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Harnessing Locality for Scalable Strongly Correlated Electron Simulations
No full textMaterials-specific predictions of large, realistic molecules and materials with strong electron correlations have been a long-standing challenge in quantum chemistry. This dissertation addresses this challenge by leveraging three forms of physical and mathematical locality—in space, energy, and rank—to develop scalable, efficient, and accurate electronic structure methods.
In Chapter 2, we use quantum embedding theory that exploits the spatial locality of electron correlations and reduces the computational cost of accurate correlated electronic structure methods, enabling accurate ab initio simulation of complicated correlated materials. In this work, we study Kondo physics, a prototypical many-body quantum phenomenon, with a full-cell extension of dynamical mean-field theory (DMFT). Our \textit{ab initio} simulation of the Kondo correlations systematically converges towards the exact zero-temperature limit, yielding material-specific Kondo temperatures that reproduce the subtle exponential trends observed experimentally and offer new insight into the underlying physics.
Chapter 3 explores the locality in energy in lanthanide single-ion magnets. Their multi-reference ground and excited states are generally challenging to compute, but fortunately, the states that govern the spin dynamics are local in the energy spectrum. We develop a theoretical protocol to compute their spin Hamiltonian by sampling only relevant states in this reduced Hilbert space, and particularly, the single-reference states accessible by the efficient density functional theory. This method surpasses the prohibitive cost of calculating multi-reference eigenstates, and with its mean-field scaling, enables studying realistic magnets of unprecedentedly large size at an accuracy comparable to the previous state-of-the-art method.
Chapter 4 focuses on the locality in the rank structure of reduced density matrices (RDMs). The 1- and 2-RDMs are the crucial ingredients in estimating energies and observables in many classical and quantum simulation methods. Their intrinsic low-rank structure makes them compressible and can be exploited to significantly reduce the measurement cost. We analyze both noiseless and noisy measurement scenarios, including shot-noise-limited quantum algorithms, and show that in the context of Gaussian (shot) noise, a low-rank approximate reconstruction of RDMs effectively removes the high-rank noises and reduces the measurement cost by orders of magnitude, therefore enabling larger-scale simulations.</p
Carbon in Flux: Measuring the Climate Sensitivity of Terrestrial Greenhouse Gas Uptake
No full textThe greenhouse gases carbon dioxide and methane exert a major control on Earth’s climate, and their accumulation in the atmosphere is tempered by biological uptake. These biological uptake processes—photosynthesis and methanotrophy—are key contributors to the carbon-climate system, but their sensitivity to ongoing environmental change remains uncertain. In this thesis, I investigate how the ecophysiology of methanotrophy and photosynthesis dictate their response to perturbations in atmospheric composition, temperature, and other environmental variables. In Chapter 1, I present the first comprehensive compilation of kinetic measurements of methanotrophy in soils, and use this dataset to explore how kinetic properties may provide additional constraints to improve global models of the soil methane sink. Chapter 2 is a study of soil methane uptake rates in California dryland ecosystems and their relationship to local climate, ecology, and edaphic properties. This study reveals unique characteristics of dry climate regions that contradict typical assumptions about soil methane cycling. In Chapter 3, I present a novel method for position-specific carbon isotope analysis of submilligram glucose samples by Orbitrap mass spectrometry, and an application of this method to glucose standards isolated from C3 and C4 plants. In Chapter 4, I apply this new method to cellulose-derived glucose from tree-ring samples. Measurements of trees grown in climate chambers show how 13C-PSIA can disentangle changes in temperature, soil moisture, and tree carbon allocation. Finally, in two appendices, I describe methodological progress toward field-portable measurements of sedimentary porewater methane and the kinetics of soil methane uptake. Taken together, this work makes progress toward a more nuanced understanding of biological greenhouse gas uptake processes and their sensitivity to climate change
The Biochemical and Structural Basis of Get3d’s Role in Photosynthesis
