Geometry Optimization of Crystals by the Quasi-Independent Curvilinear Coordinate Approximation

The quasi-independent curvilinear coordinate approximation (QUICCA) method [K. N\'emeth and M. Challacombe, J. Chem. Phys. {\bf 121}, 2877, (2004)] is extended to the optimization of crystal structures. We demonstrate that QUICCA is valid under periodic boundary conditions, enabling simultaneous relaxation of the lattice and atomic coordinates, as illustrated by tight optimization of polyethylene, hexagonal boron-nitride, a (10,0) carbon-nanotube, hexagonal ice, quartz and sulfur at the $\Gamma$-point RPBE/STO-3G level of theory.Comment: Submitted to Journal of Chemical Physics on 7/7/0

Structural Evidence for the Tetrameric Assembly of Chemokine CCL11 and the Glycosaminoglycan Arixtra™.

Understanding chemokine interactions with glycosaminoglycans (GAG) is critical as these interactions have been linked to a number of inflammatory medical conditions, such as arthritis and asthma. To better characterize in vivo protein function, comprehensive knowledge of multimeric species, formed by chemokines under native conditions, is necessary. Herein is the first report of a tetrameric assembly of the human chemokine CCL11, which was shown bound to the GAG Arixtra™. Isothermal titration calorimetry data indicated that CCL11 interacts with Arixtra, and ion mobility mass spectrometry (IM-MS) was used to identify ions corresponding to the CCL11 tetrameric species bound to Arixtra. Collisional cross sections (CCS) of the CCL11 tetramer-Arixtra noncovalent complex were compared to theoretical CCS values calculated using a preliminary structure of the complex deduced using X-ray crystallography. Experimental CCS values were in agreement with theoretical values, strengthening the IM-MS evidence for the formation of the noncovalent complex. Tandem mass spectrometry data of the complex indicated that the tetramer-GAG complex dissociates into a monomer and a trimer-GAG species, suggesting that two CC-like dimers are bridged by Arixtra. As development of chemokine inhibitors is of utmost importance to treatment of medical inflammatory conditions, these results provide vital insights into chemokine-GAG interactions

Calculation of disease dynamics in a population of households

Early mathematical representations of infectious disease dynamics assumed a single, large, homogeneously mixing population. Over the past decade there has been growing interest in models consisting of multiple smaller subpopulations (households, workplaces, schools, communities), with the natural assumption of strong homogeneous mixing within each subpopulation, and weaker transmission between subpopulations. Here we consider a model of SIRS (susceptible-infectious-recovered-suscep​tible) infection dynamics in a very large (assumed infinite) population of households, with the simplifying assumption that each household is of the same size (although all methods may be extended to a population with a heterogeneous distribution of household sizes). For this households model we present efficient methods for studying several quantities of epidemiological interest: (i) the threshold for invasion; (ii) the early growth rate; (iii) the household offspring distribution; (iv) the endemic prevalence of infection; and (v) the transient dynamics of the process. We utilize these methods to explore a wide region of parameter space appropriate for human infectious diseases. We then extend these results to consider the effects of more realistic gamma-distributed infectious periods. We discuss how all these results differ from standard homogeneous-mixing models and assess the implications for the invasion, transmission and persistence of infection. The computational efficiency of the methodology presented here will hopefully aid in the parameterisation of structured models and in the evaluation of appropriate responses for future disease outbreaks

In-the-wild residual data research and privacy

As the world becomes increasingly dependent on technology, researchers endeavor to understand how technology is used, the impact it has on everyday life and the life-cycle and span of digital information. In doing so, researchers are increasingly gathering `real-world' or `in the wild' residual data, obtained from a variety of sources without the explicit consent of the original owners. This data gathering raises significant concerns regarding privacy, ethics and legislation, as well as practical considerations concerning investigator training, data storage, overall security and disposal. This paper surveys recent studies of residual data gathered in the wild and analyses the challenges that were faced. Taking these insights, the paper presents a compendium of practices for addressing the issues that arise in in the wild residual data research. The practices presented in this paper can be used to critique current projects and assess the feasibility of proposed future research

The Influence and Application of Eastern Philosophy in the Western Musical Tradition

This paper documents my summer research on the philosophy of music. Specifically, my research focused on the connection between the philosopher Arthur Schopenhauer and the composer Richard Wagner, as is evident in the opera Tristan und Isolde. I composed a piece of music for the University of Puget Sound Wind Ensemble attempting to utilize both a more Eastern approach to Schopenhauer\u27s philosophy, relative to Wagner\u27s interpretation, and to incorporate 20th century developments in musical technique, theory and language

‘Our sentiments of sympathy for the late unwarranted, cruel, and barbarous massacre’: The American Jewish response to the Damascus Affair

By looking at four American Jewish meetings that were convened in the United States, this thesis seeks to understand why they would care about a handful of Jews in a faraway land (Damascus). In so doing, it militates against Jacob R. Marcus’ argument (which dominates the historiography) that holds that American Jews felt a special connection to Damascene Jews by virtue of their shared religion. Instead, this thesis argues the American Jewish attempt to rescue the Damascene Jews was informed by prevailing intellectual currents in Western society. A product of the culture of sensibility and Romanticism, American Jews had a heightened sense of sympathy for the well-being of others and an aversion to pain. They believed humans were given certain inviolable rights, including: 1.) The right to a fair trial; 2.) The right to live free of torture; 3.) The right to practice religion without the threat of persecution. They saw the Damascus Affair as an atrocity that flew in the face of universal human rights. Moreover, American Jews believed that the United States was an exponent of republican virtue that set a model to be followed by the rest of the world. They felt America was ordained with a divine duty to protect human rights abroad. According to American Jews, if the United States truly embodied the rights enshrined in the Constitution, it would take meaningful action to end the sufferings of the Damascene Jews. The American Jewry had a special affinity to American exceptionalism because it dovetailed with Jewish particularism. If the American Jews were a chosen people, tasked with spreading the word of God, America was a chosen nation, tasked with spreading representative government. American Jews were not an insular community, cut off from society. They were a perceptive people that bought into ideas that were pervasive in America and Western society, co-opting them to suit their own interest