12023 research outputs found
Sort by
Discovering Biological Roles of Glycosaminoglycans and Protein O-GlcNAcylation Using Chemical Tools
Get PDFCarbohydrates surround nearly every cell in the human body. Glycosaminoglycans like chondroitin sulfate and heparan sulfate on the cell surface regulate protein ligand engagement and receptor activation to control a variety of biological processes including development, angiogenesis, and neuronal growth. These polysaccharides exert activity through protein binding to their diverse chemical structures. Therefore, the development of methods to tailor glycosaminoglycan populations at the cell surface with defined structures could provide novel approaches to control biological activity. Herein, two new methods to engineer the cell surface glycocalyx with known glycosaminoglycans are reported. Together, these methods provide complementary short- and long-term approaches to change carbohydrate structures at the cell surface and guide neuronal growth and stem cell differentiation. It is also critical to identify unknown protein-carbohydrate interactions that underlie biological phenomena. Studies delineating novel GAG interactions with an orphan receptor and related soluble ligands are reported herein as well as work towards understanding the biological functions of these newly discovered interactions. These results showcase the utility of chemical biology and biochemical tools to discover and modulate various GAG-protein interactions in diverse biological systems.
Within the cell, thousands of proteins are modified by O-GlcNAc glycosylation, a process that is uniquely catalyzed by a single transferase and hydrolase pair unlike many other post-translational modifications. O-GlcNAcylation functions in many biological contexts including transcription, translation, proteostasis, and metabolism. Key to understanding its effects on these physiological phenomena is the discovery of O-GlcNAc modification sites. However, due to a number of technical challenges, O-GlcNAc proteomics has not progressed nearly as quickly as phosphoproteomics. Thus, developing new methods to enrich O-GlcNAcylated substrates and map modification sites is critical to unravel the myriad functions of O-GlcNAc. Herein, a labeling approach using a chemically cleavable tag is reported as an improved method to capture and release O-GlcNAcylated substrates. Unlike other methods, the cleavable Dde tag is quantitatively removed under mild, neutral conditions and leaves a minimal residual tag on the O-GlcNAcylated peptide to be analyzed. Moreover, the Dde linker outcompetes a previously used UV-cleavable tag both at the protein and peptide enrichment levels. Together, these results highlight the potential usefulness of this method to illuminate novel roles of O-GlcNAcylation in diverse systems.</p
Development of Cu- and Ni-Catalyzed C–C and C–N Bond Forming Reactions
Get PDFChapters 1 and 2 describe the development of photoinduced, Cu-catalyzed coupling reactions of unactivated secondary alkyl halides with amide and cyanide nucleophiles. These reactions may be conducted at room temperature under operationally simple conditions. Mechanistic studies are consistent with the intermediacy of alkyl radicals in these processes.
Chapter 3 describes progress toward the development of the first enantioselective Ni-catalyzed cross coupling of racemic alkyl halides and heteroatom nucleophiles. Borylation of secondary benzylic chlorides with B2(pin)2 may be achieved in good yield and promising levels of enantioselectivity.
Chapter 4 describes enantioselective Ni-catalyzed couplings of α-substituted lactam enolates with benzonitrile derivatives resulting in formal intermolecular C- acylation via in situ hydrolysis of an imine intermediate.</p
Fluid Dynamics with Incompressible Schrödinger Flow
Get PDFThis 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 dynamics under an ISF is shown to be an Euler equation modified with a Landau-Lifshitz term. We show that the modifying term not only enhances the dynamics of vortex filaments, but also regularizes the potentially singular behavior of incompressible flows.
