771 Works

Quantitative Characterization of Composition and Regulation of Cullin-RING Ubiquitin Ligases

Kurt Michael Reichermeier
Induced proteolysis of pathogenic proteins via degrader molecules, such as Proteolysis Targeting Chimeras (PROTACs), is emerging as a promising therapeutic strategy. In particular, induced proximity of Cullin-RING ubiquitin Ligases (CRLs) with various neo-substrates has proven successful in mediating proteasomal degradation of previously undruggable proteins. Hijacking enzymes to carry out biochemical reactions on neo-substrates stands in stark contrast to conventional pharmacological approaches and exposes degrader molecules to unusually complex pharmacodynamics. While the first PROTACs entered the...

Convex Relaxations for Graph and Inverse Eigenvalue Problems

Utkan Onur Candogan
This thesis is concerned with presenting convex optimization based tractable solutions for three fundamental problems: 1. Planted subgraph problem: Given two graphs, identifying the subset of vertices of the larger graph corresponding to the smaller one. 2. Graph edit distance problem: Given two graphs, calculating the number of edge/vertex additions and deletions required to transform one graph into the other. 3. Affine inverse eigenvalue problem: Given a subspace ε ⊂ 𝕊ⁿ and a vector of...

Unraveling scaling properties of slow-slip events

This dataset contains data used in Dal Zilio et al., (2020): Unraveling scaling properties of slow-slip events

Haze seasonal variations of Titan's upper atmosphere

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This study presents a 13 years survey of haze UV extinction profiles, monitoring the temporal evolution of the detached haze layer (DHL) in Titan's upper atmosphere (350-600 km). As reported by West et al. 2011 (GRL vol.38, L06204) at the equator, we show that the DHL is present at all latitudes below 55°N during the northern winter (2004-2009). Then, it globally sunk and disappeared in 2012. No permanent DHL was observed between 2012 and 2015....

Data for \"Statistically Steady State Large-Eddy Simulations Forced by an Idealized GCM: 1. Forcing Framework and Simulation Characteristics\"

Zhaoyi Shen, Kyle Pressel, Zhihong Tan & Tapio Schneider
This dataset provides time-averaged GCM and LES data required to produce results in the paper "Statistically Steady State Large-Eddy Simulations Forced by an Idealized GCM: 1. Forcing Framework and Simulation Characteristics". It also includes an example script that can be used to generate Figure 8.

2D Modeling of Lower Mantle Structure with WKM Synthetics

Sidao Ni
The Earth is very heterogeneous, especially in the region close to the surface of the Earth, and in regions close to the core-mantle boundary (CMB). The lowermost mantle (bottom 300km of the mantle) is the place for fast anomaly (3% faster S velocity than PREM, modeled from Scd), for slow anomaly (-3% slower S velocity than PREM, modeled from S,ScS), for extreme anomalous structure (ultra-low velocity zone, 30% lower inS velocity, 10% lower in P...

Characterization of the Physical Properties of Atmospheric Aerosols through Airborne Sampling

Donald R. Collins
Atmospheric aerosols are highly variable both in their characteristics and their concentration. Aircraft-based sampling provides a means of characterizing such a complex and variable constituent. To maximize the potential of aircraft sampling, improvements in existing aerosol instrumentation and development of new instruments is necessary. A new approach to inversion of differential mobility analyzer (DMA) data has been developed that improves the accuracy with which accelerated size distribution measurements can be made. Extensive testing of this...

Engineering multiple levels of specificity in an RNA viral vector

Xiaojing Gao, Lucy Chong, Michaela Ince, Matthew Kim & Michael Elowitz
Flow data, images, and scripts required to generate figures.

