In molecular programming, the Chemical Reaction Network model is often used to describe systems of interacting molecules. This model can describe either real systems, allowing us to analyze and determine their computational function; or describe hypothetical systems, with known computational function but perhaps no known physical example. One significant breakthrough in the field is that any Chemical Reaction Network can be approximated by a system using DNA Strand Displacement mechanisms. This allows the Chemical Reaction...

In this paper we introduce a new class of non-linear cyclic error-correcting codes, which we call subspace subcodes of Reed-Solomon (SSRS) codes. An SSRS code is a subset of a parent Reed-Solomon (RS) code consisting of codewords whose components all lie in a fixed v-dimensional vector subspace S of GF(2ᵐ). Starting from a (n, k₀, d₀) RS code over GF(2ᵐ), with any positive integer 0 ≤ v ≤ m, there is an SSRS code of...

Chapter I This chapter presents a general introduction to the cellular metabolism of calcium with particular reference to the concept of calcium pools. The importance of the ionized calcium pool of the cytosol in determining the specific function of cells and tissues is discussed. A model for stimulus-release coupling in mast cells is presented. Excitation-contraction (EC) coupling in skeletal muscle is defined and the fundamental premises required for a theory on EC coupling are given....

The neural crest is a transient population of cells that migrate away from the dorsal neural tube in the vertebrate embryo. As the developing hindbrain constricts into rhombomeres, cranial neural crest cells migrate in three discrete streams adjacent to even-numbered rhombomeres, rhombomere 2 (r2), r4, and r6. To test the role of intrinsic versus extrinsic cues in influencing an individual cell’s trajectory, we implanted physical barriers in the chick mesoderm, distal to emerging neural crest...

For centuries, historians have followed the lead of their forebears by using standardized names to refer to people and events. The use of 'Charles the Bald' to refer to Charlemagne's grandson has been reinforced via centuries of copying, paraphrasing, and citing historical documents. The sobriquet is now inextricably linked to the man. But in the simple process of writing the epithet, it is easy to forget how much complexity is distilled into one word. Any...

Curcusone C is a tricyclic diterpenoid natural product possessing potent anti-cancer activities as well as a structurally unusual 2,3,7,8-tetrahydroazulene-1,4-dione skeleton. Herein, we report our evolving synthetic efforts toward the divergent total syntheses of ent-curcusone C and several structural congeners, which commenced with a Suzuki coupling of the peripheral carbon-based rings. Whereas the boronate partner was constructed from cyclopentenone, the halide partner could be elaborated from (S)-perillaldehyde. The alcohol coupling product was next esterified, then subjected...

Paper 1: A mapping of the phase space onto itself with the same low order resonance structure as the 3/1 commensurability in the planar elliptic three-body prob­lem is derived. This mapping is approximately one thousand (1000) times faster than the usual method of numerically integrating the averaged equations of motion (as used by Schubart, Froeschlé and Scholl in their studies of the asteroid belt). This mapping exhibits some very surprising behavior that might provide the...

Area MSTd is involved in the computation of heading direction from the focus of expansion (FOE) of the visual image. Our laboratory previously found that MSTd neurons adjust their focus tuning curves to compensate for shifts in the FOE produced by eye rotation (Bradley et al., 1996) as well as for changes in pursuit speed (Shenoy et al., 2002). The translation speed of an observer also affects the shift of the FOE. To investigate whether...

As robotic platforms are put to work in an ever more diverse array of environments, their ability to deploy visuomotor capabilities without supervision is complicated by the potential for unforeseen operating conditions. This is a particular challenge within the domain of manipulation, where significant geometric, semantic, and kinetic understanding across the space of possible manipulands is necessary to allow effective interaction. To facilitate adoption of robotic platforms in such environments, this work investigates the application...

O-linked β-N-acetylglucosamine glycosylation (O-GlcNAcylation) is a dynamic, inducible post-translational modification (PTM) of thousands of intracellular proteins. There are only two enzymes responsible for O-GlcNAc cycling in higher eukaryotes, O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), which catalyze addition and removal, respectively. We hypothesized that constructing OGT substrate/interactor networks could serve as a useful foundation for understanding the functions of O-GlcNAcylation. Moreover, this approach might reveal novel insights into how OGT is able to coordinate the specific...

The atomic vibrations and thermal properties of amorphous dielectric solids are of fundamental and practical interest. For applications, amorphous solids are widely used as thermal insulators in thermopile and other detectors where low thermal conductivity directly sets the sensitivity of the detector. Amorphous solids are of fundamental interest themselves because the lack of atomic periodicity complicates theoretical development. As a result, the lower limits of thermal conductivity in solids as well as the nature of...

Solving protein structures by single-particle cryoelectron microscopy (cryo-EM) has become a crucial tool in structural biology. While exciting progress is being made toward the visualization of small macromolecules, the median protein size in both eukaryotes and bacteria is still beyond the reach of cryo-EM. To overcome this problem, we implemented a platform strategy in which a small protein target was rigidly attached to a large, symmetric base via a selectable adapter. Of our seven designs,...

[Introduction] As automated decision procedures become an increasing part of our lives, the question of how to ensure that they are fair is more relevant than ever. The freedoms, careers, and financial statuses of everyone whose lives depend on these decisions often hinge on whether the algorithms behind them are fair or not, so it is critical that algorithmic fairness is understood in a precise and rigorous manner.

