Gauge Invariant Spectral Cauchy Characteristic Extraction of Gravitational Waves in Computational General Relativity

We present a complete system for Spectral Cauchy characteristic extraction (Spectral CCE). Implemented in C++ within the Spectral Einstein Code (SpEC), the method employs numerous innovative algorithms to efficiently calculate the Bondi strain, news, and flux.

Spectral CCE was envisioned to ensure physically accurate gravitational wave-forms computed for the Laser Interferometer Gravitational wave Observatory (LIGO) and similar experiments, while working toward a template bank with more than a thousand waveforms to span the binary black hole (BBH) problem’s seven-dimensional parameter space.

The Bondi strain, news, and flux are physical quantities central to efforts to understand and detect astrophysical gravitational wave sources within the Simulations of eXtreme Spacetime (SXS) collaboration, with the ultimate aim of providing the first strong field probe of the Einstein field equation.

In a series of included papers, we demonstrate stability, convergence, and gauge invariance. We also demonstrate agreement between Spectral CCE and the legacy Pitt null code, while achieving a factor of 200 improvement in computational efficiency.

Spectral CCE represents a significant computational advance. It is the foundation upon which further capability will be built, specifically enabling the complete calculation of junk-free, gauge-free, and physically valid waveform data on the fly within SpEC.

The Molecular Basis of Lysine Acetylation: Addition, Removal, and Recognition

Acetyltransferases and deacetylases catalyze the addition and removal, respectively, of acetyl groups to the epsilon-amino group of protein lysine residues. This modification can affect the function of a protein through several means, including the recruitment of specific binding partners called acetyl-lysine readers. Acetyltransferases, deacetylases, and acetyl-lysine readers have emerged as crucial regulators of biological processes and prominent targets for the treatment of human disease. This work describes a combination of structural, biochemical, biophysical, cell-biological, and organismal studies undertaken on a set of proteins that cumulatively include all steps of the acetylation process: the acetyltransferase MEC-17, the deacetylase SIRT1, and the acetyl-lysine reader DPF2. Tubulin acetylation by MEC-17 is associated with stable, long-lived microtubule structures. We determined the crystal structure of the catalytic domain of human MEC-17 in complex with the cofactor acetyl-CoA. The structure in combination with an extensive enzymatic analysis of MEC-17 mutants identified residues for cofactor and substrate recognition and activity. A large, evolutionarily conserved hydrophobic surface patch distal to the active site was shown to be necessary for catalysis, suggesting that specificity is achieved by interactions with the alpha-tubulin substrate that extend outside of the modified surface loop. Experiments in C. elegans showed that while MEC-17 is required for touch sensitivity, MEC-17 enzymatic activity is dispensible for this behavior. SIRT1 deacetylates a wide range of substrates, including p53, NF-kappaB, FOXO transcription factors, and PGC-1-alpha, with roles in cellular processes ranging from energy metabolism to cell survival. SIRT1 activity is uniquely controlled by a C-terminal regulatory segment (CTR). Here we present crystal structures of the catalytic domain of human SIRT1 in complex with the CTR in an apo form and in complex with a cofactor and a pseudo-substrate peptide. The catalytic domain adopts the canonical sirtuin fold. The CTR forms a beta-hairpin structure that complements the beta-sheet of the NAD^+-binding domain, covering an essentially invariant, hydrophobic surface. A comparison of the apo and cofactor bound structures revealed conformational changes throughout catalysis, including a rotation of a smaller subdomain with respect to the larger NAD^+-binding subdomain. A biochemical analysis identified key residues in the active site, an inhibitory role for the CTR, and distinct structural features of the CTR that mediate binding and inhibition of the SIRT1 catalytic domain. DPF2 represses myeloid differentiation in acute myelogenous leukemia. Finally, we solved the crystal structure of the tandem PHD domain of human DPF2. We showed that DPF2 preferentially binds H3 tail peptides acetylated at Lys14, and binds H4 tail peptides with no preference for acetylation state. Through a structural and mutational analysis we identify the molecular basis of histone recognition. We propose a model for the role of DPF2 in AML and identify the DPF2 tandem PHD finger domain as a promising novel target for anti-leukemia therapeutics.

Essays in revealed preference theory and behavioral economics

Time, risk, and attention are all integral to economic decision making. The aim of this work is to understand those key components of decision making using a variety of approaches: providing axiomatic characterizations to investigate time discounting, generating measures of visual attention to infer consumers' intentions, and examining data from unique field settings.