No full textTail-anchored (TA) membrane proteins, defined by a single C-terminal transmembrane domain, are inserted into the endoplasmic reticulum (ER) membrane via the guided entry of tail-anchored proteins pathway. The central targeting factor of this pathway is Get3, an ATPase that receives TA clients from upstream chaperones and mediates their delivery to the ER. Here, we identify and characterize a unique Get3 homolog, termed Get3d, distinguished by a C-terminal α-crystallin domain (αCD). We show that Get3d is conserved across plants and photosynthetic bacteria and demonstrate that it localizes to the chloroplast in plants. We present the X-ray crystal structure of Get3d, revealing unique features including the αCD and a client-binding chamber in the closed state. Biochemical analyses confirm that Get3d is an active ATPase capable of binding TA proteins in vitro. To investigate its physiological role, we identified the plant-like Get3d homolog in Synechocystis sp. PCC 6803 and generated deletion and complementation strains. Loss of Get3d impairs cell growth and pigment production, and proteomic analyses reveal widespread dysregulation, including up-regulation of transcriptional regulators and down-regulation of redox-associated proteins—suggesting a role in redox homeostasis. Complementation studies show that ATPase activity is necessary for restoring the expression of key photosynthesis-related proteins, while the αCD is critical for maintaining Get3d protein stability in vivo. Finally, co-immunoprecipitation coupled to mass spectrometry identifies putative Get3d interaction partners enriched in membrane-associated and photosynthetic proteins. Together, these findings establish Get3d as a biochemically distinct and functionally essential member of the Get3 family, with a potential role in redox regulation and photosynthetic homeostasis in diverse photosynthetic organisms
Simulation of Electrohydrodynamic Distortion Relevant to Liquid Metal Ion Sources
No full textThe free surface of a liquid metal film in vacuum subject to an imbalance of destabilizing Maxwell (electric) and stabilizing capillary forces can undergo rapidly accelerating electrohydrodynamic (EHD) distortion which culminates in formation of protrusions from whose tips highly energetic ion beams are emitted. Such a phenomenon has been successfully leveraged into liquid metal ion sources (LMIS) which are fundamental to the operation of focused ion beam systems used for micro- and nanofabrication and even microarray devices actuating space micropropulsion. In this thesis, we have conducted a series of computational simulations using the arbitrary Lagrangian Eulerian finite element method designed to track the pre-emission EHD liquid distortion for realistic LMIS geometries characterizing a slender microemitter with a sharp (highly curved) tip positioned beneath an apertured extractor in vacuum.
The simulations unveil various stable and unstable configurations whose protrusions can occur along the liquid surface. The particular configurations are found to correlate with the Reynolds number and electric Weber number based on a handful of initial values, namely the applied electric potential, emitter apex curvature radius and initial liquid thickness. For the parameter space explored, spectral analysis of the unstable configuration yields a dominant wavenumber in close agreement to that predicted from linear stability analysis of the flat liquid layer. This can be traced to the fact that a key aspect ratio indicates that the dynamics are in the flat liquid limit. Examination of the late stage dynamical behavior of the evolving protrusions reveals self-similar growth for all configurations examined. Values of the exponents extracted from the simulations are found to cluster neatly when plotted against Reynolds number and Weber number.</p
Crystalline Records of Mafic Arc Magmas Across the Sierra Nevada Batholith, California
No full textOur planet Earth is unique among the rocky planets of the solar system in having compositionally evolved continental crust—the reason for life as we know it. Processes that create continental crust occur at subduction zones where magmas differentiate, evolving from primary mantle-derived basalt to produce a diverse range of compositions that erupt at arc volcanoes and comprise the bulk of the continental crust. Many processes for differentiation have been proposed, yet, recognizing and evaluating the role of pre-existing crust in these processes remains challenging.
This thesis includes two studies of mafic intrusions in the Sierra Nevada batholith—the well-studied Mesozoic continental arc of the western North American Cordillera. The studies are grounded in field and petrographic observations. By targeting the intrusive record, they document the time-integrated effects of mafic magmatism over tens of millions of years within a volcanic arc.
Chapter 2 is a petrologic study of the most primitive intrusive rocks of the batholith, exposed in the Emigrant Gap complex. The complex ranges compositionally from ultramafic cumulates to intermediate granodiorite. The petrology, geochemistry and field relationships of these plutonic rocks reveal that—in addition to crystallization—open-system processes (melt-mush reactions and hybridization between the mafic products and a crustally contaminated felsic magma) produced the distinctive geochemical and petrologic trends of the complex.
