Physical Sciences and Mathematics Commons^™

Proton-Electrostatic Localization: Explaining The Bioenergetic Conundrum In Alkalophilic Bacteria, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

The decades-longstanding energetic conundrum of alkalophilic bacteria as to how they are able to synthesize ATP has now, for the first time, been clearly solved using the proton-electrostatics localization hypothesis. This is a major breakthrough advance in understanding proton-coupling bioenergetics over the Nobel-prize work of Peter Mitchell’s chemiosmotic theory. The widespread textbook Mitchellian proton motive force (pmf) equation has now been significantly revised. Use of the newly derived equation results in an overall pmf value (215~233 mV) that is more than 4 times larger than that (44.3 mV) calculated from the Mitchellian equation for the alkalophilic bacteria growing at pH …

The Relative Importance Of Methanogenesis In The Decomposition Of Organic Matter In Northern Peatlands, J. Elizabeth Corbett, Malak M. Tfaily, David J. Burdige, Paul H. Glaser, Jeffrey P. Chanton

OES Faculty Publications

Using an isotope-mass balance approach and assuming the equimolar production of CO₂ and CH₄ from methanogenesis (e.g., anaerobic decomposition of cellulose), we calculate that the proportion of total CO₂ production from methanogenesis varies from 37 to 83% across a variety of northern peatlands. In a relative sense, methanogenesis was a more important pathway for decomposition in bogs (80 ± 13% of CO₂ production) than in fens (64 ± 5.7% of CO₂ production), but because fens contain more labile substrates they may support higher CH4 production overall. The concentration of CO₂ produced from methanogenesis (CO …

Effect Of Methoxy Substituents On The Activation Barriers Of The Glutathione Peroxidase-Like Mechanism Of An Aromatic Cyclic Seleninate, Craig A. Bayse, Ashley L. Shoaf

Chemistry & Biochemistry Faculty Publications

Density functional theory (DFT) models including explicit water molecules have been used to model the redox scavenging mechanism of aromatic cyclic seleninates. Experimental studies have shown that methoxy substitutions affect the rate of scavenging of reactive oxygen species differently depending upon the position. Activities are enhanced in the para position, unaffected in the meta, and decreased in the ortho. DFT calculations show that the activation barrier for the oxidation of the selenenyl sulfide, a proposed key intermediate, is higher for the ortho methoxy derivative than for other positions, consistent with the low experimental conversion rate.

Retrieval And Validation Of Carbon Dioxide, Methane, And Water Vapor For The Canary Islands Ir-Laser Occultation Experiment, V. Proschek, G. Kirchengast, S. Schweitzer, J.S. A. Brooke, P. F. Bernath, C. B. Thomas, J. G. Wang, K. A. Tereszchuk, G. González Abad, R. J. Hargreaves, C. A. Beale, J. J. Harrison, P. A. Martin, V. L. Kasyutich, C. Gerbig, O. Kolle, A. Loescher

Chemistry & Biochemistry Faculty Publications

The first ground-based experiment to prove the concept of a novel space-based observation technique for microwave and infrared-laser occultation between low-Earthorbit satellites was performed in the Canary Islands between La Palma and Tenerife. For two nights from 21 to 22 July 2011 the experiment delivered the infrared-laser differential transmission principle for the measurement of greenhouse gases (GHGs) in the free atmosphere. Such global and long-term stable measurements of GHGs, accompanied also by measurements of thermodynamic parameters and line-of-sight wind in a self-calibrating way, have become very important for climate change monitoring. The experiment delivered promising initial data for demonstrating the …

Global Ozone Chemistry And Related Trace Gas Data Records For The Stratosphere (Gozcards): Methodology And Sample Results With A Focus On Hcl, H20, And 03, L. Froidevaux, J. Anderson, H. J. Wang, R. A. Fuller, M. J. Schwartz, M. L. Santee, N. J. Livesey, H. C. Pumphrey, P. F. Bernath, J. M. Russell Iii, M. P. Mccormick

