This thesis describes laboratory experiments and electronic structure calculations on three chemical systems relevant to tropospheric ozone chemistry: peroxynitrous acid (HOONO), hydroxymethylperoxy radical formed from HO2 + HCHO (R1), and products of alkoxy isomerization (R2). R1 and R2 were studied experimentally using a gas flow cell that combined UV photolysis with cavity ringdown spectroscopy (CRDS). All chemical systems were studied using electronic structure calculations and kinetics modeling. HOONO is one of the products of the...

The amount of digital image and video data keeps increasing at an ever-faster rate. While "big data" holds the promise of leading science to new discoveries, raw image data in itself is not of much use. In order to statistically analyze the data, it must be quantified and annotated. We argue that entirely automated methods are not accurate enough to annotate data in the short term. Crowdsourcing is an alternative that provides higher accuracy, but...

This thesis describes a search for νe appearance in the two-detector long-baseline MINOS neutrino experiment at Fermilab, based on a data set representing an exposure of 8.2 x 1020 protons on the NuMI target. The analysis detailed herein represents an increase in sensitivity to the θ13 mixing angle of approximately 25% over previous analyses, due to improvements in the event discriminant and fitting technique. Based on our observation, we constrain the value of θ13 further,...

The large diffusion coefficients of sub-10 nm aerosol have posed a long-standing challenge to the aerosol community; to understand nucleation and early growth, there is a need for methods such as those presented here that transmit a strong, high resolution signal of classified charged aerosol to the detector. I introduce a framework for comparison of the Flagan Laboratory classifiers to other instruments, and I show why our instruments perform favorably relative to these alternatives. Reducing...

This thesis deals with achieving more realistic atomistic simulations of materials, by developing accurate and robust force-fields, and algorithms for practical time scales. I develop a formalism for generating interatomic potentials for simulating atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high-energy collisions. This is done by fitting against an extensive database of ab initio results, as well as to experimental measurements for mixed oxide nuclear fuels. The applicability...

My thesis centers around the study of neutron stars, especially those in massive binary systems. To this end, it has two distinct components: the observational study of neutron stars in massive binaries with a goal of measuring neutron star masses and participation in NuSTAR, the first imaging hard X-ray mission, one that is extremely well suited to the study of massive binaries and compact objects in our Galaxy. The Nuclear Spectroscopic Telescope Array (NuSTAR) is...

The Human Immunodeficiency Virus (HIV) depends on the ability to exit infected cells, mature into an infectious state, and infect new host cells. The structural details of exiting and maturation (known as the "late stage events") remain elusive, but further understanding could lead to new therapies. HIV exits cells by hijacking a host cellular complex called ESCRT (Endosomal Sorting Complex Required for Transport), which evolved to constrict membranes in multivesicular body formation and cytokinesis. Electron...

In much of classical queueing theory, workloads are assumed to be light-tailed, with job sizes being described using exponential or phase type distributions. However, over the past two decades, studies have shown that several real-world workloads exhibit heavy-tailed characteristics. As a result, there has been a strong interest in studying queues with heavy-tailed workloads. So at this stage, there is a large body of literature on queues with light-tailed workloads, and a large body of...

The fields of Network Coding and Distributed Compression have focused primarily on finding the capacity for families of problems defined by either a broad class of networks topologies (e.g., directed, acyclic networks) under a narrow class of demands (e.g., multicast), or a specific network topology (e.g. three-node networks) under different types of demands (e.g. Slepian-Wolf, Ahlswede-Körner). Given the difficulty of the general problem, it is not surprising that the collection of networks that have been...

There has been a barrage of interest in recent years to marry the fields of nanomechanics and quantum optics. Mechanical systems provide sensitive and scalable architectures for sensing applications ranging from atomic force microscopy to gravity wave interferometry. Optical resonators driven by low noise lasers provide a quiet and well-understood means to read-out and manipulate mechanical motion, by way of the radiation pressure force. Taken to an extreme, a device consisting of a high-Q nanomechanical...

We study a generalization of the famous k-center problem where each object is an affine subspace of dimension Δ, and give either the first or significantly improved algorithms and hardness results for many combinations of parameters. This generalization from points (Δ=0) is motivated by the analysis of incomplete data, a pervasive challenge in statistics: incomplete data objects in Rd can be modeled as affine subspaces. We give three algorithmic results for different values of k,...

This dissertation primarily describes structure-function studies of the prototypical Cys-loop ligand-gated ion channel, the nicotinic acetylcholine receptors (nAChRs). Agonists that bind nAChRs, including acetylcholine, nicotine, and the smoking cessation drug varenicline, share one of the longest-known, best-studied pharmacophores, consisting of a cationic N and a hydrogen bond acceptor. A major theme of this thesis is concerned with defining the nAChR residues that bind the nicotinic pharmacophore. Chapters 2 and 3 establish that a hydrogen bond...

