Ion beam modification and analysis of metal/polymer bi-layer thin films

A set of varying-thickness Au-films were thermally evaporated onto poly(styrene-co-acrylonitrile) thin film surfaces. The Au/PSA bi-layer targets were then implanted with 50 keV N+ ions to a fluence of 1 × 1016 ions/cm2 to promote metal-to-polymer adhesion and to enhance their mechanical and electrical performance. Electrical conductivity measurements of the implanted Au/PSA thin films showed a sharp percolation behavior versus the pre-implant Au-film thickness with a percolation threshold near the nominal thickness of 44 Å. The electrical conductivity results are discussed along with the film microstructure and the elemental diffusion/mixing within the Au/PSA interface obtained by scanning electron microscopy (SEM) and ion beam analysis techniques (RBS and ERD).

Frequency and temporal effects in linear optical quantum computing

Typically linear optical quantum computing (LOQC) models assume that all input photons are completely indistinguishable. In practice there will inevitably be nonidealities associated with the photons and the experimental setup which will introduce a degree of distinguishability between photons. We consider a nondeterministic optical controlled-NOT gate, a fundamental LOQC gate, and examine the effect of temporal and spectral distinguishability on its operation. We also consider the effect of utilizing nonideal photon counters, which have finite bandwidth and time response.

Novel mitochondrial gene content and gene arrangement indicate illegitimate inter-mtDNA recombination in the chigger mite, Leptotrombidium pallidum

To better understand the evolution of mitochondrial (mt) genomes in the Acari (mites and ticks), we sequenced the mt genome of the chigger mite, Leptotrombidium pallidum (Arthropoda: Acari: Acariformes). This genome is highly rearranged relative to that of the hypothetical ancestor of the arthropods and the other species of Acari studied. The mt genome of L. pallidum has two genes for large subunit rRNA, a pseudogene for small subunit rRNA, and four nearly identical large noncoding regions. Nineteen of the 22 tRNAs encoded by this genome apparently lack either a T-arm or a D-arm. Further, the mt genome of L. pallidum has two distantly separated sections with identical sequences but opposite orientations of transcription. This arrangement cannot be accounted for by homologous recombination or by previously known mechanisms of mt gene rearrangement. The most plausible explanation for the origin of this arrangement is illegitimate inter-mtDNA recombination, which has not been reported previously in animals. In light of the evidence from previous experiments on recombination in nuclear and mt genomes of animals, we propose a model of illegitimate inter-mtDNA recombination to account for the novel gene content and gene arrangement in the mt genome of L. pallidum.

Evaluation and comparison of mammalian subcellular localization prediction methods

Background: Determination of the subcellular location of a protein is essential to understanding its biochemical function. This information can provide insight into the function of hypothetical or novel proteins. These data are difficult to obtain experimentally but have become especially important since many whole genome sequencing projects have been finished and many resulting protein sequences are still lacking detailed functional information. In order to address this paucity of data, many computational prediction methods have been developed. However, these methods have varying levels of accuracy and perform differently based on the sequences that are presented to the underlying algorithm. It is therefore useful to compare these methods and monitor their performance. Results: In order to perform a comprehensive survey of prediction methods, we selected only methods that accepted large batches of protein sequences, were publicly available, and were able to predict localization to at least nine of the major subcellular locations (nucleus, cytosol, mitochondrion, extracellular region, plasma membrane, Golgi apparatus, endoplasmic reticulum (ER), peroxisome, and lysosome). The selected methods were CELLO, MultiLoc, Proteome Analyst, pTarget and WoLF PSORT. These methods were evaluated using 3763 mouse proteins from SwissProt that represent the source of the training sets used in development of the individual methods. In addition, an independent evaluation set of 2145 mouse proteins from LOCATE with a bias towards the subcellular localization underrepresented in SwissProt was used. The sensitivity and specificity were calculated for each method and compared to a theoretical value based on what might be observed by random chance. Conclusion: No individual method had a sufficient level of sensitivity across both evaluation sets that would enable reliable application to hypothetical proteins. All methods showed lower performance on the LOCATE dataset and variable performance on individual subcellular localizations was observed. Proteins localized to the secretory pathway were the most difficult to predict, while nuclear and extracellular proteins were predicted with the highest sensitivity.