Chemistry & Biochemistry Faculty Publications

We describe the publicly available data from the Global OZone Chemistry And Related trace gas Data records for the Stratosphere (GOZCARDS) project and provide some results, with a focus on hydrogen chloride (HCl), water vapor (H₂O), and ozone (O₃). This data set is a global long-term stratospheric Earth system data record, consisting of monthly zonal mean time series starting as early as 1979. The data records are based on high-quality measurements from several NASA satellite instruments and the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS) on SCISAT. We examine consistency aspects between the various data sets. …

Peptide Inhibitor Of Complement C1 (Pic1) Rapidly Inhibits Complement Activation After Intravascular Injection In Rats, Julia A. Sharp, Pamela S. Hair, Haree K. Pallera, Parvathi S. Kumar, Clifford T. Mauriello, Julius O. Nyalwidhe, Cody A. Phelps, Dalnam Park, Nicole M. Thielens, Stephen M. Pascal, Waldon Chen, Diane M. Duffy, Frank A. Lattanzio, Kenji M. Cunnion, Neel K. Krishna

Chemistry & Biochemistry Faculty Publications

The complement system has been increasingly recognized to play a pivotal role in a variety of inflammatory and autoimmune diseases. Consequently, therapeutic modulators of the classical, lectin and alternative pathways of the complement system are currently in preclinical and clinical development. Our laboratory has identified a peptide that specifically inhibits the classical and lectin pathways of complement and is referred to as Peptide Inhibitor of Complement C1 (PIC1). In this study, we determined that the lead PIC1 variant demonstrates a salt-dependent binding to C1q, the initiator molecule of the classical pathway. Additionally, this peptide bound to the lectin pathway initiator …

Plant Species Rather Than Climate Greatly Alters The Temporal Pattern Of Litter Chemical Composition During Long-Term Decomposition, Yongfu Li, Na Chen, Mark E. Harmon, Yuan Li, Xiaoyan Cao, Mark A. Chappell, Jingdong Mao

Chemistry & Biochemistry Faculty Publications

A feedback between decomposition and litter chemical composition occurs with decomposition altering composition that in turn influences the decomposition rate. Elucidating the temporal pattern of chemical composition is vital to understand this feedback, but the effects of plant species and climate on chemical changes remain poorly understood, especially over multiple years. In a 10-year decomposition experiment with litter of four species (Acer saccharum, Drypetes glauca, Pinus resinosa, and Thuja plicata) from four sites that range from the arctic to tropics, we determined the abundance of 11 litter chemical constituents that were grouped into waxes, carbohydrates, …

Role Of Low Exposure To Metals As Male Reproductive Toxicants, H. Anna Jeng, Yeou-Lih Huang, Chih-Hong Pan, Norou Diawara

Community & Environmental Health Faculty Publications

The objective of the study was to examine the associations between environmentally relevant low metal concentrations and semen quality parameters in men. The concentrations of zinc (Zn), copper (Cu), cadmium (Cd), arsenic (As), selenium (Se), and lead (Pb) in the seminal plasma and urine were measured from 196 male human subjects in Taiwan. Urinary Cd concentrations were negatively associated with sperm viability (p=0.006). Seminal plasma Cu concentrations of the normal group (>= 15 x 10(6)/ml) were significantly lower than those of the abnormal group (p=0.023). However, the linear regression analysis showed a weak association between Cu concentration and sperm …

Testing The Waters: Local Users, Sea Level Rise, And The Productive Usability Of Interactive Geovisualizations, Daniel Richards

English Faculty Publications

This paper explores the potential for technical communicators to employ usability research with risk-based interactive geovisualization technologies as a method of cultivating "critical rhetorics of risk communication" for local communities. Through integrating theories from usability studies and risk communication, I offer some new directions for thinking about the productive usability of online, participatory technologies that promote citizen engagement in science. I argue that the key tenets of productive usability afford technical communicators the opportunity to build localized knowledge of risk in real, local users, which in turn improves the capacity for a community and its stakeholders to more effectively communicate …

