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Engineering Multi Step Electron Tunneling Systems in Proteins
Get PDFMulti-step electron tunneling, or “hopping,” has become a fast-developing research field with studies ranging from theoretical modeling systems, inorganic complexes, to biological systems. In particular, the field is exploring hopping mechanisms in new proteins and protein complexes, as well as further understanding the classical biological hopping systems such as ribonuclease reductase, DNA photolyases, and photosystem II. Despite the plethora of natural systems, only a few biologically engineered systems exist. Engineered hopping systems can provide valuable information on key structural and electronic features, just like other kinds of biological model systems. Also, engineered systems can harness common biologic processes and utilize them for alternative reactions. In this thesis, two new hopping systems are engineered and characterized.
The protein Pseudomonas aeruginosa azurin is used as a building block to create the two new hopping systems. Besides being well studied and amenable to mutation, azurin already has been used to successfully engineer a hopping system. The two hopping systems presented in this thesis have a histidine-attached high potential rhenium 4,7-dimethyl-1,10-phenanthroline tricarbonyl [Re(dmp)(CO)3] + label which, when excited, acts as the initial electron acceptor. The metal donor is the type I copper of the azurin protein. The hopping intermediates are all tryptophan, an amino acid mutated into the azurin at select sites between the photoactive metal label and the protein metal site. One system exhibits an inter-molecular hopping through a protein dimer interface; the other system undergoes intra-molecular multi-hopping utilizing a tryptophan “wire.” The electron transfer reactions are triggered by excitation of the rhenium label and monitored by UV-Visible transient absorption, luminescence decays measurements, and time-resolved Infrared spectroscopy (TRIR). Both systems were structurally characterized by protein X-ray crystallography.</p
Olefin Cyclopropanation and Carbon-Hydrogen Amination via Carbene and Nitrene Transfers Catalyzed by Engineered Cytochrome P450 Enzymes
Get PDFSynthetic biology promises to transform organic synthesis by enabling artificial catalysis in living cells. I start by reviewing the state of the art in this young field and recognizing that new approaches are required for designing enzymes that catalyze nonnatural reactions, in order to expand the scope of biocatalytic transformations. Carbene and nitrene transfers to C=C and C-H bonds are reactions of tremendous synthetic utility that lack biological counterparts. I show that various heme proteins, including cytochrome P450BM3, will catalyze promiscuous levels of olefin cyclopropanation when provided with the appropriate synthetic reagents (e.g., diazoesters and styrene). Only a few amino acid substitutions are required to install synthetically useful levels of stereoselective cyclopropanation activity in P450BM3. Understanding that the ferrous-heme is the active species for catalysis and that the artificial reagents are unable to induce a spin-shift-dependent increase in the redox potential of the ferric P450, I design a high-potential serine-heme ligated P450 (P411) that can efficiently catalyze cyclopropanation using NAD(P)H. Intact E. coli whole-cells expressing P411 are highly efficient asymmetric catalysts for olefin cyclopropanation. I also show that engineered P450s can catalyze intramolecular amination of benzylic C-H bonds from arylsulfonyl azides. Finally, I review other examples of where synthetic reagents have been used to drive the evolution of novel enzymatic activity in the environment and in the laboratory. I invoke preadaptation to explain these observations and propose that other man-invented reactions may also be transferrable to natural enzymes by using a mechanism-based approach for choosing the enzymes and the reagents. Overall, this work shows that existing enzymes can be readily adapted for catalysis of synthetically important reactions not previously observed in nature
Dynamics and Scaling of Self-Excited Passive Vortex Generators for Underwater Propulsion
Get PDFA series of experiments was conducted on the use of a device to passively generate vortex rings, henceforth a passive vortex generator (PVG). The device is intended as a means of propulsion for underwater vehicles, as the use of vortex rings has been shown to decrease the fuel consumption of a vehicle by up to 40% Ruiz (2010).
The PVG was constructed out of a collapsible tube encased in a rigid, airtight box. By adjusting the pressure within the airtight box while fluid was flowing through the tube, it was possible to create a pulsed jet with vortex rings via self-excited oscillations of the collapsible tube.
