617 Works

Building a gene regulatory network in adult mouse skeletal muscle following nerve injury : transcriptome characterization and new model for functional cis-regulatory analysis in vivo

Gilberto Hernandez
The essential functional linkages of gene regulatory networks (GRNs) consist of the interactions between cis-regulatory DNA sequences and trans-acting regulatory factors. These genomically encoded regulatory interactions govern the differential gene expression programs which direct specific biological processes during development and adulthood. Detailed analysis of GRNs during development has yielded important insights regarding the structural and functional dynamics of cis-regulatory modules (CRMs) and cis-regulatory elements (CREs). Indeed, the comprehensive GRNs that have been characterized for various...

Simulations and Mechanisms of Subtropical Low-cloud Response to Climate Change

Zhihong Tan
This thesis focuses on improving the simulation skills and the theoretical understanding of the subtropical low cloud response to climate change. First, an energetically consistent forcing framework is designed and implemented for the large eddy simulation (LES) of the low-cloud response to climate change. The three representative current-day subtropical low cloud regimes of cumulus (Cu), cumulus-over-stratocumulus, and stratocumulus (Sc) are all well simulated with this framework, and results are comparable to the conventional fixed-SST approach....

Imperfection Insensitive Thin Shells

Xin Ning
The buckling of axially compressed cylindrical shells and externally pressurized spherical shells is extremely sensitive to even very small geometric imperfections. In practice this issue is addressed by either using overly conservative knockdown factors, while keeping perfect axial or spherical symmetry, or adding closely and equally spaced stiffeners on shell surface. The influence of imperfection-sensitivity is mitigated, but the shells designed from these approaches are either too heavy or very expensive and are still sensitive...

Wave-induced oscillations of small moored vessels

W. M. Keck Laboratory Of Hydraulics And Water Resources

Did Galaxies Reionize the Universe?

Matthew Aaron Schenker
The epoch of reionization remains one of the last uncharted eras of cosmic history, yet this time is of crucial importance, encompassing the formation of both the first galaxies and the first metals in the universe. In this thesis, I present four related projects that both characterize the abundance and properties of these first galaxies and uses follow-up observations of these galaxies to achieve one of the first observations of the neutral fraction of the...

Models of the Oxygen-Evolving Complex of Photosystem II

Jacob Steven Kanady
In the five chapters that follow, I delineate my efforts over the last five years to synthesize structurally and chemically relevant models of the Oxygen Evolving Complex (OEC) of Photosystem II. The OEC is nature’s only water oxidation catalyst, in that it forms the dioxygen in our atmosphere necessary for oxygenic life. Therefore understanding its structure and function is of deep fundamental interest and could provide design elements for artificial photosynthesis and manmade water oxidation...

I. Quantal effects in biochemical cooperativity and a proposed mechanism for the differentiation of calcium signaling in synaptic plasticity. II. Evolutionary algorithms for the optimization of methods in computational chemistry

William Chastang Ford
In Part 1 of this thesis, we propose that biochemical cooperativity is a fundamentally non-ideal process. We show quantal effects underlying biochemical cooperativity and highlight apparent ergodic breaking at small volumes. The apparent ergodic breaking manifests itself in a divergence of deterministic and stochastic models. We further predict that this divergence of deterministic and stochastic results is a failure of the deterministic methods rather than an issue of stochastic simulations. Ergodic breaking at small volumes...

Enantioselective Total Synthesis of Diketopiperazinecontaining Natural Products: (–)-Lansai B, (+)-Nocardioazines A and B, and (–)-Acetylapoaranotin

Haoxuan Wang
Diketopiperazine (DKP) motif is found in a wide range of biologically active natural products. This work details our efforts toward two classes of DKP-containing natural products. Class one features the pyrroloindoline structure, derived from tryptophans. Our group developed a highly enantioselective (3 + 2) formal cycloaddition between indoles and acrylates to provide pyrroloindoline products possessing three stereocenters. Utilizing this methodology, we accomplished asymmetric total synthesis of three natural products: (–)-lansai B, (+)-nocardioazines A and B....

Mechanics of Sediment Transport and Bedrock Erosion in Steep Landscapes

Joel Simon Scheingross
Erosion is concentrated in steep landscapes such that, despite accounting for only a small fraction of Earth’s total surface area, these areas regulate the flux of sediment to downstream basins, and their rugged morphology records transient changes (or lack thereof) in geologic and climatic forcing. Steep landscapes are geomorphically active; large sediment fluxes and rapid landscape evolution rates can create or destroy habitat for humans and wildlife alike, and landslides, debris flows, and floods common...

Signatures of Topological Superconductors

Shu-Ping Lee
Topological superconductors are particularly interesting in light of the active ongoing experimental efforts for realizing exotic physics such as Majorana zero modes. These systems have excitations with non-Abelian exchange statistics, which provides a path towards topological quantum information processing. Intrinsic topological superconductors are quite rare in nature. However, one can engineer topological superconductivity by inducing effective p-wave pairing in materials which can be grown in the laboratory. One possibility is to induce the proximity effect...

Multiplexed Analysis of Diverse RNA Classes via Hybridization Chain Reaction

Aneesh Acharya
Gene circuits are complex biological networks composed of numerous regulatory elements, including transcription factors, mRNAs, and microRNAs. Fluorescent in situ hybridization (FISH) is a powerful method for spatially mapping expression levels of RNA elements within an intact organism, but traditional methods exhibit at least one of the following drawbacks: low signal-to-background, arduous and/or destructive multiplexing, and non-quantitative signal. These issues are all overcome using in situ amplification based on the mechanism of hybridization chain reaction...

