An efficient Monte Carlo method for calculating ab initio transition state theory reaction rates in solution

In this article, we propose an efficient method for sampling the relevant state space in condensed phase reactions. In the present method, the reaction is described by solving the electronic Schr\"{o}dinger equation for the solute atoms in the presence of explicit solvent molecules. The sampling algorithm uses a molecular mechanics guiding potential in combination with simulated tempering ideas and allows thorough exploration of the solvent state space in the context of an ab initio calculation even when the dielectric relaxation time of the solvent is long. The method is applied to the study of the double proton transfer reaction that takes place between a molecule of acetic acid and a molecule of methanol in tetrahydrofuran. It is demonstrated that calculations of rates of chemical transformations occurring in solvents of medium polarity can be performed with an increase in the cpu time of factors ranging from 4 to 15 with respect to gas-phase calculations.Comment: 15 pages, 9 figures. To appear in J. Chem. Phy

Electrophysiological measures of flexible attentional control and visual working memory maintenance

Top-down attentional control can be used to both guide attention toward and away from items according to their goal relevance. When given a feature-based cue, such as the colour of an upcoming target, individuals can allocate attention and memory resources according to the item’s priority. This distribution of resources is continuous, such that the amount that an item receives is dependent on its likelihood of being probed. However, top-down goals are often challenged by bottom-up stimulus salience of distractors. One’s ability to avoid attentional capture by distractors is limited by attentional control over bottom-up biases. In particular, individuals with anxiety have attentional biases toward both neutral and threatening distractors, leading to unnecessary storage of distractors in visual working memory (VWM). Using electrophysiology, it is possible to study the time course of these attentional processes to gain a better understanding of how attentional selection, suppression, and VWM maintenance relate to attentional control. The present thesis explores the event-related potential (ERP) correlates and time course of flexible attentional control, as well as how individual differences in anxiety limit this ability. In the first study, I used positive and negative feature-based cues to demonstrate that attentional selection occurs earlier when guided by target information than distractor information. Additionally, it was found that greater anxiety resulted in selection of the salient distractor, demonstrating that anxiety compromises early attentional control. For the second study, I further examined deficits in attentional control in anxiety. Here, it was demonstrated that individuals with high anxiety had early selection of threat-related distractors, whereas individuals with low anxiety could pro-actively suppress them. Interestingly, this effect did not carry over to VWM maintenance, suggesting that deficits in early attentional control do not necessarily result in poor memory filtering. In the final study, I examined the link between continuous attentional allocation and VWM maintenance, finding that individuals use priority information to flexibly select and filter information from VWM. Together, in this thesis I propose that attentional control over selection, suppression, and VWM filtering processes is flexible, time-dependent, and driven both by external cues and internal biases related to individual differences in anxiety

A Textile Narrative Through the Eye of a Camera/Through the Eye of a Needle

When I began to research needlework in the early 1980s the Library of Congress Catalogue directed me not to needlework, or even embroidery, but to the letter “W” – Women’s Work – the first step in a long and tangled journey. When I recently came across an 1890s photograph of a Canadian woman and her embroidery by Hannah Maynard all I had to do was turn to Google to be directed to the BC Archives. My first reaction was glee – my second dismay – with 300+ hits how could I not know Mrs. Maynard? To date, Hannah Maynard (1834-1918), remains a relative unknown. Her work came under scrutiny in the late 1970s – for what one author described as its “freakish, goofy, and often grotesque quality” and the designation “eccentric” continues to be used in describing both the artist and her photographs. Most of these references are limited to books on Canadian photography. However, eccentric suggests that she deviated from conventional practices or patterns and as a textile historian I disagree. There is a pattern here. It is my intention to show that Maynard’s photographs, with their repeated images and lavish embellishments, are closely linked to contemporary needlework – fashionable domestic embroidery and crazy quilts – and to suggest that it was this familiarity with the decorative and the domestic that allowed Hannah Maynard to move between the private and public spheres. While the British Columbia Archives in Victoria hold a large collection of Maynard negatives and several original photographs there are few business or personal documents to provide insights into the life and work of this artist. Of the images themselves, the majority fulfil contemporary expectations regarding portraiture and photography. I have identified these as her public images and include the studio portraits, group portraits, documented events, and landscapes. That these were truly in the public domain is underscored by an American journal of 1887 which proposed that “Photographers would not lose anything were they to send to [Mrs. Maynard] and secure a set of these views, and frame and hang them in their reception rooms…