Chapter 2, co-authored with Federico Echenique and Kota Saito, presents the first revealed-preference characterizations of exponentially-discounted utility model and its generalizations. My characterizations provide non-parametric revealed-preference tests. I apply the tests to data from a recent experiment, and find that the axiomatization delivers new insights on a dataset that had been analyzed by traditional parametric methods.

Chapter 3, co-authored with Min Jeong Kang and Colin Camerer, investigates whether "pre-choice" measures of visual attention improve in prediction of consumers' purchase intentions. We measure participants' visual attention using eyetracking or mousetracking while they make hypothetical as well as real purchase decisions. I find that different patterns of visual attention are associated with hypothetical and real decisions. I then demonstrate that including information on visual attention improves prediction of purchase decisions when attention is measured with mousetracking.

Chapter 4 investigates individuals' attitudes towards risk in a high-stakes environment using data from a TV game show, Jeopardy!. I first quantify players' subjective beliefs about answering questions correctly. Using those beliefs in estimation, I find that the representative player is risk averse. I then find that trailing players tend to wager more than "folk" strategies that are known among the community of contestants and fans, and this tendency is related to their confidence. I also find gender differences: male players take more risk than female players, and even more so when they are competing against two other male players.

Chapter 5, co-authored with Colin Camerer, investigates the dynamics of the favorite-longshot bias (FLB) using data on horse race betting from an online exchange that allows bettors to trade "in-play." I find that probabilistic forecasts implied by market prices before start of the races are well-calibrated, but the degree of FLB increases significantly as the events approach toward the end.

Upconversion and fluorescence spectral studies of Er3+/Yb3+-codoped Bi(2)Q(3)-GeO2-Ga(2)Q(3)-Na2O glasses

The absorption spectra and upconversion fluorescence spectra of Er3+/-Yb3+-codoped natrium-gallium-germanium-bismuth glasses are measured and investigated. The intense green (533 and 549 nm) and red (672 nm) emission bands were simultaneously observed at room temperature. The quadratic dependence of the green and red emission on excitation power indicates that the two-photon absorption processes occur. The influence of Ga2C3 on upconversion intensity is investigated. The intensity of green emissions increases slowly with increasing Ga2O3 content, while the intensity of red emission increases significantly. The possible upconversion mechanisms for these glasses have also been discussed. The maximum phonon energy of the glasses determined based on the infrared (IR) spectral analysis is as low as 740 cm(-1). The studies indicate that Bi2O3-GeO2-Ga2O3-Na2O glasses may be potential materials for developing upconversion optical devices (c) 2006 Published by Elsevier B.V.

Sobre a possibilidade de um conteúdo estreito numa teoria bi-dimensional epistêmica

O bi-dimensionalismo epistêmico é a tese de que os estados mentais de um indivíduo tem uma dupla divisão, tendo, então, um conteúdo amplo e um conteúdo estreito. Um conteúdo amplo é aquele cuja determinação depende em parte de propriedades extrínsecas ao sujeito: ou seja, é aquele que possui relação com o mundo externo ao sujeito, seja físico ou social. Já o conteúdo estreito é o conteúdo plenamente determinado por propriedades intrísecas ao sujeito, sem precisar recorrer a nada externo. Este conteúdo estreito será, de acordo com o bi-dimensionalismo de Jackson e de Chalmers, o conteúdo representativo de um estado mental, dado através de descrições sobre aquilo que o sujeito sabe e acredita sobre o mundo ao seu redor. O objetivo desta dissertação ao tratar sobre esta forma de bi-dimensionalismo é o de apresentá-lo como uma possível resposta para dois problemas gerados pela afirmação externalista de que nomes próprios e termos de tipos naturais são designadores rígidos e pela afirmação de que todo conteúdo de um estado mental é amplo. Estes dois problemas são a incompatibilidade do conteúdo amplo com o acesso privilegiado e a sua incompatibilidade com o papel explicatório que estados mentais intencionais parecem ter em relação aos comportamentos de um indivíduo, pois, se os indivíduos não possuem um acesso privilegiado aos conteúdos dos seus estados mentais, tal conteúdo amplo não poderá ser visto como sendo um causalmente relevante para os seus comportamentos. Contudo, os argumentos apresentados pelo externalismo semântico parecem ainda convincentes demais para considerar tais consequências como sendo um bom motivo para se abandonar a tese externalista. Além disso, vários exemplos do funcionamento da linguagem (como os casos do uso de nomes próprios e termos de espécies naturais) parecem indicar que o externalismo semântico é correto. Assim, neste trabalho, analisarei a teoria bi-dimensional à luz das afirmações externalistas sobre o significado e sobre a individuação dos conteúdos dos estados mentais, ou seja, como podendo ser uma teoria que, além de ser uma capaz de fornecer uma resposta viável para estes dois problemas, é também compatível com o conteúdo amplo da forma como é afirmado pelo externalismo.