On The Shoaling Of Solitary Waves In The Presence Of Short Random Waves, Miao Tian, Alex Sheremet, James M. Kaihatu, Gangfeng Ma

Civil & Environmental Engineering Faculty Publications

Overhead video from a small number of laboratory tests conducted by Kaihatu et al. at the Tsunami Wave Basin at Oregon State University shows that the breaking point of a shoaling solitary wave shifts to deeper water if random waves are present. The analysis of the laboratory data collected confirms that solitary waves indeed tend to break earlier in the presence of random wave field, and suggests that the effect is the result of the radiation stresses gradient induced by the random wave fields. A theoretical approach based on the forced KdV equation is shown to successfully predict the shoaling …

Are Religion And Environmentalism Complements Or Substitutes?: A Club-Based Approach, Feler Bose, Timothy M. Komarek

Economics Faculty Publications

In this article, we analyze the causal link between membership in environmental groups and active participation and membership in religious groups. We use a club-based model and employ OLS and spatial econometrics with controls to test for whether membership and participation in a religious group is a substitute or complement for membership in environmental groups. Instrumental variables estimation was used as a robustness check. We found that religious participation and religious membership in evangelical groups are a substitute for environmental membership. Much of the work on environmental concerns has focused on answers to survey questions, not on membership. We used …

Climate, Environmental And Socio-Economic Change: Weighing Up The Balance In Vector-Borne Disease Transmission, Paul E. Parham, Joanna Waldock, George K. Christophides, Deborah Hemming, Folashade Agusto, Katherine J. Evans, Nina Fefferman, Holly Gaff, Abba Gumel, Shannon Ladeau

Biological Sciences Faculty Publications

Arguably one of the most important effects of climate change is the potential impact on human health. While this is likely to take many forms, the implications for future transmission of vector-borne diseases (VBDs), given their ongoing contribution to global disease burden, are both extremely important and highly uncertain. In part, this is owing not only to data limitations and methodological challenges when integrating climate-driven VBD models and climate change projections, but also, perhaps most crucially, to the multitude of epidemiological, ecological and socio-economic factors that drive VBD transmission, and this complexity has generated considerable debate over the past 10-15 …

Casitas: A Location-Dependent Ecological Trap For Juvenile Caribbean Spiny Lobsters, Panulirus Argus, Benjamin C. Gutzler, Mark J. Butler Iv, Donald C. Behringer

Biological Sciences Faculty Publications

Casitas are artificial shelters used by fishers to aggregate Caribbean spiny lobsters (Panulirus argus) for ease of capture. However, casitas may function as an ecological trap for juvenile lobsters if they are attracted to casitas and their growth or mortality is poorer compared with natural shelters. We hypothesized that juvenile lobsters may be at particular risk if attracted to casitas because they are less able than larger individuals to defend themselves, and do not forage far from shelter. We compared the nutritional condition, relative mortality, and activity of lobsters of various sizes in casitas and natural shelters in adult and …

The Effect Of Parental Size On Spermatophore Production, Egg Quality, Fertilization Success, And Larval Characteristics In The Caribbean Spiny Lobster, Panulirus Argus, Mark J. Butler Iv, Alison Macdiarmid, Gaya Gnanalingam

Biological Sciences Faculty Publications

The average size of spiny lobsters (Decapoda; Palinuridae) has decreased worldwide over the past few decades. Market forces coupled with minimum size limits compel fishers to target the largest individuals. Males are targeted disproportionately as a consequence of sexual dimorphism in spiny lobster size (i.e. males grow larger than females) and because of protections for ovigerous females. Therefore, overexploitation of males has led to sperm limitation in several decapod populations with serious repercussions for reproductive success. In the Caribbean spiny lobster, Panulirus argus, little is known about the effect of reduced male size on fertilization success or the role …

A Framework And System For A Multi-Model Decision Aid For Sustainable Farming Practices, Kasi Bharath Vegesana