Vertical and horizontal scope economies in the regulated US electricity power industry

This paper investigates vertical economies between generation and distribution of electric power, and horizontal economies between different types of power generation in the U.S. electric utility industry. Our quadratic cost function model includes three generation output measures (hydro, nuclear and fossil fuels), which allows us to analyze the effect that generation mix has on vertical economies. Our results provide (sample mean) estimates of vertical economies of 8.1% and horizontal economies of 5.4%. An extensive sensitivity analysis is used to show how the scope measures vary across alternative model specifications and firm types. © 2012 Blackwell Publishing Ltd and the Editorial Board of The Journal of Industrial Economics.

Measuring economies of horizontal and vertical integration in the US electric power industry:how costly is unbundling?

This research employs econometric analysis on a cross section of American electricity companies in order to study the cost implications associated with unbundling the operations of integrated companies into vertically and/or horizontally separated companies. Focusing on the representative sample average firm, we find that complete horizontal and vertical disintegration resulting in the creation of separate nuclear, conventional, and hydro electric generation companies as well as a separate firm distributing power to final consumers, results in a statistically significant 13.5 percent increase in costs. Maintaining a horizontally integrated generator producing nuclear, conventional, and hydro electric generation while imposing vertical separation by creating a stand alone distribution company, results in a lower but still substantial and statistically significant cost penalty amounting to an 8.1 % increase in costs relative to a fully integrated structure. As these results imply that a vertically separated but horizontally integrated generation firm would need to reduce the costs of generation by 11% just to recoup the cost increases associated with vertical separation, even the costs associated with just vertical unbundling are quite substantial. Our paper is also the first academic paper we are aware of that systematically considers the impact of generation mix on vertical, horizontal, and overall scope economies. As a result, we are able to demonstrate that the estimated cost of unbundling in the electricity sector is substantially influenced by generation mix. Thus, for example, we find evidence of strong vertical integration economies between nuclear and conventional generation, but little evidence for vertical integration benefits between hydro generation and the distribution of power. In contrast, we find strong evidence suggesting the presence of substantial horizontal integration economies associated with the joint production of hydro generation with nuclear and/or conventional fossil fuel generation. These results are significant because they indicate that the cost of unbundling the electricity sector will differ substantially in different systems, meaning that a blanket regulatory policy with regard to the appropriateness of vertical and horizontal unbundling is likely to be inappropriate.

The adaptive response of humans to exercise: Impact of exercise intensity, fibre-type specific responses and molecular patterns of response

In an attempt to improve the current understanding of the adaptive response to exercise in humans, this dissertation performed a series of studies designed to examine the impact of training intensity and mode on aerobic capacity and performance, fibre-type specific adaptations to training, and individual patterns of response across molecular, morphological and genetic factors. Project #1 determined that training intensity, session dose, baseline VO2max and total training volume do not influence the magnitude of change in VO2max by performing a meta-regression, and meta-analysis of 28 different studies. The intensity of training had no effect on the magnitude of increase in maximal oxygen uptake in young healthy participants, but similar adaptations were achieved with lower training doses following high intensity training. Project # 2 determined the acute molecular response, and training-induced adaptations in aerobic performance, aerobic capacity and muscle phenotype following high-intensity interval training (HIT) or endurance exercise (END). The acute molecular response (fibre recruitment and signal activation) and training-induced adaptations in aerobic capacity, aerobic performance, and muscle phenotype were similar following HIT and END. Project # 3 examined the impact of baseline muscle morphology and molecular characteristics on the training response, and if muscle adaptations are coordinated. The muscle phenotype of individuals who experience the largest improvements (high responders) were lower before training for some muscle characteristics and molecular adaptations were coordinated within individual participants. Project # 4 examined the impact of 2 different intensities of HIT on the expression of nuclear and mitochondrial encoded genes targeted by PGC-1α. A systematic upregulation of nuclear and mitochondrial encoded genes was not present in the early recovery period following acute HIT, but the expression of mitochondrial genes were coordinated at an individual level. Collectively, results from the current dissertation contribute to our understanding of the molecular mechanisms influencing skeletal muscle and whole-body adaptive responses to acute exercise and training in humans.