Self-Organized Criticality, Plasticity and Sensorimotor Coupling. Explorations with a Neurorobotic Model in a Behavioural Preference Task

During the last two decades, analysis of 1/f noise in cognitive science has led to a considerable progress in the way we understand the organization of our mental life. However, there is still a lack of specific models providing explanations of how 1/f noise is generated in coupled brain-body-environment systems, since existing models and experiments typically target either externally observable behaviour or isolated neuronal systems but do not address the interplay between neuronal mechanisms and sensorimotor dynamics. We present a conceptual model of a minimal neurorobotic agent solving a behavioural task that makes it possible to relate mechanistic (neurodynamic) and behavioural levels of description. The model consists of a simulated robot controlled by a network of Kuramoto oscillators with homeostatic plasticity and the ability to develop behavioural preferences mediated by sensorimotor patterns. With only three oscillators, this simple model displays self-organized criticality in the form of robust 1/f noise and a wide multifractal spectrum. We show that the emergence of self-organized criticality and 1/f noise in our model is the result of three simultaneous conditions: a) non-linear interaction dynamics capable of generating stable collective patterns, b) internal plastic mechanisms modulating the sensorimotor flows, and c) strong sensorimotor coupling with the environment that induces transient metastable neurodynamic regimes. We carry out a number of experiments to show that both synaptic plasticity and strong sensorimotor coupling play a necessary role, as constituents of self-organized criticality, in the generation of 1/f noise. The experiments also shown to be useful to test the robustness of 1/f scaling comparing the results of different techniques. We finally discuss the role of conceptual models as mediators between nomothetic and mechanistic models and how they can inform future experimental research where self-organized critically includes sensorimotor coupling among the essential interaction-dominant process giving rise to 1/f noise.

Effects of melting temperature on the broadband infrared luminescence of bi-doped and Bi/Dy co-doped chalcohalide glasses

Bismuth (Bi)-doped and Bi/Dy co-doped chalcohalide glasses are investigated as promising materials for amplifiers in optical communication. The samples synthesized at lower melting temperatures (MTs) are characterized by more intensified infrared emissions. With respect to the redox process of a liquid mixture at different MTs, we attribute an emission at 1230 nm to low-valent Bi ions. The lower MT favors the formation of LVB ions, i.e. Bi+ or Bi2+, while the higher MT promotes the production of higher-valent Bi ions Bi3+. An enhanced broadband infrared luminescence with the full-width at half-maximum over 200 nm is achieved from the present Bi/Dy co-doped chalcohalide glasses.

Ultrabroad infrared luminescences from Bi-doped alkaline earth metal germanate glasses

We report on ultrabroad infrared (IR) luminescences covering the 1000-1700-nm wavelength region, from Bi-doped 75GeO(2) 20RO-5Al(2)O(3) 1B(2)O(3) (R = Sr, Ca, and Mg) glasses. The full width at half-maximum of the IR luminescences excited at 980 nm increases (315 -> 440 -> 510 nm) with the change of alkaline earth metal (Mg2+ -> Ca2+ -> Sr2+). The fluorescence lifetime of the glass samples is 1725, 157, and 264 mu s when R is Sr, Ca, and Mg, respectively. These materials may be promising candidates for broad-band fiber amplifiers and tunable laser resources.

Ultrabroad infrared luminescence from Bi-doped aluminogermanate glasses

We report ultrabroad infrared luminescence from Bi-doped aluminogermanate glasses. The infrared luminescence almost covers the whole low loss wavelength region (1200-1650 nm) of silica glass fiber when excited by a diode laser at 980 nm. The full width at half maximum (FWHM) of the luminescence is 510 nm. The luminescence peak can be divided into three Gaussian peaks, and the fluorescence lifetime of the three emissions are 297 mu s, 470 mu s and 1725 mu s, respectively. These fluorescence properties indicate that the glasses are promising material for broadband optical amplifiers. (C) 2007 Elsevier Ltd. All rights reserved.

Effects of thermal treatment on broadband near-infrared emission from Bi-doped chalcohalide glasses

GeGaSKBr glass with Bi ions as emission centers were fabricated. An intense emission centered at around 1230 nm with the width of more than 175 nm was observed by 808 nm photo-excitation of the glass. Lower quenching rate and thermal treatment promote micro-crystallization process, thus strengthening the emission. Crown Copyright (c) 2008 Published by Elsevier Ltd. All rights reserved.