Computational Modeling & Simulation Engineering Theses & Dissertations

Decision support systems (DSS) for farmers address the need for modeling multiple processes and scenarios that affect farmer decision making. Existing DSS have various drawbacks that stop them from being deployed as decision support tools. This research proposes a multi-model simulation framework that can be used to analyze farm management practices at the crop level, individual farm level and at the community level to show the impact and alternatives for smallholder farming practices. A generic crop growth model is proposed, based on existing equations. We run sensitivity analysis on the model to identify important variables. The outputs from the crop …

De Novo Protein Structure Modeling And Energy Function Design, Lin Chen

Computer Science Theses & Dissertations

The two major challenges in protein structure prediction problems are (1) the lack of an accurate energy function and (2) the lack of an efficient search algorithm. A protein energy function accurately describing the interaction between residues is able to supervise the optimization of a protein conformation, as well as select native or native-like structures from numerous possible conformations. An efficient search algorithm must be able to reduce a conformational space to a reasonable size without missing the native conformation. My PhD research studies focused on these two directions.

A protein energy function—the distance and orientation dependent energy function of …

Modeling And Simulation Of Molecular Couette Flows And Related Flows, Wei Li

Mathematics & Statistics Theses & Dissertations

In this thesis, molecular Couette flow is clearly defined and the modeling and simulation of this kind of flow is systematically investigated. First, the integral equations for the velocity of gaseous Couette flow and related flows are derived from linearized Boltzmann BGK equation with Maxwell boundary condition and solved with high precision by using Chebyshev collocation and chunk-based collocation methods. The velocity profiles of gaseous Couette flows and related flows with a wide range of Knudsen number and the Maxwell boundary condition of various accommodation ratios are obtained. Moreover, the order of convergence of the numerical methods is also discussed …

Multi-Surface Simplex Spine Segmentation For Spine Surgery Simulation And Planning, Rabia Haq

Computational Modeling & Simulation Engineering Theses & Dissertations

This research proposes to develop a knowledge-based multi-surface simplex deformable model for segmentation of healthy as well as pathological lumbar spine data. It aims to provide a more accurate and robust segmentation scheme for identification of intervertebral disc pathologies to assist with spine surgery planning. A robust technique that combines multi-surface and shape statistics-aware variants of the deformable simplex model is presented. Statistical shape variation within the dataset has been captured by application of principal component analysis and incorporated during the segmentation process to refine results. In the case where shape statistics hinder detection of the pathological region, user-assistance is …

First Measurement Of The Polarization Observable E In The P→ (Ɣ→, Π+) In Reaction Up To 2.25 Gev, S. Strauch, W. J. Briscoe, M. Döring, E. Klempt, V. A. Nikonov, E. Pasyuk, D. Rönchen, A.V. Sarantsev, I. Strakovsky, R. Workman, K. P. Adhikari, D. Adikaram, L. El Fassi

Physics Faculty Publications

First results from the longitudinally polarized frozen-spin target (FROST) program are reported. The double-polarization observable E, for the reaction ɣ^→p^→→π+n, has been measured using a circularly polarized tagged-photon beam, with energies from 0.35 to 2.37 GeV. The final-state pions were detected with the CEBAF Large Acceptance Spectrometer in Hall B at the Thomas Jefferson National Accelerator Facility. These polarization data agree fairly well with previous partial-wave analyses at low photon energies. Over much of the covered energy range, however, significant deviations are observed, particularly in the high-energy region where high-L multipoles contribute. The data have been …

Fragmentation Of Fast Josephson Vortices And Breakdown Of Ordered States By Moving Topological Defects, Ahmad Sheikhzada, Alex Gurevich

Physics Faculty Publications

Topological defects such as vortices, dislocations or domain walls define many important effects in superconductivity, superfluidity, magnetism, liquid crystals, and plasticity of solids. Here we address the breakdown of the topologically-protected stability of such defects driven by strong external forces. We focus on Josephson vortices that appear at planar weak links of suppressed superconductivity which have attracted much attention for electronic applications, new sources of THz radiation, and low-dissipative computing. Our numerical simulations show that a rapidly moving vortex driven by a constant current becomes unstable with respect to generation of vortex-antivortex pairs caused by Cherenkov radiation. As a result, …

