Physical Sciences and Mathematics Commons^™

Critical Decisions In Metaproteomics: Achieving High Confidence Protein Annotations In A Sea Of Unknowns, Emma Timmins-Schiffman, Damon H. May, Molly Mikan, Michael Riffle, Chris Frazar, H. R. Harvey, William S. Noble, Brook L. Nunn

OES Faculty Publications

No abstract provided.

Improving Cavity Enhanced Spectroscopy Of Molecular Ions In The Mid-Infrared With Up-Conversion Detection And Brewster-Plate Spoilers, Charles R. Markus, Adam J. Perry, James N. Hodges, Benjamin J. Mccall

Chemistry & Biochemistry Faculty Publications

The performance of sensitive spectroscopic methods in the mid-IR is often limited by fringing due to parasitic etalons and the background noise in mid-infrared detectors. In particular, the technique Noise Immune Cavity Enhanced Optical Heterodyne Velocity Modulation Spectroscopy (NICE-OHVMS), which is capable of determining the frequencies of strong rovibrational transitions of molecular ions with sub-MHz uncertainty, needs improved sensitivity in order to probe weaker transitions. In this work, we have implemented up-conversion detection with NICE-OHVMS in the 3.2 - 3.9 μm region to enable the use of faster and more sensitive detectors which cover visible wavelengths. The higher bandwidth enabled …

New And Improved Infra-Red Absorption Cross Sections And Ace-Fts Retrievals Of Carbon Tetrachloride (Ccl4), Jeremy J. Harrison, Christopher D. Boone, Peter F. Bernath

Chemistry & Biochemistry Faculty Publications

Carbon tetrachloride (CCl₄) is one of the species regulated by the Montreal Protocol on account of its ability to deplete stratospheric ozone. As such, the inconsistency between observations of its abundance and estimated sources and sinks is an important problem requiring urgent attention (Carpenter et al., 2014) [5]. Satellite remote-sensing has a role to play, particularly limb sounders which can provide vertical profiles into the stratosphere and therefore validate stratospheric loss rates in atmospheric models. This work is in two parts. The first describes new and improved high-resolution infra-red absorption cross sections of carbon tetrachloride/dry synthetic air over …

Barriers To Counseling Among Human Service Professionals: The Development And Validation Of The Fit, Stigma, & Value Scale, Edward S. Neukrug, Michael T. Kalkbrenner, Sandy-Ann M. Griffith

Counseling & Human Services Faculty Publications

This study sought to confirm rates of attendance in counseling of human service professionals and validate a 32-item questionnaire designed to identify barriers to counseling seeking behavior among this population. Results indicated that a large percentage of human service professionals attend counseling, with males and females attending at similar rates and non-Caucasians attending at lower rates. A multivariate analysis of variance and descriptive statistics identified the most common barriers to attendance in counseling and examined demographic differences in participants’ sensitivity towards barriers to attendance in counseling. A Principal Factor Analysis (PFA) revealed three subscales (fit, value, and stigma), which we …

Earning A Seat At The Table: How It Departments Can Partner In Organizational Change And Innovation, Robert L. Moore, Nathan Johnson

STEMPS Faculty Publications

Few would argue that the information technology department (ITD) is not an essential part of an organization. It is hard to envision a project that does not need the support of the ITD. Despite this importance, the ITD is not always involved in the management of projects. Often, the ITD is brought into the project late in the planning and development process. In many cases, the inclusion of the ITD in an advanced project stage can result in project failure where early involvement could have prevented it. Why is it that ITDs, while clearly a vital part of project implementation, …

Effects Of Nonaerated Circulation Water Velocity On Nutrient Release From Aquaculture Pond Sediments, Xiangju Cheng, Dantong Zhu, Xixi Wang, Deguang Yu, Jun Xie

Civil & Environmental Engineering Faculty Publications

Sustaining good water quality in aquaculture ponds is vital. Without an aerator, the dissolved oxygen in ponds comes primarily from mass transfer at the water-ambient atmosphere interface. As sediment can seriously affect water quality, this study used indoor experiments to examine the nutrient (nitrogen and phosphorus) release mechanisms and fluxes from sediment in aquaculture ponds with moving water but no aeration. The results showed that the ammonia nitrogen (NH₃-N) concentration in the overlying water was inversely proportional to flow velocity and that a higher flow velocity tended to result in a lower concentration in the overlying water, a …