Another contribution of this thesis is the elucidation of a general, geometric notion of Clebsch variables. A geometric Clebsch variable is useful for analyzing the dynamics of ISF, as well as representing vortical structures in a general flow field. We also develop an algorithm of approximating a "spherical" Clebsch map for an arbitrarily given flow field, which leads to a new tool for visualizing, analyzing, and processing the vortex structure in a fluid data.</p
An Investigation of Nonstoichiometric Oxides for Solar-Driven Thermochemical Fuel Production
Get PDFIn order to realize energy independence and substantially combat global climate change, renewable and sustainable energy technologies must be developed. Solar energy is the most readily abundant, and if converted into a chemical fuel, could be stored and transported easily. Solar-driven thermochemical cycling is a method of chemical fuel production that shows great promise, but current state-of-the-art systems have very low efficiencies. This work discusses new reactor designs and cycling techniques using nonstoichiometric oxides that will enable more efficient solar to fuel energy conversion. Practical aspects of the reactor design are explored – specifically, thermochemical expansion of the reactive oxide, and morphologies aimed at enhancing the reaction kinetics. Additionally, doped fluorite- and perovskite-structured materials are evaluated for thermodynamic behavior and in-situ thermochemical cycling performance. Oxide morphology and new doped compounds show little improvement over previously established neat ceria due to thermodynamic limitations. The thermodynamic limit is explored in new reactor geometries and is shown to demonstrate significantly more efficient fuel production. Finally, different nonstoichiometry thermodynamics are explored to provide guidance for further material exploration, as well as applicable methodologies.</p
The Bag6 Complex: Biological Complexity through Modularity
Get PDFProper synthesis and targeting of membrane proteins that contain hydrophobic transmembrane domains are mediated by chaperones and targeting factors. Tail-anchored (TA) proteins are a special class of membrane proteins that are characterized by a single carboxy (C) terminal helix that anchors them to biological membranes. Fungal Guided Entry of Tail-anchored protein (GET) pathway components, which include four soluble proteins—Sgt2, Get3, Get4, Get5—and two membrane bound receptors—Get1 and Get2—mediate TA biogenesis. These proteins maintain TA protein solubility in the aqueous cytosol and target TA to the endoplasmic reticulum. While most of the components are conserved in metazoans, one additional protein, Bag6, reorganizes the sorting complex from the heterotetrameric Get4-5 to the heterotrimeric Bag6-TRC35-Ubl4A. To understand the molecular architecture and mechanism of the Bag6 complex, we took a multidisciplinary approach that combines x-ray crystallography, biochemical reconstitution, and cell biology. Our studies demonstrate that the BAG domain of Bag6 is not a canonical BAG domain. Instead, main role of the Bag6 'mock' BAG domain is to dimerize with Ubl4A. Furthermore, the truncated Bag6 complex defined in this study is sufficient to facilitate substrate transfer from SGTA to TRC40. Lastly, our results unequivocally establish TRC35 as a cytoplasmic retention factor for Bag6. These results provide structural, biochemical and cell biological bases for modular Bag6 function and regulation of nucleocytoplasmic distribution of Bag6 by TRC35
Network Effects in Small Networks: A Study of Cooperation
Get PDFCommunication over a point-to-point link is relatively well understood. However, when such a link is part of a larger network, our understanding is far from complete. Nonetheless, progress in this area has important consequences in both the theoretical and practical aspects of communication networks.
In this work, we focus on the role of a single link in networks that in addition to point-to-point links, contain "multi-terminal components." An example of a network consisting of a single multi-terminal component is the uplink in a wireless communication network where multiple transmitters communicate with a single receiver over a shared medium. We demonstrate the existence of a class of such networks where a finite capacity link results in a rate gain for each source that far exceeds the capacity of that link. This is an example of a "network effect": the phenomenon where a resource, here link capacity, is significantly more valuable in a network than in isolation. Here we measure the "value" of the finite capacity link by the sum-capacity gain per source that it enables.
The central idea behind the construction of networks that exhibit such effects is the introduction of a node, referred to as the "cooperation facilitator" (CF), that allows other network nodes to work together to reduce interference. In the setting of the classical multiple access channel (MAC), an example of a CF is a node that receives rate-limited information from each transmitter and broadcasts rate-limited information back to the transmitters through a common bottleneck link. Let the "cooperation rate" be the capacity of the CF bottleneck link. We show that for a class of MACs, the presence of a CF
leads to a sum-capacity gain that, as a function of the cooperation rate, has an infinite slope at cooperation rate zero. This means that the bottleneck link of the CF is significantly more valuable in some networks than in isolation. This class of MACs includes well-known examples such as the Gaussian MAC and the binary adder MAC.