Corrigendum To "Suppression Of ϒ Production In D + Au And Au + Au Collisions At √Sɴɴ = 200 Gev" (Phys. Lett. B Vol 735 (2014) 127-137), J. Adamczyk, J. K. Adkins, G. Agakishiev, M. M. Aggarwal, Z. Ahammed, I. Alekseev, J. Alford, C. D. Anson, A. Aparin, D. Arkhipkin, S. Bültmann

Physics Faculty Publications

No abstract provided.

Nlo Evolution Of 3-Quark Wilson Loop Operator, I. Balitsky, A. V. Grabovsky

Physics Faculty Publications

It is well known that the high-energy scattering of a meson from some hadronic target can be described by the interaction of that target with a color dipole formed by two Wilson lines corresponding to the fast quark-antiquark pair. Moreover, the energy dependence of the scattering amplitude is governed by the evolution equation of this color dipole with respect to rapidity. Similarly, the energy dependence of scattering of a baryon can be described in terms of evolution of a three-Wilson-line operator with respect to the rapidity of the Wilson lines. We calculated the evolution of the 3-quark Wilson loop operator …

The Heavy Photon Search Test Detector, M. Battaglieri, S. Boyarinov, S. Bueltmann, V. Burkert, A. Celentano, G. Charles, W. Cooper, C. Cuevas, N. Dashyan, R. Devita, L. B. Weinstein

Physics Faculty Publications

The Heavy Photon Search (HPS), an experiment to search for a hidden sector photon in fixed target electroproduction, is preparing for installation at the Thomas Jefferson National Accelerator Facility (JLab) in the Fall of 2014. As the first stage of this project, the HPS Test Run apparatus was constructed and operated in 2012 to demonstrate the experiment׳s technical feasibility and to confirm that the trigger rates and occupancies are as expected. This paper describes the HPS Test Run apparatus and readout electronics and its performance. In this setting, a heavy photon can be identified as a narrow peak in the …

Beam-Energy-Dependent Two-Pion Interferometry And The Freeze-Out Eccentricity Of Pions Measured In Heavy Ion Collisions At The Star Detector, L. Adamczyk, J.K. Adkins, G. Agakishiev, M.M. Aggarwal, Z. Ahammed, I. Koralt, Star Collaboration

Physics Faculty Publications

We present results of analyses of two-pion interferometry in Au + Au collisions at root s(NN) = 7.7, 11.5, 19.6, 27, 39, 62.4, and 200 GeV measured in the STAR detector as part of the BNL Relativistic Heavy Ion Collider Beam Energy Scan program. The extracted correlation lengths (Hanbury-Brown-Twiss radii) are studied as a function of beam energy, azimuthal angle relative to the reaction plane, centrality, and transverse mass (m(T)) of the particles. The azimuthal analysis allows extraction of the eccentricity of the entire fireball at kinetic freeze-out. The energy dependence of this observable is expected to be sensitive to …

Double Spin Asymmetries Of Inclusive Hadron Electroproduction From A Transversely Polarized He-3 Target, Y. X. Zhao, K. Allada, K. Aniol, J.R.M. Annand, T. Averett, F. Benmokhtar, M. Canan

Physics Faculty Publications

We report the measurement of beam-target double spin asymmetries (A_LT) in the inclusive production of identified hadrons, ^→e + ³He^↑ → h + X, using a longitudinally polarized 5.9-GeV electron beam and a transversely polarized ³He target. Hadrons (π^±, K^±, and proton) were detected at 16 ° with an average momentum ( P_h ) = 2.35 GeV/c and a transverse momentum (p_T) coverage from 0.60 to 0.68 GeV/c. Asymmetries from the He-3 target were observed to be nonzero for π^± production when the target was polarized …

