VictorJuiz/thesis huggingface dataset:
RF-ultrasound relay for wireless powering and communication with retinal and brain implants

Next generation neural interfaces including retinal and brain implants have the potential to treat vision loss and neurological disorders. To do so effectively, large arrays of electrical stimulation and recording channels are needed to manipulate and capture electrical activity at cellular resolution. To wirelessly power and communicate with these devices, a couple challenges need to be overcome. First, wireless power must pass through two mediums for retinal and brain implants: air and eye tissue, or skull and brain tissue. Current single modality solutions are limited in either depth or by the interface between the two mediums. Second, recording neural activity over a large array generates a huge data volume that needs to be transmitted from the implant. In this work, we will address these two challenges using a new RF-ultrasound relay architecture. First, to overcome the challenge of transmitting across two mediums, the relay architecture uses a combination of RF and ultrasound to overcome the interface loss and to transmit at depth. New rectifier and power amplifier designs are introduced in a custom CMOS chip to increase the power conversion efficiency from RF to ultrasound, and beamforming is implemented to make it more robust to implant movement. Second, we will introduce an implant compatible high data rate uplink. A 12 Mbps uplink ultrasound MIMO system is presented to handle the data volume from the recording array. The MIMO receiver is integrated onto the CMOS chip and is robust to movement and wireless power. The custom CMOS chip integrates both wireless power and data relaying capability to enable these next generation implants.

Keywords: Engineering.
Electrical Engineering.
Advisor: Arbabian Amin
Chichilnisky E. J.
Rivas-Davila Juan
Scalable open-air processing of electron transport layers for perovskite solar cells

This dissertation explores open-air processing of perovskite solar cells, specifically on the electron transport layer deposited above the perovskite layer. An inorganic titanium dioxide electron transport layer is first explored using an open-air chemical vapor deposition process. The titanium dioxide demonstrates improved mechanical stability and barrier properties against ingress of environmental species. The development of an open-air ultrasonic spray process for the deposition of an organic electron transport bilayer on top of perovskite is presented next. The successful spray deposition and resultant film quality is highly dependent on solvent composition and the inclusion of a near-infrared heating module to accelerate film drying. In addition, the second half of the bilayer is an ultrathin (sub 10 nm) film that requires sophisticated characterization to ensure that the film is of the appropriate thickness and surface morphology. The sprayed organic electron transport bilayer is integrated into perovskite solar cell devices exhibiting high efficiencies > 20%. Finally, the spray process is included in a previously developed cost model resulting in significant manufacturing cost savings.

Keywords: Engineering.
Materials Science and Engineering.
Advisor: Dauskardt R. H. (Reinhold H.)
Salleo Alberto
Saraswat Krishna
Seismic signatures of volcanic eruptions

Increases in seismic wave radiation coincident with explosive volcanic eruptions demonstrate that eruptive processes exert forces on the surrounding earth, exciting seismic waves. Studies of seismic radiation from volcanoes have been done to gain insight into internal dynamics that cannot be directly observed. However, traditional seismogram interpretation is nonunique and often ambiguously related to eruptive processes, which limits the amount of information we can learn from the seismic signal. In this dissertation, I develop a theoretical framework to rigorously connect internal fluid dynamics to associated seismic radiation in order to calculate synthetic seismograms from simulated eruptions. Based on this theoretical work, I present the procedure to translate wall shear traction and pressure changes into force and moment histories, which are then convolved with numerical Green's functions to calculate seismograms. This is referenced as the synthetic seismogram calculation workflow. This process allows for direct connection between an eruptive process and its seismic signature. This workflow is one of the first instances of using unsteady conduit flow models to quantitatively study seismicity. I then apply this workflow in the study of potential sources of commonly observed types of seismic signals at volcanic eruptions: very-long-period (VLP) waveforms and incoherent eruptive tremor. I demonstrate that rupture of a magmatic plug and fragmentation of high viscosity magma yield distinct signatures in the VLP frequency band with coincident modulations in mass eruption rate, providing observationally testable predictions. I explore an existing model for eruptive tremor based on particle impacts and turbulence in the upper conduit using steady-state conduit flow models and more rigorous treatment of wave propagation, finding extreme parameter values are required to match observed tremor amplitudes. I present a study of a potential alternative mechanism for eruption tremor due to fluctuating fragmentation, finding that stochastic fluctuations in fragmentation arising from advection of heterogeneous magma yield stochastic seismic signals.