Bdellovibrio bacteriovorus

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Atlas of Bacterial and Archaeal Cell Structure

Methylomicrobium alcaliphilum

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Atlas of Bacterial and Archaeal Cell Structure

Mechanics of the Cytoskeleton: Examining the Dynamics of Cytoplasmic Transport through Fluorescence Microscopy

Rajan P. Kulkarni
The cellular cytoplasmic space contains many different molecules and complexes confined within a small volume. Understanding how objects are transported in this crowded space is important for many potential applications. In this work, we examined various aspects of cytoskeletal mechanics, including microtubule-mediated and diffusive transport using advanced fluorescence microscopy techniques. Spatio-temporal image correlation spectroscopy (ICS) was employed to first examine microtubule-mediated transport of non-viral polyplexes within endosomes through the cytoplasm. ICS analysis of these polyplex-loaded...

Quantum Mechanical Vistas on the Road to Quantum Gravity

Ashmeet Singh
In this thesis, we lay out the goal, and a broad outline, for a program that takes quantum mechanics in its minimal form to be the fundamental ontology of the universe. Everything else, including features like space-time, matter and gravity associated with classical reality, are emergent from these minimal quantum elements. We argue that the Hilbert space of quantum gravity is locally finite-dimensional, in sharp contrast to that of conventional field theory, which could have...

Synthesis, Characterization, and Reactivity of Thiolate-Supported Metalloradicals

Nina Xiao Gu
Reactive metalloradical intermediates have been implicated in both biological and synthetic catalyst systems for small molecule activation processes, including proton reduction and ammonia oxidation. Towards a greater mechanistic understanding of such transformations on well-defined model complexes, this thesis explores relevant H–H and N–N bond-forming reactions mediated by trivalent Fe and Ni species, as well as catalytic N–N bond cleavage mediated by an open-shell VFe bimetallic complex. First, a pair of thiolate-supported, S = ½ iron...

Probing the Progression, Properties, and Progenies of Magnetic Reconnection

Young Dae Yoon
Magnetic reconnection is a plasma phenomenon in which opposing magnetic fields annihilate and release their magnetic energy into other forms of energy. In this thesis, various aspects of collisionless magnetic reconnection are studied analytically and numerically, and an experimental diagnostic for magnetic fields in a plasma is described. The progression of magnetic reconnection is first illustrated through the formulation of a framework that revolves around canonical vorticity flux, which is ideally a conserved quantity. The...

Directed Evolution of the Transcriptional Activator LuxR

Cynthia Hollie Collins
LuxR-type proteins are responsible for density-dependent transcriptional regulation in quorum-sensing systems that employ acyl-homoserine lactones (acyl-HSLs) as signal molecules. The Vibrio fischeri lux operon, which includes LuxR, has been well studied and shown to function in E. coli. The components of the lux operon have been used to engineer de novo genetic circuits because they provide a versatile intercellular communications system. We have used directed evolution to engineer LuxR to generate new components for engineering...

Searching for the Astrophysical Gravitational-Wave Background and Prompt Radio Emission from Compact Binaries

Thomas Alfred, III Callister
Gravitational-wave astronomy is now a reality. During my time at Caltech, the Advanced LIGO and Virgo observatories have detected gravitational waves from dozens of compact binary coalescences. All of these gravitational-wave events occurred in the relatively local Universe. In the first part of this thesis, I will instead look towards the remote Universe, investigating what LIGO and Virgo may be able to learn about cosmologically-distant compact binaries via observation of the stochastic gravitational-wave background. The...

Cell-Selective Proteomic Profiling in Complex Biological Systems

Xinran Liu
Cells within biological systems are constantly adjusting their protein synthesis in response to various environmental changes. To study the rapid cellular regulations in complex biological systems, global proteomic profiling provides important information on system-level regulations, yet physiological properties characteristic of individual cellular subpopulations could be hidden under the characterization. Instead, cell-selective proteomic profiling allows researchers to reveal the heterogeneities in biological systems with phenotypically and even genetically distinct subpopulations under different microenvironments. Chapter 1 describes...