Organic compounds contribute a significant mass fraction of ambient aerosol and play a role in determining the physiochemical properties of ambient aerosol. A significant fraction of organic aerosol is secondary organic aerosol (SOA), which is produced when the volatile organic compounds (VOCs) originated from various anthropogenic and biogenic sources react with atmospheric oxidants such as ozone, hydroxyl radicals, and nitrate radicals to form lower volatility organic compounds, which subsequently partition into the particle phase. Understanding...

DNA has been used in vitro as a computational substrate due to programmable base-pairing interactions. This allows the construction of logic gates, self-assembled shapes, motors, walkers and other nanoscale devices comprised of DNA strands. These strands must be carefully designed in order to correctly perform their function, which requires effective models of the DNA system. The thermodynamics of multiple interacting DNA strands is a well-studied model which can make equilibrium predictions on these systems, but...

During embryogenesis, the central nervous system (CNS) transforms from what seems like an amorphous mass of cells to a rod-like structure, and then to a fully functional and complex system of tissues composed of multiple cell types. Using confocal laser scanning microscopy (CLSM), I demonstrate a modified version of in toto imaging to track normal spinal cord organization in zebrafish from bud stage, ~ 11 hours post-fertilization (hpf), to 48 hpf. I also assisted in...

Translocation of membrane proteins from the point of synthesis to their integration in the membrane is critical to the function of the cell. Tail-anchored (TA) proteins are an important class of membrane proteins with a single transmembrane domain (TMD) close to the carboxyl-terminus. They are defined topologically by having their amino-terminus in the cytosol and their carboxyl-terminus on the exterior side of the membrane. Since the TMD is sequestered by the ribosome during translation, co-translational...

In part I, the 3D velocity and attenuation structure of the Cocos subduction zone in Mexico is imaged using earthquakes recorded by two temporary seismic arrays and local stations. Inversion results reveal low-attenuation and high-velocity Cocos slab. The slab dip angle increases from almost flat in central Mexico near Mexico City to about 30 degrees in southern Mexico near the Isthmus of Tehuantepec. High attenuation and low velocity in the crust beneath the Trans-Mexico Volcanic...

Basic questions regarding the interaction between changes in human activity and the atmosphere remain unanswered. Among these, the link between aerosol particles and cloud formation and development, especially in an altered climate, is a large point of uncertainty in recent climate projections. This should come as no surprise given the uncertainty in model parameters required to predict droplet activation, even in the most detailed models used for climate predictions. Here, a detailed spectral mixed-phase microphysics...

The advantages of Proton Exchange Membrane (PEM) fuel cells include lower operating temperature than other fuel cells and size small enough to fit into a car. Improving the cost and durability of PEM fuel cell materials is a hot topic of research today. The Nafion membrane and cathode catalysts are two areas where PEM fuel cells have issues of cost, durability, and efficiency. In order to improve these materials, researchers need a better understanding of...

Many gene regulatory motifs in both prokaryotes and eukaryotes involve physical manipulations of the genetic material, often on length scales short enough that the mechanical properties of the DNA significantly impact gene expression. One class of such manipulations, called “action at a distance”, includes transcription factor-mediated DNA looping, in which a binding site some distance away on the DNA is brought into close proximity with the transcription machinery at the promoter. DNA looping is a...

In this thesis, we explore examples of each of the three primary strategies for the detection of particle dark matter: indirect detection, direct detection, and collider production. We first examine the indirect detection of weakly interacting massive particle (WIMP) dark matter via the gamma-ray photons produced by astrophysical WIMP annihilation. Such photons may be observed by the Fermi Gamma-ray Space Telescope. We propose the gamma-ray-flux probability distribution function (PDF) as a probe of the Galactic...

Neuroeconomics has produced a number of insights into economics, psychology, and neuroscience in its relatively short existence. Here, I show how neuroeconomics can inform these fields through three studies in social decision making and decision making under risk. Specifically, I focus on computational biases inherent in our daily decisions. First, using functional magnetic resonance imaging (fMRI), I examine how we make decisions for others compared to ourselves. I find that overlapping areas of the ventromedial...

A wide variety of astrophysical observations indicate that approximately 85% of the matter in the universe is nonbaryonic and nonluminous. Understanding the nature of this "dark matter" is one of the most important outstanding questions in cosmology. Weakly Interacting Massive Particles (WIMPs) are a leading candidate for dark matter since they would be thermally produced in the early universe in the correct abundance to account for the observed relic density of dark matter. If WIMPs...

Glaucoma is an eye disease that gradually steals vision. Open angle glaucoma is one of the most common glaucoma forms, in which eye fluid (aqueous humor) produced by the ciliary body cannot be drained away normally by patients’ eyes. The accumulated eye fluid inside the anterior chamber causes high intraocular pressure (IOP), which is transmitted onto the retina in the back of the eyeball (globe), continuously suppressing and damaging the patient’s optic nerves; this may...

Vector-borne diseases have a profound impact on world health. The two most well-known and costly diseases are dengue fever and malaria, both spread by mosquito vectors. In the last decade, many new solutions to halting the spread of these diseases have been sought, including vector-mediated disease suppression. The work presented here seeks to generate alleles to effect this suppression, and engineer a drive system to replace the native population. Additional work on systems to keep...