Unification Of Gravity And Quantum Theory, Adam Daniels

Faculty-Sponsored Student Research & Capstones

An overview of the four fundamental forces of physics as described by the Standard Model (SM) and prevalent unifying theories beyond it is provided. Background knowledge of the particles governing the fundamental forces is provided, as it will be useful in understanding the way in which the unification efforts of particle physics has evolved, either from the SM, or apart from it. It is shown that efforts to provide a quantum theory of gravity have allowed supersymmetry (SUSY) and M-Theory to become two of the prevailing theories for unifying gravity with the remaining non-gravitational forces.

Accounting For Locational, Temporal, And Physical Similarity Of Residential Sales In Mass Appraisal Modeling: The Development And Application Of Geographically, Temporally, And Characteristically Weighted Regression, Paul E. Bidanset, Michael Mccord, John R. Lombard, Peadar Davis, William J. Mccluskey

School of Public Service Faculty Publications

Geographically weighted regression (GWR) has been recognized in the assessment community as a viable automated valuation model (AVM) to help overcome, at least in part, modeling hurdles associated with location, such as spatial heterogeneity and spatial autocorrelation of error terms. Although previous researchers have adjusted the GWR weights matrix to also weight by time of sale or by structural similarity of properties in AVMs, the research described in this paper is the first that has done so by all three dimensions (i.e., location, structural similarity, and time of sale) simultaneously. Using 24 years of single-family residential sales in Fairfax, Virginia, …

Impact Of Disease On The Survival Of Three Commercially Fished Species, John M. Hoenig, Maya L. Groner, Matthew W. Smith, Wolfgang K. Vogelbein, David M. Taylor, Donald F. Landers Jr., John T. Swenarton, David T. Gauthier

Biological Sciences Faculty Publications

Recent increases in emergent infectious diseases have raised concerns about the sustainability of some marine species. The complexity and expense of studying diseases in marine systems often dictate that conservation and management decisions are made without quantitative data on population-level impacts of disease. Mark-recapture is a powerful, underutilized, tool for calculating impacts of disease on population size and structure, even in the absence of etiological information. We applied logistic regression models to mark-recapture data to obtain estimates of disease-associated mortality rates in three commercially important marine species: snow crab (Chionoecetes opilio) in Newfoundland, Canada, that experience sporadic epizootics …

Rapid Adaptive Responses To Climate Change In Corals, Gergely Torda, Jennifer M. Donelson, Manuel Aranda, Daniel J. Barshis, Line Bay, Michael L. Berumen, David G. Bourne, Neal Cantin, Sylvain Foret, Mikhail Matz

Biological Sciences Faculty Publications

Pivotal to projecting the fate of coral reefs is the capacity of reef-building corals to acclimatize and adapt to climate change. Transgenerational plasticity may enable some marine organisms to acclimatize over several generations and it has been hypothesized that epigenetic processes and microbial associations might facilitate adaptive responses. However, current evidence is equivocal and understanding of the underlying processes is limited. Here, we discuss prospects for observing transgenerational plasticity in corals and the mechanisms that could enable adaptive plasticity in the coral holobiont, including the potential role of epigenetics and coral-associated microbes. Well-designed and strictly controlled experiments are needed to …

Investigating Coral Bleaching In A Changing Climate: Our State Of Understanding And Opportunities To Push The Field Forward, Mark E. Warner, Daniel Barshis, Sarah Davies, Andréa G. Grottoli, Todd C. Lajeunesse, Robert Van Woesik

Biological Sciences Faculty Publications

[First Paragraph]

Coral reefs throughout the world are facing the consequences of large-scale changes in Earth’s climate. In particular, ocean warming is leading to frequent coral bleaching, which is threatening the long-term stability of coral reefs. Coral bleaching is a stress response that results in the disassociation of the mutualistic symbioses (i.e., dysbiosis) between corals and their endosymbiotic algae (Symbiodinium spp.). In the past two decades, there have been four substantial bleaching events, which have affected large geographic areas across the globe, including the worst recorded bleaching event on the Great Barrier Reef in 2016 (Berkelmans et al. 2004; Eakin …