E00-110 Experiment At Jefferson Lab Hall A: Deeply Virtual Compton Scattering Off The Proton At 6 Gev, M. Defurne, M. Amaryan, K. A. Aniol, M. Beaumel, H. Benaoum, P. Bertin, C. E. Hyde, P.E. Ulmer, Jefferson Lab Hall A Collaboration

Physics Faculty Publications

We present final results on the photon electroproduction (^→e p → epγ) cross section in the deeply virtual Compton scattering (DVCS) regime and the valence quark region from Jefferson Lab experiment E00-110. Results from an analysis of a subset of these data were published before, but the analysis has been improved, which is described here at length, together with details on the experimental setup. Furthermore, additional data have been analyzed, resulting in photon electroproduction cross sections at new kinematic settings for a total of 588 experimental bins. Results of the Q² and x_B dependencies of both …

Λλ Correlation Function In Au + Au Collisions At √S(Nn)=200 Gev, L. Adamczyk, J. K. Adkins, G. Agakishiev, M. M. Aggarwal, S. Bültmann, I. Koralt

Physics Faculty Publications

We present ΛΛ correlation measurements in heavy-ion collisions for Au + Au collisions at √s_NN = 200 GeV using the STAR experiment at the Relativistic Heavy-Ion Collider. The Lednicky-Lyuboshitz analytical model has been used to fit the data to obtain a source size, a scattering length and an effective range. Implications of the measurement of the ΛΛ correlation function and interaction parameters for dihyperon searches are discussed.

Measurement Of The Target-Normal Single-Spin Asymmetry In Quasielastic Scattering From The Reaction ³He↑(E, E'), Y. W. Zhang, E. Long, M. Mihoviloviĉ, G. Gin, M Canan, S. Golge, R. Schiavilla

Physics Faculty Publications

We report the first measurement of the target single-spin asymmetry, A_y, in quasielastic scattering from the inclusive reaction ³He↑(e, e') on a ³He gas target polarized normal to the lepton scattering plane. Assuming time-reversal invariance, this asymmetry is strictly zero for one-photon exchange. A nonzero A_y can arise from the interference between the one-and two-photon exchange processes which is sensitive to the details of the substructure of the nucleon. An experiment recently completed at Jefferson Lab yielded asymmetries with high statistical precision at Q² = 0.13, 0.46, and 0.97 GeV2. These measurements demonstrate, for the first …

Precision Measurement Of The Longitudinal Double-Spin Asymmetry For Inclusive Jet Production In Polarized Proton Collisions At √S= 200gev, L. Adamczyk, J.K. Adkins, G. Agakishiev, S. Bültmann, I. Koralt, Star Collaboration

Physics Faculty Publications

We report a new measurement of the midrapidity inclusive jet longitudinal double-spin asymmetry, A_LL, in polarized pp collisions at center-of-mass energy √s = 200 GeV. The STAR data place stringent constraints on polarized parton distribution functions extracted at next-to-leading order from global analyses of inclusive deep-inelastic scattering (DIS), semi-inclusive DIS, and RHIC pp data. The measured asymmetries provide evidence at the 3σ level for positive gluon polarization in the Bjorken-x region x > 0.05.

Precision Measurements Of Aⁿ1 In The Deep Inelastic Regime, D. S. Parno, D. Flay, M. Posik, M. Canan, C. Hyde, The Jefferson Lab Hall A Collaboration

Physics Faculty Publications

We have performed precision measurements of the double-spin virtual-photon asymmetry A₁ on the neutron in the deep inelastic scattering regime, using an open-geometry, large-acceptance spectrometer and a longitudinally and transversely polarized ³He target. Our data cover a wide kinematic range 0.277 <= x <= 0.548 at an average Q² value of 3.078(GeV/c)², doubling the available high-precision neutron data in this xrange. We have combined our results with world data on proton targets to make a leading-order extraction of the ratio of polarized-to-unpolarized parton distribution functions for up quarks and for down quarks in the same kinematic range. Our data are consistent with …