A study of PVG integration into an existing autonomous underwater vehicle (AUV) system was conducted. A small AUV was used to retrofit a PVG with limited alterations to the original vehicle. The PVG-integrated AUV was used for self-propelled testing to measure the hydrodynamic (Froude) efficiency of the system. The results show that the PVG-integrated AUV had a 22% increase in the Froude efficiency using a pulsed jet over a steady jet. The maximum increase in the Froude efficiency was realized when the formation time of the pulsed jet, a nondimensional time to characterize vortex ring formation, was coincident with vortex ring pinch-off. This is consistent with previous studies that indicate that the maximization of efficiency for a pulsed jet vehicle is realized when the formation of vortex rings maximizes the vortex ring energy and size.
The other study was a parameter study of the physical dimensions of a PVG. This study was conducted to determine the effect of the tube diameter and length on the oscillation characteristics such as the frequency. By changing the tube diameter and length by factors of 3, the frequency of self-excited oscillations was found to scale as f~D_0^{-1/2} L_0^0, where D_0 is the tube diameter and L_0 the tube length. The mechanism of operation is suggested to rely on traveling waves between the tube throat and the end of the tube. A model based on this mechanism yields oscillation frequencies that are within the range observed by the experiment.</p
Investigations of Secondary Organic Aerosol Formation in Laboratory Chambers
Get PDFSecondary organic aerosol (SOA) is produced in the atmosphere by oxidation of volatile organic compounds. Laboratory chambers are used understand the formation mechanisms and evolution of SOA formed under controlled conditions. This thesis presents studies of SOA formed from anthropogenic and biogenic precursors and discusses the effects of chamber walls on suspended vapors and particles.
During a chamber experiment, suspended vapors and particles can interact with the chamber walls. Particle wall loss is relatively well-understood, but vapor wall losses have received little study. Vapor wall loss of 2,3-epoxy-1,4-butanediol (BEPOX) and glyoxal was identified, quantified, and found to depend on chamber age and relative humidity.
Particles reside in the atmosphere for a week or more and can evolve chemically during that time period, a process termed aging. Simulating aging in laboratory chambers has proven to be challenging. A protocol was developed to extend the duration of a chamber experiment to 36 h of oxidation and was used to evaluate aging of SOA produced from m-xylene. Total SOA mass concentration increased and then decreased with increasing photooxidation suggesting a transition from functionalization to fragmentation chemistry driven by photochemical processes. SOA oxidation, measured as the bulk particle elemental oxygen-to-carbon ratio and fraction of organic mass at m/z 44, increased continuously starting after 5 h of photooxidation.
The physical state and chemical composition of an organic aerosol affect the mixing of aerosol components and its interactions with condensing species. A laboratory chamber protocol was developed to evaluate the mixing of SOA produced sequentially from two different sources by heating the chamber to induce particle evaporation. Using this protocol, SOA produced from toluene was found to be less volatile than that produced from a-pinene. When the two types of SOA were formed sequentially, the evaporation behavior most closely represented that of SOA from the second parent hydrocarbon, suggesting that the structure of the mixed SOA particles resembles a core of SOA from the first precursor coated by a layer of SOA from the second precursor, indicative of limiting mixing.</p
GRAph Parallel Actor Language: A Programming Language for Parallel Graph Algorithms
Get PDFWe introduce a domain-specific language, GRAph Parallel Actor Language, that enables parallel graph algorithms to be written in a natural, high-level form. GRAPAL is based on our GraphStep compute model, which enables a wide range of parallel graph algorithms that are high-level, deterministic, free from race conditions, and free from deadlock. Programs written in GRAPAL are easy for a compiler and runtime to map to efficient parallel field programmable gate array (FPGA) implementations. We show that the GRAPAL compiler can verify that the structure of operations conforms to the GraphStep model. We allocate many small processing elements in each FPGA that take advantage of the high on-chip memory bandwidth (5x the sequential processor) and process one graph edge per clock cycle per processing element. We show how to automatically choose parameters for the logic architecture so the high-level GRAPAL programming model is independent of the target FPGA architecture. We compare our GRAPAL applications mapped to a platform with four 65 nm Virtex-5 SX95T FPGAs to sequential programs run on a single 65 nm Xeon 5160. Our implementation achieves a total mean speedup of 8x with a maximum speedup of 28x. The speedup per chip is 2x with a maximum of 7x. The ratio of energy used by our GRAPAL implementation over the sequential implementation has a mean of 1/10 with a minimum of 1/80
Navigating Earthquake Physics with High-Resolution Array Back-Projection
Get PDFUnderstanding earthquake source dynamics is a fundamental goal of geophysics. Progress toward this goal has been slow due to the gap between state-of-art earthquake simulations and the limited source imaging techniques based on conventional low-frequency finite fault inversions. Seismic array processing is an alternative source imaging technique that employs the higher frequency content of the earthquakes and provides finer detail of the source process with few prior assumptions. While the back-projection provides key observations of previous large earthquakes, the standard beamforming back-projection suffers from low resolution and severe artifacts. This thesis introduces the MUSIC technique, a high-resolution array processing method that aims to narrow the gap between the seismic observations and earthquake simulations.