Enhancement Of The Physicochemical Properties Of Pt(Dien)(Nucleobase) (2+) For Hivncp7 Targeting, S. D. Tsotsoros, P. B. Lutz, A. G. Daniel, E. J. Peterson, R. E. F. De Paiva, E. Rivera, Y. Qu, C. A. Bayse, N. P. Farrell

Chemistry & Biochemistry Faculty Publications

Physicochemical properties of coordination compounds can be exploited for molecular recognition of biomolecules. The inherent π-π stacking properties of [Pt(chelate)(N-donor)]²⁺([PtN₄]) complexes were modulated by systematic variation of the chelate (diethylenetriamine and substituted derivatives) and N-donor (nucleobase or nucleoside) in the formally substitution-inert PtN₄ coordination sphere. Approaches to target the HIV nucleocapsid protein HIVNCp7 are summarized building on (i) assessment of stacking interactions with simple tryptophan or tryptophan derivatives to (ii) the tryptophan-containing C-terminal zinc finger and (iii) to the full two-zinc finger peptide and its interactions with RNA and DNA. The xanthosine nucleoside was identified …

The Conservation Status Of Marine Bony Shorefishes Of The Greater Caribbean, Kent E. Carptenter, Christi Linardich, Gina Ralph, N. Cox, D. R. Robertson, H. Harwell, A. Acero P., W. Anderson Jr., F. Barthelat, J. -L. Bouchereau, J. J. Brown, J. Buchanan, D. Buddo, B. Collette, M. Comeros-Raynal, M. Craig, M. Curtis, T. Defex, J. Dooley, W. Driggers Iii, C. Elfes Livsey, T. Fraser, R. Gilmore Jr., L. Grijalba Bendeck, A. Hines, R. Kishore, K. Lindeman, J. -P. Maréchal, J. Mceachran, R. Mcmanus, J. Moore, T. Munroe, H. Oxenford, F. Pezold, F. Pina Amargós, A. Polanco Fernandez, B. Polidoro, C. Pollock, R. Robins, B. Russell, C. Sayer, S. Williams

Biological Sciences Faculty Publications

The greater Caribbean biogeographic region covered in this report (representing 38 countries and territories) encompasses an outstanding marine bony shorefish richness of approximately 1,360 species, with many (53%) being endemic. This report provides an overview of the conservation status of greater Caribbean shorefishes, with detailed information available through the IUCN Red List, and gives recommendations.

Fit To Predict? Ecoinformatics For Predicting The Catchability Of A Pelagic Fish In Near Real-Time, Kylie L. Scales, Elliot L. Hazen, Sara M. Maxwell, Heidi Dewar, Suzanne Kohin, Michael G. Jacox, Christopher A. Edwards, Dana K. Briscoe, Larry B. Crowder, Rebecca L. Lewison, Steven J. Bograd

Biological Sciences Faculty Publications

The ocean is a dynamic environment inhabited by a diverse array of highly migratory species, many of which are under direct exploitation in targeted fisheries. The timescales of variability in the marine realm coupled with the extreme mobility of ocean-wandering species such as tuna and billfish complicates fisheries management. Developing ecoinformatics solutions that allow for near real-time prediction of the distributions of highly mobile marine species is an important step towards the maturation of dynamic ocean management and ecological forecasting. Using 25 years (1990-2014) of NOAA fisheries' observer data from the California drift gillnet fishery, we model relative probability of …

Fast Multipole Method Using Cartesian Tensor In Beam Dynamic Simulation, He Zhang, He Huang, Rui Li, Jie Chen, Li-Shi Luo

Mathematics & Statistics Faculty Publications

The fast multipole method (FMM) using traceless totally symmetric Cartesian tensor to calculate the Coulomb interaction between charged particles will be presented. The Cartesian tensor based FMM can be generalized to treat other non-oscillating interactions with the help of the differential algebra or the truncated power series algebra. Issues on implementation of the FMM in beam dynamic simulations are also discussed. © 2017 Author(s).