Chapters 3 and 4 represent a broad study of mafic intrusions within a 250 km by 100 km swath of the central Sierra Nevada (37±0.5°N latitude). This regional perspective on mafic magmatism spans ~110 million years and crosses several tectonically-assembled belts, each with distinctive geology. The two chapters document systematic differences in field relationships and geochemistry of the mafic intrusions that vary by geologic belt, as the mafic magmas interacted with heterogeneous crust. Chapter 3 presents field relationships, ages, and major and trace element chemistry. Chapter 4 presents isotopic compositions (O, Hf, Sr, and Nd), revealing that contamination of mafic magmas by ~10–20% assimilation of the local crustal column is inevitable, and that it occurs early during differentiation.</p
Two Categorifications of the Local Langlands Correspondence for the Torus
No full textThe stack of local Langlands parameters is a Picard stack when the relevant reductive group is a torus. We explicitly determine its Picard dual and show that the Fourier-Mukai transform gives rise to the integral categorical local Langlands correspondence for the torus. This is the categorification of the local Langlands correspondence and answers a conjecture of X. Zhu. Moreover, we establish a geometric version of this correspondence. This second categorification relates to the previous correspondence in the sense that taking the categorical trace construction allows one to reproduce the previous result
Low Noise at Low Cost for Large Radio Astronomy Arrays
No full textThe 2020s is the decade of survey instruments in astronomy. Radio astronomy is no exception, with Caltech's proposed DSA-2000 being the most powerful radio interferometer in the world, costing much less than competing instruments. Key to this achievement are two core breakthroughs: a completely ambient-temperature receiver and a “radio camera” backend that images the sky in real time. DSA-2000 will have record-breaking survey speed and sensitivity, enabled by these two key breakthroughs, giving astronomers all over the world open access to exquisite all-sky maps to enable the discovery of billions of new radio sources, precise timing of pulsars, and localization of fast radio bursts. The array will produce enough data to keep astronomers busy for a century.
In this thesis, we discuss the development of one of the key breakthroughs, the ambient-temperature receiver. Specifically, we focus on the design, testing, and implementation of the wideband, ambient-temperature low noise amplifier. We cover the design from analytic first principles through precision measurement of its performance. We follow this with a discussion of the design and implementation of the analog signal path, including a high performance, RF over fiber link. Finally, we discuss the Galactic Radio Explorer (GReX) instrument, designed as a global experiment probing the brightest radio transients in the local universe.</p
Insights Into the Core’s Structure, Formation and Evolution from First-Principles Calculations
No full textUnderstanding the formation, composition, and evolution of planetary cores is essential to unraveling the early history and internal dynamics of terrestrial planets. However, direct constraints on the physical and chemical properties of liquid metal under core-forming conditions remain limited due to the inaccessibility of the core and the challenges of reproducing its extreme pressures and temperatures in the laboratory. This thesis integrates first-principles molecular dynamics(FPMD)simulations with high-pressure experimental data to investigate the thermodynamics, chemical partitioning, and seismic implications of multicomponent metal liquids in the deep interiors of Earth and other differentiated bodies.