TCCON data from Lamont (US), Release GGG2014.R1

P. O. Wennberg, D. Wunch, C. M. Roehl, J.-F. Blavier, G. C. Toon & N. T. Allen
The Total Carbon Column Observing Network (TCCON) is a network of ground-based Fourier Transform Spectrometers that record direct solar absorption spectra of the atmosphere in the near-infrared. From these spectra, accurate and precise column-averaged abundances of atmospheric constituents including CO2, CH4, N2O, HF, CO, H2O, and HDO, are retrieved. This data set contains observations from the TCCON station at Lamont, U.S.A..

TCCON data from Jet Propulsion Laboratory (US), 2011, Release GGG2014.R1

P. O. Wennberg, C. M. Roehl, J.-F. Blavier, D. Wunch & N. T. Allen
The Total Carbon Column Observing Network (TCCON) is a network of ground-based Fourier Transform Spectrometers that record direct solar absorption spectra of the atmosphere in the near-infrared. From these spectra, accurate and precise column-averaged abundances of atmospheric constituents including CO2, CH4, N2O, HF, CO, H2O, and HDO, are retrieved. This data set contains observations from the TCCON station at the Jet Propulsion Laboratory, Pasadena, U.S.A..

TCCON data from Indianapolis (US), Release GGG2014.R1

L. T. Iraci, J. R. Podolske, P. W. Hillyard, C. Roehl, P. O. Wennberg, J.-F. Blavier, J. Landeros, N. Allen, D. Wunch, J. Zavaleta, E. Quigley, G. B. Osterman, E. Barrow & J. Barney
The Total Carbon Column Observing Network (TCCON) is a network of ground-based Fourier Transform Spectrometers that record direct solar absorption spectra of the atmosphere in the near-infrared. From these spectra, accurate and precise column-averaged abundances of atmospheric constituents including CO2, CH4, N2O, HF, CO, H2O, and HDO, are retrieved. This data set contains observations from the TCCON station at Indianapolis, U.S.A..

TCCON data from Edwards (US), Release GGG2014.R1

L. T. Iraci, J. R. Podolske, P. W. Hillyard, C. Roehl, P. O. Wennberg, J.-F. Blavier, J. Landeros, N. Allen, D. Wunch, J. Zavaleta, E. Quigley, G. B. Osterman, R. Albertson, K. Dunwoody & H. Boyden
The Total Carbon Column Observing Network (TCCON) is a network of ground-based Fourier Transform Spectrometers that record direct solar absorption spectra of the atmosphere in the near-infrared. From these spectra, accurate and precise column-averaged abundances of atmospheric constituents including CO2, CH4, N2O, HF, CO, H2O, and HDO, are retrieved. This data set contains observations from the TCCON station at Edwards, U.S.A..

Lock Acquisition and Sensitivity Analysis of Advanced LIGO Interferometers

Denis V. Martynov
Laser interferometer gravitational wave observatory (LIGO) consists of two complex large-scale laser interferometers designed for direct detection of gravitational waves from distant astrophysical sources in the frequency range 10Hz - 5kHz. Direct detection of space-time ripples will support Einstein's general theory of relativity and provide invaluable information and new insight into physics of the Universe. Initial phase of LIGO started in 2002, and since then data was collected during six science runs. Instrument sensitivity was...

Aryne Reactions in the Synthesis of Heterocyclic Molecules

Christopher Keating Haley
Reactive intermediates play an important the within the realm of chemical synthesis. Their high energy and transient nature make them difficult to observe and characterize, but it is these same properties that empower them to form bonds traditionally seen as difficult to prepare and unusual architectures quickly and efficiently. Herein, two reactive intermediates, arynes and transitient (2azaaryl)-cuprates, are exploited for their abilities to prepare important chemical motifs. Both serve as an avenue into the functionalization...

High-Latitude Ocean Convection and Gyre Dynamics

Zhan Su
High-latitude ocean deep convection substantially contributes to vertical mixing, vertical heat transport, deep-water formation, and sea-ice budget in the World Ocean. However, the extent of this contribution remains poorly constrained. The concept of ocean convective available potential energy (OCAPE) have been developed to improve the understanding and the prediction for these deep convection events. The kinetic energy (KE) budget of deep convection is explored analytically and numerically based on the observations in the Weddell Sea....

From Molecules to Organs : Microscopy and Multi-Scale Nature of Development

Vikas Trivedi
Morphogenesis is a phenomenon of intricate balance and dynamic interplay between processes occurring at a wide range of scales (spatial, temporal and energetic). During development, a variety of physical mechanisms are employed by tissues to simultaneously pattern, move, and differentiate based on information exchange between constituent cells, perhaps more than at any other time during an organism's life. To fully understand such events, a combined theoretical and experimental framework is required to assist in deciphering...

The Bin Model

Computer Science Technical Reports

Structural Characterizations of the Dimeric Anti-HIV Antibody 2G12 and the HIV-2 Envelope Glycoprotein

Yunji Wu
More than thirty years after the discovery that Human Immunodeficiency Virus (HIV) was the causative agent of Acquired Immunodeficiency Syndrome (AIDS), the disease remains pandemic as long as no effective universal vaccine is found. Over 34 million individuals in the world are infected with the virus, and the vast majority of them have no access to the antiretroviral therapies that have largely reduced HIV to a chronic disease in the developed world. The first chapter...

Analysis of air-bubble plumes

W. M. Keck Laboratory Of Hydraulics And Water Resources

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