplished through surface chemistry, and lower recombination rates, through lower NT,s values, have been demonstrated in this work for surfaces chemically treated to produce methoxylated, Si-O-CH3, overlayers. The H-Si(111)...

The recognition of DNA base mismatches is of considerable interest for both the diagnosis and treatment of mismatch repair-deficient cancers. Two new mismatch recognition complexes have been synthesized. The first, [Rh(bpy)2(phzi)]3+ (phzi=benzo[a]phenazine-5,6-quinone diimine), recognizes DNA mismatches with high specificity and affinity, 1 x 107 Mm-1, two orders of magnitude stronger than [Rh(bpy)2(chrysi)]3+ (chrysi=chrysene-5,6-quinone diimine), the parent complex that binds single thermodynamically-destabilized base-mismatch sites in duplex DNA. The second, [Rh(bqdi)2(chrysi)]3+, is able to recognize more stable...

The DNA pi stack provides an efficient pathway for transport of electron and electron holes. Ground-state electron transport is furthermore extremely sensitive to subtle DNA structural perturbations, such as a single base mismatch, that alter pi-stacking. As a result, DNA-modified electrodes have allowed the development of highly sensitive diagnostic devices for the detection of base mismatches, lesions, and mutations. We have been able to apply DNA-mediated charge transduction, using a methylene blue/ferricyanide electrocatalytic cycle, in...