The MUSIC is a high-resolution method taking advantage of the higher order signal statistics. The method has not been widely used in seismology yet because of the nonstationary and incoherent nature of the seismic signal. We adapt MUSIC to transient seismic signal by incorporating the Multitaper cross-spectrum estimates. We also adopt a “reference window” strategy that mitigates the “swimming artifact,” a systematic drift effect in back projection. The improved MUSIC back projections allow the imaging of recent large earthquakes in finer details which give rise to new perspectives on dynamic simulations. In the 2011 Tohoku-Oki earthquake, we observe frequency-dependent rupture behaviors which relate to the material variation along the dip of the subduction interface. In the 2012 off-Sumatra earthquake, we image the complicated ruptures involving orthogonal fault system and an usual branching direction. This result along with our complementary dynamic simulations probes the pressure-insensitive strength of the deep oceanic lithosphere. In another example, back projection is applied to the 2010 M7 Haiti earthquake recorded at regional distance. The high-frequency subevents are located at the edges of geodetic slip regions, which are correlated to the stopping phases associated with rupture speed reduction when the earthquake arrests.</p
Synthesis and Thermodynamic Studies of Physisorptive Energy Storage Materials
Get PDFPhysical adsorption of hydrogen or other chemical fuels on the surface of carbonaceous materials offers a promising avenue for energy storage applications. The addition of a well-chosen sorbent material to a compressed gas tank increases the volumetric energy density of the system while still permitting fast refueling, simplicity of design, complete reversibility, high cyclability, and low overall cost of materials. While physical adsorption is most effective at temperatures below ambient, effective storage technologies are possible at room temperature and modestly high pressure. A volumetric Sieverts apparatus was designed, constructed, and commissioned to accurately measure adsorption uptake at high pressures and an appropriate thermodynamic treatment of the experimental data is presented.
In Chapter 1, the problem of energy storage is introduced in the context of hydrogen as an ideal alternative fuel for future mobile vehicle applications, and with methane in mind as a near-term solution. The theory of physical adsorption that is relevant to this work is covered in Chapter 2. In-depth studies of two classes of materials are presented in the final chapters. Chapter 3 presents a study of the dissociative “hydrogen spillover” effect in the context of its viability as a practical hydrogen storage solution at room temperature. Chapters 4-5 deal with zeolite-templated carbon, an extremely high surface-area material which shows promise for hydrogen and methane storage applications. Studies of hydrogen adsorption at high pressure (Chapter 4) and anomalous thermodynamic properties of methane adsorption (Chapter 5) on ZTCs are presented. The concluding chapter discusses the impact of and possible future directions for this work.</p
Modeling, Simulation, and Design of Self-Assembling Space Systems: Accurate Collision Detection, Robust Time Integration, and Optimal Control
Get PDFMotivated by issues inherent in modeling and designing self-assembling systems (e.g. multiple collisions, collisions between non-smooth bodies, clumping and jamming behaviors, etc.), the goal of this thesis is to develop robust numerical tools that enable ecient and accurate direct simulation of self assembling systems and the application of optimal control methods to this type of system. The systems will be alternately modeled using linear nite elements, rigid bodies, or chains of rigid bodies. To this end, this work begins with development of a linear programming based collision detection algorithm for general convex polyhedral bodies. The resulting linear program has several features which render it extremely useful in determining the force system at the time of contact in numerical collision integrators. With robust collision detection in hand, three related numerical integration methods for dynamics with collisions are treated; a direct potential-based approach, and exact collision integrator in a discrete variational setting, and a decomposition-based algorithm, again in the discrete variational setting. Finally, several control problems are treated in the Discrete Mechanics and Optimal Control{Constrained (DMOCC) framework in which collisions between non-smooth bodies either need to be avoided or explicitly included in the optimal control problem. A globally stable feedback controller and a family of trajectories for spacecraft docking are also developed and tested with an accurate representation of an optimized CubeSat docking system