Keywords: Humanities and Sciences.
Physics.
Advisor: Burchat Patricia
Dunham Eric
Pamukcu Ayla Susan
Segall Paul
Sensitivity analysis in structured optimization problems methods and applications to power systems models

This work presents developments in differentiable optimization, with applications to the computation of marginal emissions in power system models. First, we discuss how recent results in differentiable optimization can be used readily to compute any emissions sensitivity metric (including marginal emissions) in optimization-based models. Second, we develop a general decentralized scheme for differentiation of graph-structured optimization problems. The methodology is efficient and can be made fully distributed, with convergence guarantees. Finally, we come full circle and illustrate the benefits of the decentralized framework in the computation of marginal emission factors. Using historical data, we demonstrate how the proposed approach allows for efficient computation of marginal emissions in large network models.

Keywords: Engineering.
Electrical Engineering.
Advisor: Pavone Marco
El Gamal Abbas
Pilanci Mert
A sensory neuron driver circuit in the colon

Within the gastrointestinal (GI) tract resides an entire nervous system devoted to coordinating its function autonomously, and which does not require any instruction from the brain. The enteric nervous system is composed of motor neurons, interneurons, and crucially its own intrinsic sensory neurons. These sensory neurons respond to local stimuli and coordinate movement of contents along the GI tract by instructing motility circuitry to relax and contract the gut. Additionally, in the colon, widespread synchro-nous oscillatory 1-2Hz activation of the ENS occurs at a set pace, every few minutes, resulting in rhythmic contractions all along its length. This motility pattern is called the colonic motor complex (CMC). Though sensory neurons were initially proposed as drivers of CMCs, that theory has long been discounted for a lack of further evidence of sensory neuron interconnectivity, synaptic input, or participation in CMCs. Here, I iden-tify cadherin-6 (Cdh6) as a novel marker of colonic sensory neurons, confirmed by im-munohistochemical, morphological, and electrophysiological methods, including the first recording of IH, a rhythmicity-associated current, in mouse colonic sensory neurons. A homophilic synaptic cell adhesion protein, Cdh6 expression only in sensory neurons suggests the presence of an interconnected sensory neuron network. I then show that optogenetic activation of Cdh6+ sensory neurons is sufficient to evoke CMCs. Finally, I demonstrate that pharmacologic blockade of IH in sensory neurons abolishes spontane-ous CMCs. These results revive a largely abandoned decades old theory of a sensory neuron driver circuit in the colon, and place sensory neurons firmly back in control of the entire ENS, not just local microcircuits.

Keywords: Engineering.
Chemical Engineering.
Advisor: Kaltschmidt Julia
Khosla Chaitan
Becker Laren
Kauer Julie
Soot mitigation potential of multiple injection strategies for fuel-rich combustion in compression-ignition engines

Conventional direct-injection, compression-ignition (DI/CI) engines operate at overall lean equivalence ratios (Phi < 0.7) to avoid excessive amounts of engine-out soot emissions. In order to overcome this equivalence ratio barrier, while keeping the soot levels low, oxygenated fuels (such as methanol and ethanol) have previously shown promising results in stoichiometric DI/CI combustion strategy. Although these fuels are difficult to autoignite, utilizing thermal barrier coatings on in-cylinder surfaces have resulted in reliable operation at stoichiometric conditions while keeping the soot emissions orders of magnitude below the soot levels for Diesel fuel. Moreover, these developments have enabled the use of DI/CI engines as work-producing, fuel-reforming devices operating at fuel-rich regimes. This work presents original data collected on single-cylinder, low-heat rejection (LHR), direct-injection, compression-ignition engine using ethanol and E85 (a mixture of 85% ethanol and 15% gasoline by volume) in stoichiometric to fuel-rich equivalence ratios. The equivalence ratio sweep data show that ethanol soot concentrations continue to increase up to an equivalence ratio of 1.4 and exhibit a plateau beyond this point. The E85 soot concentration profile shows a similar trend. However, compared to ethanol, the presence of longer chain hydrocarbon components and aromatics in the E85 increases the soot levels dramatically. The experiments in this study focus on investigating soot mitigation potential of multiple injection strategies for ethanol in fuel-rich and E85 in stoichiometric operations. Furthermore, the effects of multiple injection strategies on engine performance and other engine-out emissions in fuel-rich and stoichiometric equivalence ratios are discussed. Experimental findings show that it is possible to mitigate engine-out-soot by at least a factor of two without hindering the engine performance in both fuel-rich and stoichiometric DI/CI operation. In order to be able to interpret the experimental findings, a phenomenological model referred to as Multi-Zone NSL (MZ-NSL) model for DI/CI engines was developed to capture the in-cylinder inhomogeneity and to accommodate multiple injection operating conditions. The model was able to capture the trends of exhaust species and in-cylinder pressure of multiple injection experiments.

