### Stationary Subdivision and Multiresolution Surface Representations

Computer Science Technical Reports

### Expanding the repertoire of DNA-mediated signaling in DNA repair

Timothy Paul Mui
DNA damage is extremely detrimental to the cell and must be repaired to protect the genome. DNA is capable of conducting charge through the overlapping π-orbitals of stacked bases; this phenomenon is extremely sensitive to the integrity of the π-stack, as perturbations attenuate DNA charge transport (CT). Based on the E. coli base excision repair (BER) proteins EndoIII and MutY, it has recently been proposed that redox-active proteins containing metal clusters can utilize DNA CT...

### On the Concentration of Space Charge in the Vicinity of an Insulating Surface

Benedict Cassen
The purpose of this investigation is the determination of the order of magnitude of the highest densities of space charge experimentally producible in the immediate vicinity of an insulating surface. The first section of the paper is a theoretical analysis of the problem while the second section describes some simple experiments undertaken in order to obtain the necessary data to get a numerical answer for some particular insulating surfaces.

### Optical Phase Conjugation and Its Applications in Biology

Mooseok Jang
Optical phase conjugation is a process where an incoming electromagnetic wave is reflected with a reversed phase. The propagation direction of an incoming beam (equivalently, local phase gradient) can thereby be precisely reversed by the phase conjugate beam. This intriguing effect, so called "time-reversal of electromagnetic waves," allows cancellation of spatial distortion introduced into the incoming beam. Recently, this concept has provided a new avenue to overcome or utilize random scattering in the field of...

### Perchloric Acid from Ammonium Perchlorate and Oxides of Nitrogen

Alfred Wheelock Knight
No Abstract.

### Characteristics of transverse mixing in open-channel flows

W. M. Keck Laboratory Of Hydraulics And Water Resources

### Searches for New Physics at the Compact Muon Solenoid Experiment and Precision Timing Calorimetry

Cristián Peña Herrera
In this thesis, we present several searches for beyond the standard model physics in proton-proton collisions recorded by the Compact Muon Solenoid Experiment at center-of-mass energy of 8 and 13\TeV. We search for particle dark matter in events with two or more jets and missing transverse momentum at $\sqrt{s} = 8$ TeV, in this search we use the razor variables to discriminate signal from background events and thus improve the overall sensitivity of the analysis....

### A Multiple-Mechanism Developmental Model for Defining Self-Organizing Geometric Structures

Computer Science Technical Reports

### A 25 Input Pulse Height Recording System

J. H. Marshall & D. E. Groom
A general description is given of a data recording system which provides a link between counter experiments in high-energy physics and a high-speed digital computer. The instrument described can accept as many as 25 simultaneous photomultiplier tube signals and pulse height analyze them into 100 channels each. Six bits of digital data may be substituted for any unused pulse height input. The usual output is perforated paper tape with a binary coded decimal format for...

### Concentration Inequalities of Random Matrices and Solving Ptychography with a Convex Relaxation

Yuhua Richard Chen
Random matrix theory has seen rapid development in recent years. In particular, researchers have developed many non-asymptotic matrix concentration inequalities that parallel powerful scalar concentration inequalities. In this thesis, we focus on three topics: 1) estimating sparse covariance matrix using matrix concentration inequalities, 2) constructing the matrix phi-entropy to derive matrix concentration inequalities, 3) developing scalable algorithms to solve the phase recovery problem of ptychography based on low-rank matrix factorization. Estimation of covariance matrix is...

### Biophysics of V(D)J recombination and Genome Packaging: In singulo studies on RAG, HMGB1, and TFAM

Geoffrey A. Lovely
The recombination-activating gene products, RAG1 and RAG2, initiate V(D)J recombination during lymphocyte development by cleaving DNA adjacent to conserved recombination signal sequences (RSSs). The reaction involves DNA binding, synapsis, and cleavage at two RSSs located on the same DNA molecule and results in the assembly of antigen receptor genes. Since their discovery full-length, RAG1 and RAG2 have been difficult to purify, and core derivatives are shown to be most active when purified from adherent 293-T...

### Terahertz and Microwave Spectroscopy of Liquids and Hydrogen-Bonded Clusters

Ian Alan Finneran
The microwave (MW, 0.3-100 GHz) and terahertz (THz, 0.1-10 THz) regions of the electromagnetic spectrum are replete with a rich set of molecular motions, including soft inter- and intramolecular vibrations, torsions, and rotations. At room temperature these motions are well populated, and play an active role in condensed-phase chemistry on Earth. This work details the development of one MW and two THz spectrometers along with their application to the study of liquids and hydrogen-bonded clusters....