Topological Quantum Field Theory and the Geometric Langlands Correspondence
Get PDFIn the pioneering work of A. Kapustin and E. Witten, the geometric Langlands program of number theory was shown to be intimately related to duality of GL-twisted N=4 super Yang-Mills theory compactified on a Riemann surface. In this thesis, we generalize Kapustin-Witten by investigating compactification of the GL-twisted theory to three dimensions on a circle (for various values of the twisting parameter t). By considering boundary conditions in the three-dimensional description, we classify codimension-two surface operators of the GL-twisted theory, generalizing those surface operators studied by S. Gukov and E. Witten. For t=i, we propose a complete description of the 2-category of surface operators in terms of module categories, and, in addition, we determine the monoidal category of line operators which includes Wilson lines as special objects. For t=1 and t=0, we discuss surface and line operators in the abelian case.
We generalize Kapustin-Witten also by analyzing a separate twisted version of N=4, the Vafa-Witten theory. After introducing a new four-dimensional topological gauge theory, the gauged 4d A-model, we locate the Vafa-Witten theory as a special case. Compactification of the Vafa-Witten theory on a circle and on a Riemann surface is discussed. Several novel two- and three-dimensional topological gauge theories are studied throughout the thesis and in the appendices.
In work unrelated to the main thread of the thesis, we conclude by classifying codimension-one topological defects in two-dimensional sigma models with various amounts of supersymmetry.</p
An Ultra-Low-Energy, Variation-Tolerant FPGA Architecture Using Component-Specific Mapping
Get PDFAs feature sizes scale toward atomic limits, parameter variation continues to increase, leading to increased margins in both delay and energy. Parameter variation both slows down devices and causes devices to fail. For applications that require high performance, the possibility of very slow devices on critical paths forces designers to reduce clock speed in order to meet timing. For an important and emerging class of applications that target energy-minimal operation at the cost of delay, the impact of variation-induced defects at very low voltages mandates the sizing up of transistors and operation at higher voltages to maintain functionality.
With post-fabrication configurability, FPGAs have the opportunity to self-measure the impact of variation, determining the speed and functionality of each individual resource. Given that information, a delay-aware router can use slow devices on non-critical paths, fast devices on critical paths, and avoid known defects. By mapping each component individually and customizing designs to a component's unique physical characteristics, we demonstrate that we can eliminate delay margins and reduce energy margins caused by variation.
To quantify the potential benefit we might gain from component-specific mapping, we first measure the margins associated with parameter variation, and then focus primarily on the energy benefits of FPGA delay-aware routing over a wide range of predictive technologies (45 nm--12 nm) for the Toronto20 benchmark set. We show that relative to delay-oblivious routing, delay-aware routing without any significant optimizations can reduce minimum energy/operation by 1.72x at 22 nm. We demonstrate how to construct an FPGA architecture specifically tailored to further increase the minimum energy savings of component-specific mapping by using the following techniques: power gating, gate sizing, interconnect sparing, and LUT remapping. With all optimizations considered we show a minimum energy/operation savings of 2.66x at 22 nm, or 1.68--2.95x when considered across 45--12 nm. As there are many challenges to measuring resource delays and mapping per chip, we discuss methods that may make component-specific mapping more practical. We demonstrate that a simpler, defect-aware routing achieves 70% of the energy savings of delay-aware routing. Finally, we show that without variation tolerance, scaling from 16 nm to 12 nm results in a net increase in minimum energy/operation; component-specific mapping, however, can extend minimum energy/operation scaling to 12 nm and possibly beyond.</p