Maternal and paternal growth regulatory factor expression in hybrid sunfish.

Unidirectional hybridization between bluegill (Lepomis macrochirus) and pumpkinseed (L. gibbosus) sunfish enables researchers to explore the relative expression of paternal and maternal alleles in hybrids. Past studies have found that the metabolic dysfunction in bluegill-pumpkinseed hybrids may be due to incompatibilities between nuclear and mitochondrial genomes. However, the consequences of hybridization on body size and muscle growth have not been examined. This topic is particularly interesting because hybrids grow larger than parentals despite the fact that they are often sired by smaller, precociously mature bluegills. In order to improve our understanding of growth dynamics in hybrid sunfish, I conducted real-time quantitative PCR using species-specific primers on the white muscle tissue of bluegills, pumpkinseeds, and hybrids collected from Lake Opinicon, ON. Five growth factors that have been linked to muscle growth and body size demonstrated similar expression for maternal and paternal alleles. While about half of the hybrids showed the same pattern with myogenin, about half showed very low levels of mRNA for the paternal (bluegill) gene. While this did not explain the heterosis seen in hybrids, it may explain the small body phenotype of the cuckholding bluegill males. I explored the upstream genetic structure of bluegill myogenin and established that four alleles exist within the population. Furthermore, I uncovered a relationship in hybrids between the proximal promoter/ 5’ UTR of myogenin and its transcript level. I found that the hybrids demonstrating low paternal myogenin expression unfailingly possessed A3 or A4 alleles, but future studies will be needed to reveal the molecular links between the genotype and the growth phenotype. A similar genotype-phenotype association was not obvious in parentals, even those that were homozygous for these alleles. Whether this relationship can provide insight into the genetic determinants of bluegill alternative mating strategies has yet to be determined.

Genetic analyses reveal high levels of seed and pollen flow in hawthorn (Crataegus monogyna Jacq.), a key component of hedgerows

Hedgerows represent important components of agri-environment landscapes that are increasingly coming under threat from climate change, emergent diseases, invasive species and land use change. Given that population genetic data can be used to inform best-practice management strategies for woodland and hedgerow tree species, we carried out a study on hawthorn (Crataegus monogyna Jacq.), a key component of hedgerows, on a regional basis using a combination of nuclear and chloroplast microsatellite markers. We found that levels of genetic diversity were high and comparable to, or slightly higher than, other tree species from the same region. Levels of population differentiation for both sets of markers, however, were extremely low, suggesting extensive gene flow via both seed and pollen. These findings suggest that a holistic approach to woodland management, one which does not necessarily rely on the concept of “seed zones” previously suggested, but which also takes into account populations with high and/or rare chloroplast (i.e. seed-specific) genetic variation, might be the best approach to restocking and replanting.

Energy levels and radiative rates for Cr-like Cu VI and Zn VII

Energy levels and radiative rates (. A-values) for transitions in Cr-like Cu VI and Zn VII are reported. These data are determined in the quasi-relativistic approach (QR), by employing a very large configuration interaction (CI) expansion which is highly important for these ions. No radiative rates are available in the literature to compare with our results, but our calculated energies are in close agreement with those compiled by NIST and other available theoretical data, for a majority of the levels. The A-values (and resultant lifetimes) are listed for all significantly contributing E1, E2 and M1 radiative transitions among the energetically lowest 322 levels of each ion.