Comparing An Atomic Model Or Structure To A Corresponding Cryo-Electron Microscopy Image At The Central Axis Of A Helix, Stephanie Zeil, Julio Kovacs, Willy Wriggers, Jing He

Computer Science Faculty Publications

Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM …

Target Mass Effects In Parton Quasi-Distributions, A. V. Radyushkin

Physics Faculty Publications

We study the impact of non-zero (and apparently large) value of the nucleon mass M on the shape of parton quasi-distributions Q(y, p₃), in particular on its change with the change of the nucleon momentum p_3. We observe that the usual target-mass corrections induced by the M-dependence of the twist-2 operators are rather small. Moreover, we show that within the framework based on parametrizations by transverse momentum dependent distribution functions (TMDs) these corrections are canceled by higher-twist contributions. We identify a novel source of kinematic target-mass dependence of TMDs and build models corrected for …

Kinematics Of Current Region Fragmentation In Semi-Inclusive Deeply Inelastic Scattering, M. Boglione, J. Collins, L. Gamberg, José O. Gonzalez-Hernandez, Ted C. Rogers, N. Sato

Physics Faculty Publications

Different kinematical regions of semi-inclusive deeply inelastic scattering (SIDIS) processes correspond to different underlying partonic pictures, and it is important to understand the transition between them. We find criteria in semi-inclusive deeply inelastic scattering (SIDIS) for identifying the current fragmentation region-the kinematical region where a factorization picture with fragmentation functions is appropriate, especially for studies of transverse-momentum-dependent (TMD) functions. This region is distinguished from the central (soft) and target fragmentation regions. The basis of our argument is in the errors in approximations used in deriving factorization. As compared with previous work, we show that it is essential to take account …

Imaging Of Super-Fast Dynamics And Flow Instabilities Of Superconducting Vortices, L. Embon, Y. Anahory, Ž L. Jelić, E. O. Lachman, Y. Myasoedov, M. E. Huber, G. P. Mikitik, A. V. Silhanek, M. V. Milošević, A Gurevich, E. Z. Zeldov

Physics Faculty Publications

Quantized magnetic vortices driven by electric current determine key electromagnetic properties of superconductors. While the dynamic behavior of slow vortices has been thoroughly investigated, the physics of ultrafast vortices under strong currents remains largely unexplored. Here, we use a nanoscale scanning superconducting quantum interference device to image vortices penetrating into a superconducting Pb film at rates of tens of GHz and moving with velocities of up to tens of km/s, which are not only much larger than the speed of sound but also exceed the pair-breaking speed limit of superconducting condensate. These experiments reveal formation of mesoscopic vortex channels which …

First Measurement Of Unpolarized Semi-Inclusive Deep-Inelastic Scattering Cross Sections From A He 3 Target, X. Yan, K. Allada, K. Aniol, J. R. M. Annand, T. Averett, F. Benmokhtar, W. Bertozzi, P. C. Bradshaw, P. Bosted, A. Camsonne, M. Canan

Physics Faculty Publications

The unpolarized semi-inclusive deep-inelastic scattering (SIDIS) differential cross sections in ³He(e,e′π^±)X have been measured for the first time in Jefferson Lab experiment E06-010 with a 5.9GeV e- beam on a ³He gas target. The experiment focuses on the valence quark region, covering a kinematic range 0.12<x_bj<0.45,1<Q²<4(GeV/c)²,0.45<z_h<0.65, and 0.05<P_t<0.55GeV/c. The extracted SIDIS differential cross sections of π^± production are compared with existing phenomenological models while the ³He nucleus approximated as two protons and one neutron in a plane-wave picture, in multidimensional bins. Within …

Nonperturbative Evolution Of Parton Quasi-Distributions, A. V. Radyushkin

Physics Faculty Publications

Using the formalism of parton virtuality distribution functions (VDFs) we establish a connection between the transverse momentum dependent distributions (TMDs) F(x,k²_⊥) and quasi-distributions (PQDs) Q(y,p₃) introduced recently by X. Ji for lattice QCD extraction of parton distributions f(x). We build models for PQDs from the VDF-based models for soft TMDs, and analyze the p₃ dependence of the resulting PQDs. We observe a strong nonperturbative evolution of PQDs for small and moderately large values of p₃ reflecting the transverse momentum dependence of TMDs. Thus, the study of PQDs on the lattice …