In addition to sum-capacity gain, cooperation under the CF model also improves reliability. Specifically, in the case of the MAC with two transmitters, whenever the CF has full access to both messages, the maximal- and average error capacity regions coincide. This effect is observed even when the cooperation rate is "negligible"; that is, the cooperation rate grows sublinearly in the number of channel uses. An implication of this result is the existence of a network whose maximal-error sum-capacity is not continuous with respect to the capacities of its edges; this means that in some networks, even a negligible cooperation rate leads to a positive sum-capacity gain.</p
Full Spectrum Ultrahigh Efficiency Photovoltaics: System Design, Integration, and Characterization
Get PDFThe sun is an immense source of power, radiating more energy than all known non-renewable reserves onto the Earth every year in the form of sunlight. In spite of this abundant availability, photovoltaic electricity conversion provides less than 1% of the of the global energy consumption. This lack of deployment is largely a consequence of the cost of photovoltaics relative to other technologies, but increased efficiency is a strong driver for cost reduction due to its ability to impact both photovoltaic module and balance of systems costs. In this thesis, we present enabling technologies for achieving increased efficiency and energy yield for photovoltaic conversion of sunlight. First, we develop finite element cell modeling and electrical contact optimization tools. These models are used to deploy unconstrained optimization techniques that expand the design space of solar cell contacts. Additionally, constrained optimization techniques are used to design solar cell electrical contacts for lateral spectrum-splitting photovoltaic submodules. The lateral spectrum-splitting submodule uses a series of filters to divide broadband sunlight into seven wavelength bands, sending each onto a solar cell with bandgap chosen to minimize thermalization and sub-bandgap transmission losses. By employing a wholistic design model covering limiting efficiency, material constraints, optical ray tracing, and electrical modeling, we generate designs capable of ultrahigh (>50%) efficiency. We then design, integrate, and prototype the first photovoltaic converter with seven unique bandgaps. Characterization of this prototype and its constituent components shows an integrated 84.5% optical efficiency and 30.2% submodule efficiency. The exemplary optical performance highlights the promise of the design with further development of the cells. Finally, we develop module circuit and power combination topologies that enable independent electrical connection to two or more subcells in a multijunction photovoltaic converter. This circuit architecture enables independent power production from each device, which reduces the module sensitivity to diurnal and seasonal spectral changes and increases panel annual energy yield. The photovoltaic technologies developed herein often break with convention and demonstrate a feasible pathway to very high (>40%) and ultrahigh (>50%) efficiency modules
Programming Complex Behavior in DNA-based Molecular Circuits and Robots
Get PDFIntegrated electronic circuits, like those found in cellphones and computers, are ubiquitous in our information-driven society. The success of electronics has, in part, been due its modular architecture that enables individual components to be independently improved while the overall device functionality remains unchanged. Over the last two decades the emerging field of dynamic DNA nanotechnology has been trying to apply the underlying philosophy of electronics to biochemical circuits. DNA nanotechnology employs rationally designed DNA molecules as building blocks of biochemical circuits that can, in principle, enable powerful applications like diagnostics and therapeutics.
Researchers in the field of DNA nanotechnology have developed simple elements to construct biomolecular systems with desired functions. They have also developed molecular compilers for defining design principles. The cost of DNA synthesis has decreased by over three orders of magnitude in the past decade. This has lead to a non-trivial number of small scale circuits, like DNA-based logic gates and chemical oscillators, being implemented. However, the scalability of this approach has yet to be clearly demonstrated. n this thesis, we will discuss our main contributions to facilitating the advancement of DNA nanotechnology by developing systematic approaches for constructing modular DNA building blocks. These modules can be used to construct biochemical circuits and molecular robotic systems. The performance of the modules can be individually tuned and integrated into large-scale systems.
