Physical Sciences and Mathematics Commons^™

Identification Of Arabidopsis Gpat9 (At5g60620) As An Essential Gene Involved In Triacylglycerol Biosynthesis, Jay Shockey, Anushobha Regmi, Kimberly Cotton, Neil Adhikari, John Bowse, Philip D. Bates

Faculty Publications

The first step in the biosynthesis of nearly all plant membrane phospholipids and storage triacylglycerols is catalyzed by a glycerol-3-phosphate acyltransferase (GPAT). The requirement for an endoplasmic reticulum (ER)-localized GPAT for both of these critical metabolic pathways was recognized more than 60 years ago. However, identification of the gene(s) encoding this GPAT activity has remained elusive. Here, we present the results of a series of in vivo, in vitro, and in silico experiments in Arabidopsis (Arabidopsis thaliana) designed to assign this essential function to AtGPAT9. This gene has been highly conserved throughout evolution and is …

Elevation Promotes Long-Term Survival Of Pinus Elliottii Var. Densa, A Foundation Species Of The Endangered Pine Rockland Ecosystem In The Florida Keys, Grant L. Harley, Justin T. Maxwell, George T. Raber

Faculty Publications

The pine rockland community in southern Florida, which supports numerous state- and federally listed flora and fauna species, is considered endangered. Without its foundation species, Pinus elliottii var. densa, habitat and species diversity are lost to tropical hardwood hammock. Here, we investigate the landscape factors that contribute to the long-term persistence of pine rocklands on the 2 islands that contain the largest remaining habitat in the Florida Keys: Big Pine Key and No Name Key. Plot-level biophysical data and island-scale remotely sensed vegetation data were collected from pine rockland savannas and examined with multi-dimensional analysis. On both islands, vegetation …

No Reef Is An Island: Integrating Coral Reef Connectivity Data Into The Design Of Regional-Scale Marine Protected Area Networks, Steven R. Schill, George T. Raber, Jason J. Roberts, Eric A. Treml, Jorge Brenner, Patrick N. Halpin

Faculty Publications

We integrated coral reef connectivity data for the Caribbean and Gulf of Mexico into a conservation decision-making framework for designing a regional scale marine protected area (MPA) network that provides insight into ecological and political contexts. We used an ocean circulation model and regional coral reef data to simulate eight spawning events from 2008–2011, applying a maximum 30-day pelagic larval duration and 20% mortality rate. Coral larval dispersal patterns were analyzed between coral reefs across jurisdictional marine zones to identify spatial relationships between larval sources and destinations within countries and territories across the region. We applied our results in Marxan, …

An Enantiodivergent Synthesis Of CΑ-Methyl Nipecotic Acid Analogues From δ-Lactam Derivatives Obtained Through A Highly Stereoselective Cyclization Strategy, Souvik Banerjee, Emily R. Vogel, Daniel Hinton, Michael Sterling, Douglas S. Masterson

Faculty Publications

A stereoselective and enantiodivergent strategy for the construction of δ-lactams is described. The strategy utilizes chiral malonic esters prepared from enantiomerically enriched mono esters of disubstituted malonic acid. A cyclization occurs with the selective displacement of a substituted benzyl alcohol as the leaving group. The resulting δ-lactams are then converted into nipecotic acid analogues using straightforward transformations. The resulting nipecotic acid analogues proved capable organocatalysts in Mannich reactions.

Cooling Atomic Gases With Disorder, Ehsan Khatami, Thereza Paiva, Shuxiang Yang, Valéry Rousseau, Mark Jarrell, Juana Moreno, Randall Hulet, Richard Scalettar

Faculty Publications

Cold atomic gases have proven capable of emulating a number of fundamental condensed matter phenomena including Bose-Einstein condensation, the Mott transition, Fulde-Ferrell-Larkin-Ovchinnikov pairing, and the quantum Hall effect. Cooling to a low enough temperature to explore magnetism and exotic superconductivity in lattices of fermionic atoms remains a challenge. We propose a method to produce a low temperature gas by preparing it in a disordered potential and following a constant entropy trajectory to deliver the gas into a nondisordered state which exhibits these incompletely understood phases. We show, using quantum Monte Carlo simulations, that we can approach the Néel temperature of …

Supporting Data For The Characterization Of Pna-Dna Four-Way Junctions, Douglas Van Iverson Ii, Crystal C. Serrano, Ann Marie Brahan, Arik Shams, Filbert Totsingan, Anthony J. Bell Jr.