This thesis focuses on two fundamental properties of the core: its thermodynamic behavior and its chemical interaction with the silicate mantle during differentiation. The first part of the thesis develops a thermodynamic model for multicomponent metallic liquids—including Fe–Ni systems with light elements such as O, S, Si, C, and H–based on FPMD simulations and calibrated against experimental data. This model accurately reproduces pressure–volume–temperature relations and mixing behavior, and is consistent with both diamond anvil cell and shock wave measurements. The model forms the basis for a forward seismic modeling framework that allows direct comparison between core composition and observed density and velocity profiles in Earth’s outer core. The second part of the thesis investigates the chemical partitioning of elements that record early planetary formation and evolution—specifically Sm, Nd, I, and Pu—between metal and silicate liquids at high temperatures. Two different approaches are employed to determine the partition coefficients: thermodynamic integration based on first-principles molecular dynamics for Sm and Nd, and two-phase FPMD simulations for I and Pu. With these partitioning behaviors quantified, the study further models core formation processes in differentiated planetesimals and Earth, providing new constraints on the extent of metal–silicate chemical exchange and fresh insights into the isotopic and volatile evolution of planetary mantles.</p
Surface Evolution on Basaltic Bodies: Tectonic, Geomorphic, and Diagenetic Modification on Io and Mars
No full textAll planets and moons in the Solar System evolve over geologic timescales, though the processes affecting each body vary widely depending on gravity, atmosphere thickness and composition, volcanic activity, and perhaps most importantly, the presence of a hydrologic cycle. This dissertation investigates the surface evolution of two basaltic bodies in our Solar System: one that has barely changed in 3.5 billion years, and one that changes almost daily. Jupiter’s moon Io is continually resurfaced by large-scale volcanic eruptions of low-viscosity lava and sulfur dioxide gas, driven by interior heating generated by diurnal tidal stresses. Such tidal stresses have been linked to eruptive activity and tectonic ridge formation on other moons like Titan and Europa; while they strongly influence Io, they are orders of magnitude weaker than the crustal subsidence stresses which control the expression of tectonic features on the surface (kilometers-tall mountains and caldera-like volcanic features called paterae). Chapter 2 investigates whether tidal stresses may have any influence on the formation of mountains and paterae. Though no global trends have been identified, I suggest that local correlations between patera orientations and the large volcanic center of Loki Patera may provide insight into the magma plumbing pathways of this unique volcano. As soon as tectonic mountains are uplifted on Io, they are subject to gravity- and seismicity-driven erosional processes tearing them down. In Chapter 3, I present the first regional geologic map of a trio of mountains named Cocytus Montes and identify a new geologic unit—a blocky deposit composed of kilometer-scale slab-shaped blocks of crust—that are visible thanks to the favorable resolution and near-terminator lighting conditions of new Junocam imagery. I explore several new erosional mechanisms for Io that could create these blocks, determining regolith creep-modified cliff collapse to be the most likely. The orders of magnitude higher resolution imagery collected by the Mars Science Laboratory Curiosity rover provides a backdrop for much closer analysis of how sediments moved, deposited, lithified, and were subsequently modified by diagenetic fluids on ancient Mars. Chapter 4 takes advantage of hand-sample scale data to categorize a diverse array of diagenetic fabrics (nodules, pits, color variations) that correlate with the stratigraphy in a region defined by a transition from clay-bearing rocks to sulfate-bearing rocks. I present several hypotheses to explain how the Mg sulfate detected in these nodules and pore-filling cements may have precipitated at depth, to complement current evaporite-driven models. These hypotheses could be tested in the coming years of Mars exploration by the rover, and will provide insights into the longevity of a groundwater system after surface water ceased to flow on ancient Mars. Overall, this work explores the well-studied terrestrial processes of surface modification, degradation, and diagenesis under distinctly alien conditions throughout the Solar System
Active Acquisition Methods for Single Cell Genomics
Get PDFWe introduce two novel computational methodologies, ActiveSVM and Active Cell Inference, aimed at reducing the costs and enhancing the efficiency of single-cell mRNA sequencing and spatial transcriptomics, respectively. ActiveSVM employs an active learning approach to identify minimal yet highly informative gene sets for cell-type classification, physiological state identification, and genetic perturbation responses in single-cell datasets. By focusing on misclassified cells through an iterative process, ActiveSVM efficiently scales to analyze over a million cells, demonstrating around 90% accuracy across various datasets, including cell atlas and disease characterization studies.
Active Cell Inference complements this by utilizing ordered gene sets, developed through ActiveSVM, to streamline spatial genomics measurements. This end-to-end pipeline significantly reduces measurement time and costs by up to 100-fold in scientific and clinical settings. It optimizes the gene probing process by identifying well-classified cells early, allowing for targeted gene application based on cell classification certainty. This method's efficacy is further enhanced by a temporal scaling calibration scheme, improving calibration accuracy throughout its iterative process.
Both methodologies were rigorously tested on the expansive Human Cell Atlas dataset, using the advanced computational tool, CellxGene-Census, involving over 60 million cells. This integration facilitated the creation of precise gene sets for various human tissues, dramatically improving the efficiency and reliability of these cutting-edge genomic techniques. Together, ActiveSVM and Active Cell Inference represent significant advancements in the application of genomics to clinical diagnostics, therapeutic discovery, and genetic screens, promising substantial reductions in the operational complexities and costs associated with next-generation sequencing technologies.</p