Neurons that Control Social States in Drosophila melanogaster

Yonil Jung
Animal behaviors are influences not only by the immediate stimuli they are receiving but also by internal states. Internal states such as fear, hunger, and arousal can change subjective "feeling", and result in complex behavioral outcome even if animals receive the same stimuli. In most cases, these state-dependent behavioral changes persist long after the sensory input that caused internal state change is removed, and affect future behavior, reflexing previous experience. This feature of state-control allows...

First-Principles Calculations of Electron-Defect Interactions and Defect-Limited Charge Transport

I-Te Lu
Crystallographic defects and impurities govern charge transport at low temperature, where the electron-defect (e-d) interactions limit the carrier mobility and manifest themselves in a wide range of phenomena of broad relevance in condensed matter physics. Theoretical treatments of e-d interactions have so far relied on heuristic approaches and analytic models. However, the band structure, electronic wave functions, and defect perturbation potential are far more complex in real materials than in these simplified models. First-principles calculations...

Protein-Mediated Colloidal Assembly

Bradley Ross Silverman
The assembly of colloidal-sized particles into larger structures by the manipulation of inter-particle forces has been a subject of significant research towards applications in materials science, soft matter physics, and synthetic biology. To date, much of this work has utilized manipulation of electrostatic or depletion interactions to drive the aggregation of the particles. More recently, specific (bio)-chemical interactions have been harnessed, particularly the use of deoxyribonucleic acid (DNA) linkers to program particle interactions by Watson-Crick...

Structure, Function, and Application of Bacterial ABC Transporters

Chengcheng Fan
The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog from Novosphingobium aromaticivorans (NaAtm1) can export glutathione derivatives and confer protection against heavy metal toxicity. To establish the structural framework underlying the NaAtm1 transport mechanism, we determined eight structures by X-ray crystallography and single particle cryo-EM in distinct conformational states, stabilized by individual disulfide crosslinks and nucleotides. As NaAtm1 progresses through the transport cycle, conformational changes in transmembrane...

Suspended Trace Air-Gap Resonators for Low Loss Superconducting Circuits

Michael Tianyu Fang
Quantum memories and networks for distributed quantum information processing require links between the microwave, mechanical, and optical domains. Coherent integration of long-lived superconducting qubits (SCQs) with optomechanical and photonic devices (OMPDs) remains an outstanding challenge. We present a step towards coherent integration using a suspended trace air-gap resonator (STAR): a superconducting resonator on a silicon-on-insulator (SOI) substrate with the signal trace suspended by silicon tethers above and between galvanically connected ground metal planes. As a...

3D Microfluidics for Environmental Pathogen Detection and Single-cell Phenotype-to-Genotype Analysis

Yanzhe Zhu
The emergence of microfluidic technologies has enabled the miniaturization of cell analysis processes, including nucleic acid analysis, single cell phenotypic analysis, single cell DNA and RNA sequencing, etc. Traditional chip fabrication via soft lithography cost thousands of dollars just in personnel training and capital cost. The design of these systems is also confined to two dimensions limited by their fabrication. To address the needs of smooth transition from technology to adoption by end-users, less complexity...

Optimizing Deep Neural Networks for Single Cell Segmentation

Can (Sunny) Cui
Analysis of live-cell imaging experiments at the resolution of single cells provides exciting insights into the inner workings of biological systems. Advances in biological imaging and computer vision allow for segmentation of natural images with a high degree of accuracy. However, automation of the segmentation pipeline at the single cell resolution remains a challenging task. Complex deep learning models require large, well-annotated datasets that are rarely available in biology. In this research, we explore various...

Data Visualization 101

Kristin Briney
This is a recording from the Data Visualization 101 workshop held on 2020-05-21 over Zoom. This workshop covered how to choose the right chart type for your data and how good design choices will make your chart easier to understand. The workshop focused on visualization best practices, independent of any specific visualization software, and consisted of lecture and hands on activities.

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