Using automated circuit-design software and cheap unpurified DNA, we demonstrated the design and construction of a complex synthetic biochemical circuit consisting of 78 distinct DNA species. The circuit is capable of computing the transition rules of a cell updating its state based on its neighboring cells, defined in a classic computational model called cellular automata. Using a bottom-up approach, we first characterized the component necessary for basic Boolean logic computation. We then systematically integrated more circuit elements and eventually constructed the full circuit. By developing a systematic procedure for building DNA-based circuits using unpurified components, we significantly simplified the experimental procedure. By using unpurified DNA components, we reduced the cost and technical barrier for circuit construction, thus making the design and synthesis of complex DNA circuits accessible to even novice researchers.
Next we demonstrated a cargo sorting DNA nano-robot, using a simple algorithm and modular building blocks. The DNA robot has a leg and two foot domains for exploring a two-dimensional DNA origami surface, and an arm and hand domain for picking up randomly located cargos and dropping them off at their designated locations. It is completely autonomous and is programmed to perform a random walk without requiring an external energy source. Further, we demonstrated sorting multiple copies of two distinct cargo species on the same origami. Additionally, by compartmentalizing each sorting task on a single origami, we showed that two distinct sorting tasks can be implemented on different origami simultaneously in the same test tube. The recognition of a cargo is embedded in its destination, therefore it is possible to scale up the system simply by having multiple types of cargos. The same robot design can be used for performing multiple instances of distinct tasks in parallel. The different modules can be integrated to perform diverse functions, including applications in time-release targeted therapeutics.</p
Structures and Reactions of Diplatinum Complexes
Get PDFA d8−d8 complex [Pt2(μ-P2O5(BF2)4]4− (abbreviated Pt(pop-BF2)4−) undergoes two 1e− reductions at E1/2 = −1.68 and Ep = −2.46 V (vs Fc+/Fc) producing reduced Pt(pop-B2)5− and superreduced Pt(pop-BF2)6− species, respectively. The EPR spectrum of Pt(pop-BF2)5− and UV−vis spectra of both the reduced and the superreduced complexes, together with TD-DFT calculations, reveal successive filling of the 6pσ orbital accompanied by gradual strengthening of Pt−Pt bonding interactions and, because of 6pσ delocalization, of Pt−P bonds in the course of the two reductions. Both reduction steps proceed without changing either d8 Pt electronic configuration, making the superreduced Pt(pop-BF2)6− a very rare 6p2 σ-bonded binuclear complex. However, the Pt−Pt σ bonding interaction is limited by the relatively long bridging-ligand-imposed Pt−Pt distance accompanied by repulsive electronic congestion. Pt(pop-BF2)4− is predicted to be a very strong photooxidant (potentials of +1.57 and +0.86 V are estimated for the singlet and triplet dσ*pσ excited states, respectively).
Further study of the electronic excited states of Pt(pop-BF2)4- in the presence of luminescence quenchers revealed Stern-Volmer type dynamic quenching of the triplet state by trialkyl and triaryl amines. Quenching of the singlet as well as the triplet was observed in the presence of CoII trisbipyridine complexes, but sample decomposition and the observed presence of simultaneous static and dynamic quenching behaviors hampered quantitative analysis.</p
Highly Enantioselective Palladium-Catalyzed Allylic Alkylation Reactions of Carbocyclic Enaminones and Acyclic Substrates
Get PDFThis report details the studies of the palladium-catalyzed asymmetric allylic alkylation reactions of carbocyclic substrates, specifically of vinylogous amides and enaminones, resulting in the discovery of a new substrate class (enaminones) with the highest enantioselectivies observed for this catalytic system to date. Moreover, conditions were discovered and developed for the asymmetric allylic alkylation of acyclic substrates by the selective formation of fully substituted enolates and application of a novel C2-symmetric Pd ligand.</p