Keywords: Engineering.
Mechanical Engineering.
Advisor: Edwards C. F. (Christopher Francis)
Kar Kenneth C.
Wang Hai
Species-specific characteristics of biological processes in development and aging

The evolutionary process of speciation divides a population into separate groups, which with time, develop characteristics that differentiate it from each other. Despite this, they contain remnants, whether it be physical characteristics or at the molecular level, which tie them to a common ancestor. These similarities have allowed us to use model organisms to deduce biological phenomena in different species. This is an extremely valuable and important resource, especially for understanding human biology, where the study of certain biological processes, such as early development using human embryos, is ethically prohibited. However, despite the availability of these resources, many of these processes remain understudied. And while species with shorter evolutionary distance often retain more of the same physical features, this does not guarantee that all biological processes function the same. This reminds us to proceed with caution as we make cross-species interpretations. This thesis addresses these issues by interrogating the similarities and differences between species through two different angles. (1) The first is a direct comparison of the same biological process, early pregnancy, in various species. Through this work, we identify and characterize these novel species-specific features. (2) I will also hone in on the biological process of one species to identify how both conserved and species-specific characteristics can change depending on the experimental environment (in vivo and ex vivo) and with aging. To do this, I look at mouse hematopoiesis, blood cell production, identifying these changes throughout the whole organismal life span, starting from development to aging. Both approaches shed a new light on our understanding of what factors underly species specificity and conserved characteristics.

Keywords: Medicine.
Genetics.
Advisor: Baker Julie (Professor of genetics)
Nakauchi Hiromitsu
Bhatt Ami (Ami Siddharth)
Villeneuve Anne
Stabilized discretizations for fluid flows and coupled poromechanics

In this thesis we develop various stabilized spatial discretizations for fluid flow problems and coupled poromechanics. We start by considering isogeometric collocation methods, which have arisen as an efficient alternative to Galerkin discretizations for high-order simulations of mechanics. We wish to apply theses schemes to incompressible flow problems, which requires the development of appropriate stabilization strategies. The classical SUPG method is extended to a collocation setting, which stabilizes spline collocation schemes in highly advective regimes. Simultaneously, we show that PSPG stabilization allows one to collocation mixed problems with an equal-order scheme. We show that these stabilizations are effective are removing instabilities while also retaining the inherent high-order accuracy of spline collocation methods when applied to the scalar advection, incompressible Stokes, and incompressible Navier-Stokes equations. Continuing the focus on isogeometric collocation methods, we move on to consider applications in compressible flows. Stabilization strategies are again needed, in this case so that the scheme can handle shocks. We extend a residual-based, artificial viscosity method for this purpose, and we develop a projection-inspired alternative to SUPG stabilization. Results on a variety of conservation laws show the robustness of the stabilized scheme, again without sacrificing accuracy on smooth problems. We then turn away from isogeometric collocation methods and pure fluid flow problems. The latter half of the thesis considers coupled poromechanics, or the coupled problem of flow through a deformable porous media. We consider spatial discretization using a coupled finite element - finite volume approach using piecewise linear and piecewise constant representations for mechanics and flow, respectively. While commonly used in practice, this discretization choice will exhibit pressure instabilities as undrained conditions are approached due to a lack of inf-sup stability. We show that pressure jump stabilization is effective at removing spurious pressure oscillations that appear in the nearly undrained burden regions when simulating CO2 sequestration, and study numerical properties such as the proper selection of stabilization constants for different meshes. Finally, we consider the performance of iteratively, or sequentially, coupled schemes for poromechanics when undrained regions are present. We clarify the relationship between fractional step schemes and the inf-sup condition, and in particular note that the fact that sequential schemes do not form or invert the full saddle-point matrix at any point is not enough to conclude that spurious pressure oscillations will not appear. However, pressure jump stabilization can be trivially extended to the fixed-stress method considered, and this both removes spurious pressure oscillations and improves the efficiency of the scheme.