In Part I of this thesis, petrographic and electron microprobe data are reported for samples from a series of high-grade Archaean gneisses, collected on Langø, an island in the northwest corner of the Godthåb District of West Greenland. Rocks with a wide variety of bulk compositions occur that all preserve evidence for two distinct episodes of metamorphic mineral growth. Syn- to post-tectonic hornblende granulite grade metamorphism (MI) was followed by post-tectonic amphibolite grade metamorphism (MII)...

Olfactory receptor neurons respond to odorant stimulation with a rapid and transient increase in intracellular cAMP that opens cyclic nucleot..ide-gated ( cng) cation channels. Cng channels in rat olfactory neurons are activated by cAMP in the low micromolar range and are outwardly rectifying. The cloned rat olfactory cng channel, (rOCNCl), however, is much less sensitive to cAMP and exhibits very weak rectification. We have investigated this discrepancy between native and cloned channels, and have cloned...

A detector for the study of neutrino oscillations with a projected sensitivity to Δm² of 10⁻³ eV² and to sin²2θ of 0.1 is described. It is to be installed 800 m from three pressurized water reactors at the Palo Verde Nuclear Generating Station near Phoenix, Arizona. The detector is segmented and filled with 12 tons of gadolinium-loaded liquid scintillator. It will be placed in an underground vault with an overburden of 46 mwe and surrounded...

Conditions are described for the synthesis of long cDNA transcripts of Sindbis virus 26S and 49S RNA in high yield. This single-stranded cDNA could be cut with Type II restriction endonucleases including Hae III, Hha I, Rsa I, or Taq I to give reproducible patterns of discrete, virus-specific fragments which were suitable for subsequent end-labeling and direct sequence analysis. Using these methods, the strategy used for obtaining nearly the entire 26S RNA sequence from cDNA...

This thesis presents a mathematical framework to model trading of financial assets on an exchange. The interaction between agents on the exchange is modeled as the Nash equilibrium of a demand schedule auction. The submission of demand schedules in the auction is meant to proxy for the submission of limit and market orders on an exchange. Chapter 1 considers this auction in a one-period setting, highlighting the importance of noisy flow for obtaining a unique...

Chapter 1 When coated with a polymer surface layer and suspended on 3-D textured glass electrodes, the hybrid combination of polymer and graphene yields sensitive chemiresistive vapor sensors. The expansion and contraction of the polymer layer when it absorbs/reacts with the VOCs, is proposed to produce tremendous train on the suspended graphene. Hence, when VOCs permeates into the polymer layer, sizable electrical resistive changes as folds and creases is induced in the graphene due to...

The physics of transport of heat-carrying atomic vibrations in amorphous and semi-crystalline solids is a topic of fundamental interest. Diverse tools have been employed to study thermal transport in these materials, including cryogenic thermal conductivity measurements and various inelastic scattering tools. However, unambiguously identifying the damping mechanisms of few THz and smaller frequency excitations remains difficult owing to the lack of the experimental probes in the frequency band. As a result, debate has remained regarding...

The holographic stereogram, a hologram synthesized from ordinary stereoscopic component photographs, is investigated as an alternative to classical holograms and to previous types of stereograms for three-dimensional perfect imagery. The process is partly holographic in nature, but it provides images of naturally illuminated objects, and its application is not limited by the technology of laser illumination. The pinhole camera stereogram and the fly's eye lens stereogram are also analyzed, since the principles of their operation...

Part I: Mitigating the Richtmyer-Meshkov instability (RMI) is critical for energy production in inertial confinement fusion. Suitable plasma models are required to study the hydrodynamic and electromagnetic interactions associated with the RMI in a conducting medium. First, a sequence of asymptotic expansions in several small parameters, as formal limits of the non-dissipative and non-resistive two-fluid plasma equations, leads to five simplified plasma/magnetohydrodynamics (MHD) systems. Each system is characterized by its own physical range of validity...

Solar fuels devices produce hydrogen fuel from water and sunlight and address a critical societal need for inexpensive, long-duration energy storage. Such devices are prepared from combinations of light-absorbing semiconductors and catalysts to sunlight to drive thermodynamically uphill reactions. This dissertation puts forth strategies for controlling the three-dimensional structure of semiconductors, electrocatalysts, and the film of gas bubbles evolved on the top and bottom of a solar fuels device. High-aspect ratio features led to unexpected...

Measurements of ¹⁸O/¹⁶O, ¹³C/¹²C and D/H ratios have been made on rocks and minerals from wells drilled in active hydrothermal systems as an aid to the understanding of various factors which govern the ongoing natural interactions between rocks and fluids, leading to a more thor­ough understanding of rock-fluid interactions that have taken place in the geologic past in such processes as diagenesis, metamorphism, and hydrothermal alteration. Samples from four active hydrothermal systems have been analyzed:...

The electronic absorption spectroscopy of ferrous iron is sensitive to the geometry of the coordination site in which it resides. This sensitivity enables ferrous iron in multiple sites in a mineral to be distinguished. The spectra of ferrous iron in the M(2) site in orthopyroxene, (Mg,Fe)SiO₃, are used as a model for the spectroscopic properties of iron in a distorted site. The splitting of the ⁵T_(2G) ground state is observed to be 2350 cm⁻¹ enabling...