498 Works

Covalent Functionalization of Metal-Oxide Surfaces with Non-Traditional Ligands

Carl Michael Blumenfeld
Herein detailed are the syntheses, properties, and applications of metal-oxide nanosubstrates covalently functionalized with two classes of materials, inorganic macrocycles called corroles, and genomic deoxyribonucleic acid (DNA). These products have found biomedical applications in tumor imaging and chemotherapeutic sequestration, respectively. Both classes of prepared materials are the first of their kind. Corroles are tetrapyrrolic macrocycles, which have found applications in tumor imaging and treatment, catalysis, solar fuels, and energy conversion. The direct functionalization of metal-oxides...

First-Principles-Based Simulations for G Protein-Coupled Receptor Activation and for Large-Scale Nonadiabatic Electron Dynamics

Sijia S. Dong
This thesis focuses on simulating large molecular systems within and beyond the Born-Oppenheimer framework from first principles. Two approaches have been developed for very different but important applications. The first one is a hybrid method based on classical force fields that predicts the high-energy ensemble of three-dimensional structures of a class of proteins critical in human physiology: the G protein-coupled receptors (GPCRs). GPCRs' functions rely on their activation marked by a series of conformational changes...

Fluid Dynamics with Incompressible Schrödinger Flow

Albert Ren-Haur Chern
This thesis introduces a new way of looking at incompressible fluid dynamics. Specifically, we formulate and simulate classical fluids using a Schrödinger equation subject to an incompressibility constraint. We call such a fluid flow an incompressible Schrödinger flow (ISF). The approach is motivated by Madelung's hydrodynamical form of quantum mechanics, and we show that it can simulate classical fluids with particular advantage in its simplicity and its ability of capturing thin vortex dynamics. The effective...

Forces, Stresses, and the (Thermo?) Dynamics of Active Matter: The Swim Pressure

Sho C. Takatori
A core feature of many living systems is their ability to move, self-propel, and be active. From bird flocks to bacteria swarms, to even cytoskeletal networks, active matter systems exhibit collective and emergent dynamics owing to their constituents' ability to convert chemical fuel into mechanical activity. Active matter systems generate their own internal stress, which drives them far from equilibrium and thus frees them from conventional thermodynamic constraints, and by so doing they can control...

Integrated Ultra-high-Q Nonlinear Photonic Platform for On-chip Optoelectronic Systems

Kiyoul Yang
Silicon technology provided a concrete basis of the integrated microelectronics revolution, and it might usher disruptive advances in photonics again. An integrated photonic system can potentially revolutionize instrumentation, time standards, spectroscopy, and navigation. Driven by these applications, various high-Q platforms have emerged over the last decade. However, applications require to satisfy challenging combinations of ultra-high-Q (UHQ) cavity performance, monolithic integration, and nonlinear cavity designs: the monolithic integration of UHQ devices still remains elusive. In this...

Revealing the Mechanism of Xist-mediated Silencing

Chun-Kan Chen
Xist initiates XCI by spreading across the future inactive X-chromosome, excluding RNA polymerase II, recruiting the polycomb repressive complex and its associated repressive chromatin modifications, and repositioning active genes into a transcriptionally silenced nuclear compartment. While much is known about the events that occur during XCI, the mechanism by which Xist carries out these various roles remains unclear. Here we identify ten proteins that directly associate with Xist, and we further show that three of...

Development and Characterization of Catalytic Systems for Biomass-Derived Chemical Feedstocks

Marat Orazov
Heterogeneous catalysis by Brønsted and/or Lewis acid sites isolated within microporous environments is a topic that is perpetually growing in scope and importance. While Brønsted acid sites in zeolites have been studied and applied extensively in the petrochemical industry, new opportunities for green processes based on renewable chemical feedstocks call for applications of new microporous materials that possess Lewis acid sites (e.g., zeotypes with framework Sn, Ti, Zr, or Hf). Characterization of such materials and...