The Heavy Photon Search Beamline And Its Performance, N. Baltzell, H. Egiyan, M. Ehrhart, C. Field, A. Freyberger, F.-X. Girod, M. Holtrop, J. Jaros, G. Kalicy, T. Maruyama, H. Vance

Physics Faculty Publications

The Heavy Photon Search (HPS) is an experiment to search for a hidden sector photon, aka a heavy photon or dark photon, in fixed target electroproduction at the Thomas Jefferson National Accelerator Facility (JLab). The HPS experiment searches for the e⁺e^- decay of the heavy photon with bump hunt and detached vertex strategies using a compact, large acceptance forward spectrometer, consisting of a silicon microstrip detector (SVT) for tracking and vertexing, and a PbWO₄ electromagnetic calorimeter for energy measurement and fast triggering. To achieve large acceptance and good vertexing resolution, the first layer of silicon detectors …

Dynamic Transition Of Vortices Into Phase Slips And Generation Of Vortex-Antivortex Pairs In Thin Film Josephson Junctions Under Dc And Ac Currents, Ahmad Sheikhzada, Alex Gurevich

Physics Faculty Publications

We present theoretical and numerical investigations of vortices driven by strong dc and ac currents in long Josephson junctions described by a nonlinear integro-differential equation which takes into account nonlocal electrodynamics of films, vortex bremsstrahlung, and Cherenkov radiation amplified by the attraction of vortices to the edges of the junction. This work focuses on the dynamics of vortices in Josephson junctions in thin films where the effects of Josephson nonlocality are essential but London screening is negligible. We obtained an exact solution for a vortex driven by an arbitrary time-dependent current in an overdamped junction where the vortex turns into …

Photon Beam Asymmetry Σ For Η And Η′ Photoproduction From The Proton, P. Collins, B. G. Ritchie, M. Dugger, A. V. Anisovich, M. Doring, E. Klempt, V. A. Nikonov, D. Rönchen, D. Sadasivan, A. Sarantsev, M. J. Amaryan, A. Klein

Physics Faculty Publications

Measurements of the linearly-polarized photon beam asymmetry Σ for photoproduction from the proton of η and η ′ mesons are reported. A linearly-polarized tagged photon beam produced by coherent bremsstrahlung was incident on a cryogenic hydrogen target within the CEBAF Large Acceptance Spectrometer. Results are presented for the γ p → η p reaction for incident photon energies from 1.070 to 1.876 GeV, and from 1.516 to 1.836 GeV for the γ p → η ′ p reaction. For γ p → η p , the data reported here considerably extend the range of measurements to higher energies, and are …

Measurement Of Two-Photon Exchange Effect By Comparing Elastic E ± P Cross Sections, D. Rimal, D. Adikaram, B. A. Raue, L. B. Weinstein, J. Arrington, W. K. Brooks, M. Ungaro, K. P. Adhikari, A. V. Afanasev, Z. Akbar

Physics Faculty Publications

Background: The electromagnetic form factors of the proton measured by unpolarized and polarized electron scattering experiments show a significant disagreement that grows with the squared four-momentum transfer (Q²) . Calculations have shown that the two measurements can be largely reconciled by accounting for the contributions of two-photon exchange (TPE). TPE effects are not typically included in the standard set of radiative corrections since theoretical calculations of the TPE effects are highly model dependent, and, until recently, no direct evidence of significant TPE effects has been observed.

Purpose: We measured the ratio of positron-proton to electron-proton elastic-scattering cross …

Inclusive Neutrino Scattering Off The Deuteron At Low Energies In Chiral Effective Field Theory, A. Baroni, R. Schiavilla

Physics Faculty Publications

Cross sections for inclusive neutrino scattering off the deuteron induced by neutral and charge-changing weak currents are calculated from threshold up to 150 MeV energies in a chiral effective field theory including high orders in the power counting. Contributions beyond leading order (LO) in the weak current are found to be small, and increase the cross sections obtained with the LO transition operators by a couple of percent over the whole energy range 0–150 MeV. The cutoff dependence is negligible, and the predicted cross sections are within ∼2% of, albeit consistently larger than, corresponding predictions obtained in conventional meson-exchange frameworks.