Quantum Criticality at the Origin of Life

Why life persists at the edge of chaos is a question at the very heart of evolution. Here we show that molecules taking part in biochemical processes from small molecules to proteins are critical quantum mechanically. Electronic Hamiltonians of biomolecules are tuned exactly to the critical point of the metal-insulator transition separating the Anderson localized insulator phase from the conducting disordered metal phase. Using tools from Random Matrix Theory we confirm that the energy level statistics of these biomolecules show the universal transitional distribution of the metal-insulator critical point and the wave functions are multifractals in accordance with the theory of Anderson transitions. The findings point to the existence of a universal mechanism of charge transport in living matter. The revealed bio-conductor material is neither a metal nor an insulator but a new quantum critical material which can exist only in highly evolved systems and has unique material properties.Comment: 10 pages, 4 figure

Measuring association with recursive rank binning

Pairwise measures of dependence are a common tool to map data in the early stages of analysis with several modern examples based on maximized partitions of the pairwise sample space. Following a short survey of modern measures of dependence, we introduce a new measure which recursively splits the ranks of a pair of variables to partition the sample space and computes the $\chi^2$ statistic on the resulting bins. Splitting logic is detailed for splits maximizing a score function and randomly selected splits. Simulations indicate that random splitting produces a statistic conservatively approximated by the $\chi^2$ distribution without a loss of power to detect numerous different data patterns compared to maximized binning. Though it seems to add no power to detect dependence, maximized recursive binning is shown to produce a natural visualization of the data and the measure. Applying maximized recursive rank binning to S&P 500 constituent data suggests the automatic detection of tail dependence.Comment: 59 pages, 22 figure

Optimal Structured Matrix Approximation for Robustness to Incomplete Biosequence Data

We propose a general method for optimally approximating an arbitrary matrix $\mathbf{M}$ by a structured matrix $\mathbf{T}$ (circulant, Toeplitz/Hankel, etc.) and examine its use for estimating the spectra of genomic linkage disequilibrium matrices. This application is prototypical of a variety of genomic and proteomic problems that demand robustness to incomplete biosequence information. We perform a simulation study and corroborative test of our method using real genomic data from the Mouse Genome Database. The results confirm the predicted utility of the method and provide strong evidence of its potential value to a wide range of bioinformatics applications. Our optimal general matrix approximation method is expected to be of independent interest to an even broader range of applications in applied mathematics and engineering

Balancing central and marginal rejection when combining independent significance tests

A common approach to evaluating the significance of a collection of $p$-values combines them with a pooling function, in particular when the original data are not available. These pooled $p$-values convert a sample of $p$-values into a single number which behaves like a univariate $p$-value. To clarify discussion of these functions, a telescoping series of alternative hypotheses are introduced that communicate the strength and prevalence of non-null evidence in the $p$-values before general pooling formulae are discussed. A pattern noticed in the UMP pooled $p$-value for a particular alternative motivates the definition and discussion of central and marginal rejection levels at $\alpha$. It is proven that central rejection is always greater than or equal to marginal rejection, motivating a quotient to measure the balance between the two for pooled $p$-values. A combining function based on the $\chi^2_{\kappa}$ quantile transformation is proposed to control this quotient and shown to be robust to mis-specified parameters relative to the UMP. Different powers for different parameter settings motivate a map of plausible alternatives based on where this pooled $p$-value is minimized.Comment: 55 page, 18 figures, public technical repor