Magnetic Field Effects and Biophysical Studies on DNA Charge Transport and Repair

Theodore Joseph Zwang
DNA-mediated charge transport (DNA CT) is well established in both ground and excited state systems. Although theoretical models are still being developed, it is clear that the integrity of the extended π-stack of the aromatic heterocycles, the nucleic acid bases, plays a critical role. Electron donors and acceptors must be electronically well coupled into the π-stack, typically via intercalation. Perturbations that distort the π-stack, such as single-base mismatches, abasic sites, base lesions, and protein binding...

Gas Phase Spectroscopy and Kinetics of Atmospheric Radicals

Leah G. Dodson
An important goal for atmospheric and combustion chemists is continued improvement in our understanding of the gas phase reactivity of free radical intermediates formed during hydrocarbon oxidation. The primary focus of this thesis was to measure gas phase kinetics of prototypical free radicals relevant to atmospheric and combustion chemistry, a goal that requires spectroscopy, quantitative product detection, and computational chemistry in order to address these complex chemical systems. Near-infrared cavity ringdown spectroscopy was used to...

Studies in Palladium-Catalyzed Allylic Alkylation: Enantioselective Total Syntheses of Structurally Diverse Alkaloids

Beau Patrick Pritchett
Presented herein are three projects, all unified by the use of palladium-catalyzed, enantioconvergent, decarboxylative allylic alkylations to synthesize stereochemically rich, nitrogen-containing small molecules. The ubiquity of nitrogen in biologically active natural products and pharmaceutical ingredients necessitates perpetual exploration and development of relevant small molecules. Highly robust palladium-catalyzed allylic alkylation reactions of non-stabilized enolates enable the construction of sterically encumbered all-carbon quaternary and tetrasubstituted tertiary stereocenters present within such targets. The successful development of a novel...

Bio-Inspired Homometallic and Heterometallic Clusters Relevant to the Oxygen-Evolving Complex of Photosystem II

Kurtis Mickel Carsch
The following two chapters delineate several endeavors to isolate and characterize functional models of the oxygen-evolving complex (OEC) of photosystem II. Understanding the electronic structure and the precise mechanism of the O–O bond coupling step in the Kok cycle affords insight into this fundamental process and will guide the design of new earth-abundant catalysts to perform water oxidation under environmentally benign conditions. Nature performs this transformation by a heterometallic CaMn4O5 cluster arranged a tetra-metallic cubane...

Improving the Speed and Performance of Point-of-Care Diagnostics with Microfluidics

Travis Stratton Schlappi
Microfluidic devices play an important role in improving global health because they reduce the study of biological phenomena into physiological scales and lay the foundation for point-of-care (POC) diagnostics. Health is improved and lives are saved because POC diagnostics can enable earlier diagnosis of diseases and therefore more effective treatment. Accurate and available diagnostics also prevent accelerated drug resistance that stems from overtreatment or mistreatment with antibiotics, which is projected to cause up to $100...

Photonic Crystal Waveguides for Integration into an Atomic Physics Experiment

Andrew Corby McClung
Strongly interacting systems of atoms and photons are an important resource in many active areas of research, including quantum information science, quantum simulation, and metrology. Frequently, the strength of these interactions is enhanced by using an optical resonator to confine light to a small volume. In recent years, there have been efforts to replace traditional Fabry–Pérot resonators, formed from macroscopic mirrors, with micro- and nano-fabricated systems, leveraging techniques and infrastructure from semiconductor manufacture to scalably...

Achieving Higher Fidelity Building Response through Emerging Technologies and Analytical Techniques

Anthony Thomas Massari
The integration of sensor technology into the built environment has created an opportunity for a new approach to infrastructure development and management. Using collected data and principles of general physics, we discuss means and methods of using low cost dense instrumentation to perform damage detection, structural identification, and the benefits of cyber physical systems to community resilience. A nonlinear damping strategy for braced frame structures is introduced incorporating capped levels of damping forces. The study...

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