Connecting Different Tmd Factorization Formalisms In Qcd, John Collins, Ted C. Rogers

Physics Faculty Publications

In the original Collins-Soper-Sterman (CSS) presentation of the results of transverse-momentum-dependent (TMD) factorization for the Drell-Yan process, results for perturbative coefficients can be obtained from calculations for collinear factorization. Here we show how to use these results, plus known results for the quark form factor, to obtain coefficients for TMD factorization in more recent formulations, e.g., that due to Collins, and apply them to known results at order α²s and α³s. We also show that the "nonperturbative" functions as obtained from fits to data are equal in the two schemes. We compile the higher-order perturbative …

Differential Cross Section Measurements For Γn→Π-P Above The First Nucleon Resonance Region, P. T. Mattione, D. S. Carman, I. I. Strakovsky, R. L. Workman, A. E. Kudryavtsev, A. Svarc, V. E. Tarasov, K. P. Adhikari, S. Adhikari, D. Adikaram, G. Charles, M. Khachatryan, A. Klein, Y. Prok, Z. W. Zhao

Physics Faculty Publications

The quasifree γd→π^-p(p) differential cross section has been measured with CLAS at photon beam energies E_γ from 0.445 to 2.510 GeV (corresponding to W from 1.311 to 2.366 GeV) for pion center-of-mass angles cosθπc.m. from -0.72 to 0.92. A correction for final state interactions has been applied to these data to extract the γn→π^-p differential cross sections. These cross sections are quoted in 8428 (E_γ,cosθπc.m.) bins, a factor of nearly 3 increase in the world statistics for this channel in this kinematic range. These new data …

Photon Beam Asymmetry Σ In The Reaction →Γ P → Pω For Eγ = 1.152 To 1.876 Gev, P. Collins, B. G. Ritchie, M. Dugger, F. J. Klein, A. V. Anisovich, E. Klempt, V. A. Nikonov, A. Sarantsev, K. P. Adhikari, S. Adhikari, D. Adikaram, G. Charles, M. Khachatryan, A. Klein, Y. Prok, J. Zhang, Z. W. Zhao

Physics Faculty Publications

Photon beam asymmetry Σ measurements for ω photoproduction in the reaction γ → p → ω p are reported for photon energies from 1.152 to 1.876 GeV. Data were taken using a linearly-polarized tagged photon beam, a cryogenic hydrogen target, and the CLAS spectrometer in Hall B at Jefferson Lab. The measurements obtained markedly increase the size of the database for this observable, extend coverage to higher energies, and resolve discrepancies in previously published data. Comparisons of these new results with predictions from a chiral-quark-based model and from a dynamical coupled-channels model indicate the importance of interferences between t-channel meson …

Measurement Of The Helicity Asymmetry E In Ω→Π+ΠˉΠᵒ Photoproduction, Z. Akbar, P. Roy, S. Park, V. Crede, A. V. Anisovich, I. Denisenko, E. Klempt, V. A. Nikonov, A. V. Sarantsev, K. P. Adhikari, M. J. Amaryan, G. Charles, A. Klein, Y. Prok, J. Zhang, Z. W. Zhao

Physics Faculty Publications

The double-polarization observable E was studied for the reaction γp→pω using the CEBAF Large Acceptance Spectrometer (CLAS) in Hall B at the Thomas Jefferson National Accelerator Facility and the longitudinally polarized frozen-spin target (FROST). The observable was measured from the charged decay mode of the meson, ω→π⁺π^-π⁰, using a circularly polarized tagged-photon beam with energies ranging from the ω threshold at 1.1 to 2.3 GeV. A partial-wave analysis within the Bonn-Gatchina framework found dominant contributions from the 3/2⁺ partial wave near threshold, which is identified with the subthreshold N(1720)3/2⁺ nucleon …