### Development of Synthetic Strategies for the Total Synthesis of Ent-Kauranoid and Diterpenoid Alkaloid Natural Products

Victor Wei-Dek Mak
As part of an ongoing synthetic effort directed towards biologically active ent-kauranoid natural products, the preparation of two structurally unique natural products, (–)-trichorabdal A and (–)-longikaurin E, is presented. The syntheses intercept an early intermediate from the synthetic route towards the rearranged natural product (–)-maoecrystal Z, and thus, represents a unified synthetic strategy to access structurally unique ent-kauranoids. Specifically, the syntheses are enabled by a palladium-mediated oxidative cyclization of a silyl ketene acetal to install...

### Concurrent Simulations of Plasma Reactors for VLSI Manufacturing

Computer Science Technical Reports

### The structure of the geothermal industry through 1974

Environmental Quality Laboratory

### Microstructural Effects on Diffusion and Mechanical Properties in Different Material Systems

Shi Luo
Material microstructures is a very broad subject that encompasses most of the field of materials science. Advances in materials characterization and small scale mechanical experiments have brought about progress in the understanding of microstructural features and mechanisms down to the nanometer scale. In contrast to bulk features and properties, the small length scale of these microstructures lead to many interesting properties, and often requires a material-by-material, and even localized region-by-region study. While a thorough understanding...

### How Polymers Shape the Physicochemical Environment of the Gut

Asher Preska Steinberg
The gut is where food is digested and nutrients are absorbed, therapeutics are often delivered, and many infections take hold. The gut microbiota is in symbiosis with its host, and can influence host health and behavior. Though the gut holds these central roles, little is understood about the physics of how soft materials interact with and shape the physicochemical environment of the gut. Soft materials abound in the gut in the form of particulates (e.g.,...

### Leading to a Kind Description Language: Thoughts on Component Specification

Computer Science Technical Reports

### TCCON data from Réunion Island (RE), Release GGG2014.R0

M. De Mazière, M. K. Sha, F. Desmet, C. Hermans, F. Scolas, N. Kumps, J.-M. Metzger, V. Duflot & J.-P. Cammas
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 on Réunion Island.

### Measurement of R(D) and R(D*) Using Semileptonic Tags and Hadronic τ Decays

Jae Hong Kim
We present a measurement of R(D(*)) = B(B → D̅(*) τντ)/B(B → D̅(*) ℓνℓ) using semileptonic tagging and hadronic τ decays on the 433 fb-1 of data collected at the Υ(4S) resonance using the BaBar detector at the PEP-II collider. We obtain a high statistics data sample using loose selection criteria. The signal is extracted by performing a 2-dimensional fit of the component densities to the kernel density estimate of the data, which is made...

### The Rhetoric of Change

Christina Y. Lin
The early 20th century saw a plethora of declarations, proclamations, and calls to arms for change in China. Some authors, such as Mao Zedong, represented prominent political movements, while others, like Lu Xun, expressed their ideas in passing through a preface to a collection of short stories. Among these writers, some take a practical approach, reflecting a belief that revolution begins with concrete, tangible changes that will improve the lives of the common man. Others...

### A ratiometric-based measure of gene co-expression

Anna Cecilia Therese Abelin
Current measures of global gene expression analyses, such as correlation and mutual information-based approaches, largely depend on the degree of association between mRNA levels and to a lesser extent on variability. I develop and implement a new approach, called the Ratiometric method, which is based on the coefficient of variation of the expression ratio of two genes, relying more on variation than previous methods. The advantage of such modus operandi is the ability to detect...

### Detecting Actions of Fruit Flies

Eyrun Arna Eyjolfsdottir
In this thesis we describe a system that tracks fruit flies in video and automatically detects and classifies their actions. We introduce Caltech Fly-vs-Fly Interactions, a new dataset that contains hours of video showing pairs of fruit flies engaging in social interactions, and is published with complete expert annotations and articulated pose trajectory features. We compare experimentally the value of a frame-level feature representation with the more elaborate notion of bout features that capture the...

### The Bromination of Para-Cresol in the Presence of Strong Acids

Richard Clyde Datin
The purpose of this work has been to determine whether or not the formation of an oxonium compound of a cresol would change the directing influence of the hydroxyl group.

### Noncovalent Immobilization of Electrocatalysts on Carbon Electrodes via a Pyrenyl Ligand

Ayush Gupta
There are many problems that need to be overcome if solar energy is to be viable on a global scale. Photons must be harvested and stored in a usable to allow efficient use of energy throughout the day. The functionalization of electrode surfaces with molecular catalysts is an attractive route for assembling (photo)electrochemical devices that convert renewable energy into chemical fuels. This work focuses on one method of noncovalently attaching molecular catalysts to graphitic surfaces....

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