Energy levels and radiative rates for transitions in Cr-like Co IV and Ni V

We report calculations of energy levels and radiative rates (A-values) for transitions in Cr-like Co IV and Ni V. The quasi-relativistic Hartree-Fock (QRHF) code is adopted for calculating the data although grasp (general-purpose relativistic atomic structure package) and flexible atomic code (fac) have also been employed for comparison purposes. No radiative rates are available in the literature to compare with our results, but our calculated energies are in close agreement with those compiled by NIST for a majority of the levels. However, there are discrepancies for a few levels of up to 3%. The A-values are listed for all significantly contributing E1, E2 and M1 transitions, and the corresponding lifetimes reported, although unfortunately no previous theoretical or experimental results exist to compare with our data.

Radiative rates for E1, E2, M1, and M2 transitions in S-like to F-like tungsten ions (W LIX to W LXVI)

Calculations of energy levels, radiative rates and lifetimes are reported for eight ions of tungsten, i.e. S-like (W LIX) to F-like (W LXVI). A large number of levels have been considered for each ion and extensive configuration interaction has been included among a range of configurations. For the calculations, the general-purpose relativistic atomic structure package (. grasp) has been adopted, and radiative rates (as well as oscillator strengths and line strengths) are listed for all E1, E2, M1, and M2 transitions of the ions. Comparisons have been made with earlier available experimental and theoretical energies, although these are limited to only a few levels for most ions. Therefore for additional accuracy assessments, particularly for energy levels, analogous calculations have been performed with the flexible atomic code (. fac).

Radiative rates for E1, E2, M1, and M2 transitions in Br-like ions with 43≤Z≤50

Energies and lifetimes are reported for the eight Br-like ions with 43≤Z≤50, namely Tc IX, Ru X, Rh XI, Pd XII, Ag XIII, Cd XIV, In XV, and Sn XVI. Results are listed for the lowest 375 levels, which mostly belong to the 4s²4p⁵, 4s²4p⁴4ℓ, 4s4p⁶,4s²4p⁴5ℓ, 4s²4p³4d², 4s4p⁵4ℓ, and 4s4p⁵5ℓ configurations. Extensive configuration interaction among 39 configurations (generating 3990 levels) has been considered and the general-purpose relativistic atomic structure package (grasp) has been adopted for the calculations. Radiative rates are listed for all E1, E2, M1, and M2 transitions involving the lowest 375 levels. Previous experimental and theoretical energies are available for only a few levels of three, namely Ru X, Rh XI and Pd XII. Differences with the measured energies are up to 4% but the present results are an improvement (by up to 0.3 Ryd) in comparison to other recently reported theoretical data. Similarly for radiative rates and lifetimes, prior results are limited to those involving only 31 levels of the 4s²4p⁵, 4s²4p⁴4d, and 4s4p⁶ configurations for the last four ions. Moreover, there are generally no discrepancies with our results, although the larger calculations reported here differ by up to two orders of magnitude for a few transitions.

Radiative rates for E1, E2, M1, and M2 transitions in F-like ions with 37≤Z≤53

Calculations of energy levels, radiative rates and lifetimes are reported for 17 F-like ions with 37≤Z≤53. For brevity, results are only presented among the lowest 113 levels of the 2s²2p⁵, 2s2p⁶, 2s²2p⁴3ℓ, 2s2p⁵3ℓ, and 2p⁶3ℓ configurations, although the calculations have been performed for up to 501 levels in each ion. The general-purpose relativistic atomic structure package (grasp) has been adopted for the calculations, and radiative rates (along with oscillator strengths and line strengths) are listed for all E1, E2, M1, and M2 transitions of the ions. Comparisons are made with earlier available experimental and theoretical energies, although these are limited to only a few levels for most ions. Therefore for additional accuracy assessments, particularly for energy levels, analogous calculations have been performed with the Flexible Atomic Code (fac), for up to 72 259 levels. Limited previous results are available for radiative rates for comparison purposes, and no large discrepancy is observed for any transition and/or ion.