Keywords: Engineering.
Advisor: Tchelepi Hamdi
Dunham Eric
Evans John A. (Professor of computational mechanics)
Strontium clock atom interferometry for fundamental physics

Clock atom interferometers, quantum sensors based on the interference of atomic matter-waves excited by resonant pulses of light, show promise for measurements of industrial use as well as tests of fundamental physics. The fundamental advance of clock atom interferometry is the use of optical transitions with exceptional lifetime as the basis of the interferometer, giving new capabilities to what has become a standard technique. Although they are already showing performance that by some metrics surpasses the best devices using conventional matter-wave optics, more development is required for clock atom interferometers to be deployed in next-generation sensors. This thesis documents the development of two future experiments that aim to apply clock atom interferometry to questions in fundamental physics. The QMATCH experiment is designed to measure the electric charge of nominally neutral atoms beyond the limits of the best classical tests, using the scalar Aharonov-Bohm effect. MAGIS-100, currently under construction at Fermilab, is a 100 m-scale atom interferometer that aims to search for ultralight dark matter and to serve as a pathfinder for future gravitational wave observatories based on clock atom interferometry. In addition, this thesis reports a novel technique for matter-wave optics in alkaline earth atoms, exciting the 3P0 clock state of bosonic Sr-88 using a novel three-photon process in a collinear geometry.

Keywords: Humanities and Sciences.
Physics.
Advisor: Hogan Jason
Hollberg Leo (Leo William
Schleier-Smith Monika
A structural and functional investigation of inhibitory synaptic transmission

Gamma-aminobutyric acid (GABA) is the primary inhibitory neurotransmitter of the mammalian central nervous system. Neurons release GABA to shunt or prevent action potentials from propagating in target cells, and this process is critical to providing a dynamic regulation of overall neural circuitry. Chapter 1: I briefly introduce neurotransmission and focus on inhibitory neurotransmission mediated by GABA signaling. Chapter 2: I describe the development of an anti-vGAT recombinant Fab domain used to purify intact inhibitory GABA SVs from mouse brains and the subsequent structural characterization of these vesicles using electron microscopy. I also describe the use of these vesicles in a functional assay that directly probes the membrane association and membrane fusion of GABA synaptic vesicles. The results in this chapter have been published in the journal Current Research in Physiology in their special edition issue on neurotransmitter transporters. Chapter 3: Following the success of the vGAT Fab domain in purifying GABASVs, I describe the development of a molecular toolbox for the isolation and study of other types of vesicular neurotransmitter transporters and SVs using the recombinant Fab domain approach. The results shared in this chapter are preliminary, and the work is ongoing. Chapter 4: I use the recombinant anti-vGAT Fab domain to isolate detergent-solubilized vGAT from rat brains for structural characterization via CryoEM. The results shared in this chapter are preliminary, and the work is ongoing. Chapter 5: I describe an orthogonal structural characterization of purified GABA synaptic vesicles using high-resolution CryoEM. More specifically, the structure of the native vacuolar ATPase was investigated in the context of GABA SV membranes to determine its direct binding partners. The results shared in this chapter are preliminary, and the work is ongoing.

Keywords: Medicine.
Structural Biology.
Advisor: Brünger Axel T.
Feng Liang
Reimer Richard J.
SShen Kang
Systems and synthetic biology approaches enable first-principles models of transcription in human cells

The binding of multiple transcription factors (TFs) to genomic enhancers activates gene expression in mammalian cells. However, the molecular details that link enhancer sequence to TF binding, promoter state, and gene expression levels remain opaque. We applied single-molecule footprinting (SMF) to measure the simultaneous occupancy of TFs, nucleosomes, and components of the transcription machinery on engineered enhancer/promoter constructs with variable numbers of TF binding sites for both a synthetic and an endogenous TF. We find that activation domains enhance a TF's capacity to compete with nucleosomes for binding to DNA in a BAF-dependent manner, TF binding on nucleosome-free DNA is consistent with independent binding between TFs, and average TF occupancy linearly contributes to promoter activation rates. We also decompose TF strength into separable binding and activation terms, which can be tuned and perturbed independently. Finally, we develop thermodynamic and kinetic models that quantitatively predict both the binding microstates observed at the enhancer and subsequent time-dependent gene expression. Chapters 2-4 provide a template for quantitative dissection of distinct contributors to gene activation, including the activity of chromatin remodelers, TF activation domains, chromatin acetylation, TF concentration, TF binding affinity, and TF binding site configuration. Chapter 5 demonstrates how novel large serine recombinases can facilitate highly controlled and fast parallel DNA reporter assays by integrating linear DNA library members into landing pads. Chapter 6 characterizes how transcriptional run-on between two tandem genes can lead to unexpected gene expression dynamics in synthetic gene systems. Taken together, this thesis provides novel biological insights and tools to advance understanding and engineering of gene expression in human cells.

Keywords: Engineering.
Bioengineering.
Advisor: Bintu Lacramioara
Greenleaf William James
Fordyce Polly