Seattle University: 1891-1966

A history of Seattle University from its founding in 1891 to its diamond jubilee celebration in 1966, this dissertation traces the physical, academic and administrative growth of the university.https://scholarworks.seattleu.edu/cronin-dissertation/1000/thumbnail.jp

In Silico Prediction of Organ Level Toxicity: Linking Chemistry to Adverse Effects

In silico methods to predict toxicity include the use of (Quantitative) Structure-Activity Relationships ((Q)SARs as well as grouping (category formation) allowing for read-across. A challenging area for in silico modelling is the prediction of chronic toxicity and the No Observed (Adverse) Effect Level (NO(A)EL) in particular. A proposed solution to the prediction of chronic toxicity is to consider organ level effects, as opposed to modelling the NO(A)EL itself. This study has focussed on the use of structural alerts to identify potential liver toxicants. In silico profilers, or groups of structural alerts, were developed based on mechanisms of action and informed by current knowledge of Adverse Outcome Pathways. These profilers are robust and can be coded computationally to allow for prediction. However, they do not cover all mechanisms or modes of liver toxicity and recommendations for the improvement of these approaches are given

Scaling properties of high p_T inclusive hadron production

We analyze the scaling properties of inclusive hadron production in proton-proton and in heavy ion collisions from fixed target to collider energies. At large transverse momentum p_T, the invariant cross section exhibits a power-like behavior Ed^3\sigma/d^3p\propto p_T^{-n} at fixed transverse x, x_T=2p_T/\sqrt{s}, and fixed center-of-mass scattering angle \theta_{cm}. Knowledge of the exponent n allows one to draw conclusions about the production mechanisms of hadrons, which are poorly known, even at high p_T. We find that high-p_T hadrons are produced by different mechanisms at fixed-target and collider energies. For pions, higher-twist subprocesses where the pion is produced directly dominate at fixed target energy, while leading-twist partonic scattering plus fragmentation is the most important mechanism at collider energies. High-p_T baryons on the other hand appear to be produced by higher-twist mechanisms at all available energies. The higher-twist mechanism of direct proton production can be verified experimentally by testing whether high p_T protons are produced as single hadrons without accompanying secondaries. In addition, we find that medium-induced gluon radiation in heavy ion collisions can violate scaling.Comment: 14 pages, 3 figure

Light-Front Holography, Light-Front Wavefunctions, and Novel QCD Phenomena

Light-Front Holography, a remarkable feature of the AdS/CFT correspondence, maps amplitudes in anti-de Sitter (AdS) space to frame-independent light-front wavefunctions of hadrons in physical space-time. The model leads to an effective confining light-front QCD Hamiltonian and a single-variable light-front Schrodinger equation which determines the eigenspectrum and the light-front wavefunctions of hadrons for general spin and orbital angular momentum. The coordinate z in AdS space is identified with a Lorentz-invariant coordinate zeta which measures the separation of the constituents within a hadron at equal light-front time and determines the off-shell dynamics of the bound-state wavefunctions and the fall-off in the invariant mass of the constituents. The soft-wall holographic model, modified by a positive-sign dilaton metric, leads to a remarkable one-parameter description of nonperturbative hadron dynamics -- a semi-classical frame-independent first approximation to the spectra and light-front wavefunctions of meson and baryons. The model predicts a Regge spectrum of linear trajectories with the same slope in the leading orbital angular momentum L of hadrons and the radial quantum number n. The hadron eigensolutions projected on the free Fock basis provides the complete set of valence and non-valence light-front Fock state wavefunctions which describe the hadron's momentum and spin distributions needed to compute measures of hadron structure at the quark and gluon level. The effective confining potential also creates quark- antiquark pairs. The AdS/QCD model can be systematically improved by using its complete orthonormal solutions to diagonalize the full QCD light-front Hamiltonian or by applying the Lippmann-Schwinger method to systematically include the QCD interaction terms. A new perspective on quark and gluon condensates is also presented.Comment: Presented at LIGHTCONE 2011, 23 - 27 May, 2011, Dallas, T

Evading the CKM Hierarchy: Intrinsic Charm in B Decays

We show that the presence of intrinsic charm in the hadrons' light-cone wave functions, even at a few percent level, provides new, competitive decay mechanisms for B decays which are nominally CKM-suppressed. For example, the weak decays of the B-meson to two-body exclusive states consisting of strange plus light hadrons, such as B\to\pi K, are expected to be dominated by penguin contributions since the tree-level b\to s u\bar u decay is CKM suppressed. However, higher Fock states in the B wave function containing charm quark pairs can mediate the decay via a CKM-favored b\to s c\bar c tree-level transition. Such intrinsic charm contributions can be phenomenologically significant. Since they mimic the amplitude structure of ``charming'' penguin contributions, charming penguins need not be penguins at all.Comment: 28 pages, 6 figures, published version. References added, minor change

A critical review of adverse effects to the kidney: mechanisms, data sources and in silico tools to assist prediction

Introduction: The kidney is a major target for toxicity elicited by pharmaceuticals and environmental pollutants. Standard testing which often does not investigate underlying mechanisms has proven not to be an adequate hazard assessment approach. As such, there is an opportunity for the application of computational approaches that utilise multi-scale data based on the Adverse Outcome Pathway (AOP) paradigm, coupled with an understanding of the chemistry underpinning the molecular initiating event (MIE) to provide a deep understanding of how structural fragments of molecules relate to specific mechanisms of nephrotoxicity. The aim of this investigation was to review the current scientific landscape related to computational methods, including mechanistic data, AOPs, publicly available knowledge bases and current in silico models, for the assessment of pharmaceuticals and other chemicals with regard to their potential to elicit nephrotoxicity. A list of over 250 nephrotoxicants enriched with, where possible, mechanistic and AOP-derived understanding was compiled. Expert opinion: Whilst little mechanistic evidence has been translated into AOPs, this review identified a number of data sources of in vitro, in vivo and human data that may assist in the development of in silico models which in turn may shed light on the inter-relationships between nephrotoxicity mechanisms

Heavy quarkonium 2S states in light-front quark model

We study the charmonium 2S states $\psi'$ and $\eta_c'$, and the bottomonium 2S states $\Upsilon'$ and $\eta_b'$, using the light-front quark model and the 2S state wave function of harmonic oscillator as the approximation of the 2S quarkonium wave function. The decay constants, transition form factors and masses of these mesons are calculated and compared with experimental data. Predictions of quantities such as Br$(\psi' \to \gamma \eta_c')$ are made. The 2S wave function may help us learn more about the structure of these heavy quarkonia.Comment: 5 latex pages, final version for journal publicatio

Molecular Fingerprint-Derived Similarity Measures for Toxicological Read-Across: Recommendations for Optimal Use

Computational approaches are increasingly used to predict toxicity, in part due to pressures to find alternatives to animal testing. Read-across is the “new paradigm” which aims to predict toxicity by identifying similar, data rich, source compounds. This assumes that similar molecules tend to exhibit similar activities, i.e. molecular similarity is integral to read-across. Various molecular fingerprints and similarity measures may be used to calculate molecular similarity. This study investigated the value and concordance of the Tanimoto similarity values calculated using six widely used fingerprints within six toxicological datasets. There was considerable variability in the similarity values calculated from the various molecular fingerprints for diverse compounds, although they were reasonably concordant for homologous series acting via a common mechanism. The results suggest generic fingerprint-derived similarities are likely to be optimally predictive for local datasets, i.e. following sub-categorisation. Thus, for read-across, generic fingerprint-derived similarities are likely to be most predictive after chemicals are placed into categories (or groups), then similarity is calculated within those categories, rather than for a whole chemically diverse dataset

Nuclear dependence coefficient α(A,qT)\alpha(A,q_T) for the Drell-Yan and J/ψ\psi production

Define the nuclear dependence coefficient $\alpha(A,q_T)$ in terms of ratio of transverse momentum spectrum in hadron-nucleus and in hadron-nucleon collisions: $\frac{d\sigma^{hA}}{dq_T^2}/ \frac{d\sigma^{hN}}{dq_T^2}\equiv A^{\alpha(A,q_T)}$. We argue that in small $q_T$ region, the $\alpha(A,q_T)$ for the Drell-Yan and J/$\psi$ production is given by a universal function:\ $a+b q_T^2$, where parameters a and b are completely determined by either calculable quantities or independently measurable physical observables. We demonstrate that this universal function $\alpha(A,q_T)$ is insensitive to the A for normal nuclear targets. For a color deconfined nuclear medium, the $\alpha(A,q_T)$ becomes strongly dependent on the A. We also show that our $\alpha(A,q_T)$ for the Drell-Yan process is naturally linked to perturbatively calculated $\alpha(A,q_T)$ at large $q_T$ without any free parameters, and the $\alpha(A,q_T)$ is consistent with E772 data for all $q_T$.Comment: latex, 28 pages, 10 figures, updated two figures, and add more discussion

Charmless Exclusive Baryonic B Decays

We present a systematical study of two-body and three-body charmless baryonic B decays. Branching ratios for two-body modes are in general very small, typically less than $10^{-6}$, except that \B(B^-\to p \bar\Delta^{--})\sim 1\times 10^{-6}. In general, $\bar B\to N\bar\Delta>\bar B\to N\bar N$ due to the large coupling constant for $\Sigma_b\to B\Delta$. For three-body modes we focus on octet baryon final states. The leading three-dominated modes are $\bar B^0\to p\bar n\pi^-(\rho^-), n\bar p\pi^+(\rho^+)$ with a branching ratio of order $3\times 10^{-6}$ for $\bar B^0\to p\bar n\pi^-$ and $8\times 10^{-6}$ for $\bar B^0\to p\bar n\rho^-$. The penguin-dominated decays with strangeness in the meson, e.g., $B^-\to p\bar p K^{-(*)}$ and $\bar B^0\to p\bar n K^{-(*)}, n\bar n \bar K^{0(*)}$, have appreciable rates and the $N\bar N$ mass spectrum peaks at low mass. The penguin-dominated modes containing a strange baryon, e.g., $\bar B^0\to \Sigma^0\bar p\pi^+, \Sigma^-\bar n\pi^+$, have branching ratios of order $(1\sim 4)\times 10^{-6}$. In contrast, the decay rate of $\bar B^0\to\Lambda\bar p\pi^+$ is smaller. We explain why some of charmless three-body final states in which baryon-antibaryon pair production is accompanied by a meson have a larger rate than their two-body counterparts: either the pole diagrams for the former have an anti-triplet bottom baryon intermediate state, which has a large coupling to the $B$ meson and the nucleon, or they are dominated by the factorizable external $W$-emission process.Comment: 46 pages and 3 figures, to appear in Phys. Rev. D. Major changes are: (i) Calculations of two-body baryonic B decays involving a Delta resonance are modified, and (ii) Penguin-dominated modes B-> Sigma+N(bar)+p are discusse