Faculty Publications

Holliday or DNA four-way junctions (4WJs) are cruciform/bent structures composed of four DNA duplexes. 4WJs are key intermediates in homologous genetic recombination and double-strand break repair. To investigate 4WJs in vitro, junctions are assembled using four asymmetric DNA strands. The presence of four asymmetric strands about the junction branch point eliminates branch migration, and effectively immobilizes the resulting 4WJ. The purpose of these experiments is to show that immobile 4WJs composed of DNA and peptide nucleic acids (PNAs) can be distinguished from contaminating labile nucleic acid structures. These data compare the electrophoretic mobility of hybrid PNA–DNA junctions vs. …

Structural Characterization Of A Newly Identified Component Of Α-Carboxysomes: The Aaa+ Domain Protein Csocbbq, Markus Sutter, Evan W. Roberts, Raul C. Gonzalez, Cassandra Bates, Salma Dawoud, Kimberly Landry, Gordon C. Cannon, Sabine Heinhorst, Cheryl A. Kerfeld

Faculty Publications

Carboxysomes are bacterial microcompartments that enhance carbon fixation by concentrating ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and its substrate CO₂ within a proteinaceous shell. They are found in all cyanobacteria, some purple photoautotrophs and many chemoautotrophic bacteria. Carboxysomes consist of a protein shell that encapsulates several hundred molecules of RuBisCO and contain carbonic anhydrase and other accessory proteins. Genes coding for carboxysome shell components and the encapsulated proteins are typically found together in an operon. The α-carboxysome operon is embedded in a cluster of additional, conserved genes that are presumably related to its function. In many chemoautotrophs, products of the expanded carboxysome …

Linkages Among Fluorescent Dissolved Organic Matter, Dissolved Amino Acids And Lignin-Derived Phenols In River-Influenced Ocean Margins, Youhei Yamashita, Cédric G. Fichot, Yuan Shen, Rudolf Jaffé, Ronald Benner

Faculty Publications

Excitation emission matrix (EEM) fluorescence spectroscopy coupled with parallel factor analysis (PARAFAC) is commonly used to investigate the dynamics of dissolved organic matter (DOM). However, a lack of direct comparisons with known biomolecules makes it difficult to substantiate the molecular composition of specific fluorescent components. Here, coincident surface-water measurements of EEMs, dissolved lignin, and total dissolved amino acids (TDAA) acquired in the northern Gulf of Mexico were used to investigate the relationships between specific fluorescent components and DOM biomolecules. Two terrestrial humic-like components identified by EEM-PARAFAC using samples obtained from river to offshore waters were strongly linearly correlated with dissolved …

Comparison Of Microfacet Brdf Model To Modified Beckmann-Kirchhoff Brdf Model For Rough And Smooth Surfaces, Samuel D. Butler, Stephen E. Nauyoks, Michael A. Marciniak

Faculty Publications

A popular class of BRDF models is the microfacet models, where geometric optics is assumed. In contrast, more complex physical optics models may more accurately predict the BRDF, but the calculation is more resource intensive. These seemingly disparate approaches are compared in detail for the rough and smooth surface approximations of the modified Beckmann-Kirchhoff BRDF model, assuming Gaussian surface statistics. An approximation relating standard Fresnel reflection with the semi-rough surface polarization term, Q, is presented for unpolarized light. For rough surfaces, the angular dependence of direction cosine space is shown to be identical to the angular dependence in the microfacet …

Abundance, Stable Isotopic Composition, And Export Fluxes Of Doc, Poc, And Dic From The Lower Mississippi River During 2006-2008, Yihua Cai, Laodong Guo, Xuri Wang, George Aiken

Faculty Publications

Sources, abundance, isotopic compositions, and export fluxes of dissolved inorganic carbon (DIC), dissolved and colloidal organic carbon (DOC and COC), and particulate organic carbon (POC), and their response to hydrologic regimes were examined through monthly sampling from the Lower Mississippi River during 2006–2008. DIC was the most abundant carbon species, followed by POC and DOC. Concentration and δ¹³C of DIC decreased with increasing river discharge, while those of DOC remained fairly stable. COC comprised 61 ± 3% of the bulk DOC with similar δ¹³C abundances but higher percentages of hydrophobic organic acids than DOC, suggesting its …

Preparation And Preliminary Dielectric Characterization Of Structured C60-Thiol-Ene Polymer Nanocomposites Assembled Using The Thiol-Ene Click Reaction, Hanaa Mohammed Ahmed, Amber Danielle Windham, Maryam M. Al-Ejji, Noora H. Al-Qahtani, Mohammad K. Hassan, Kenneth A. Mauritz, Randy K. Buchanan, J. Paige Buchanan

Faculty Publications

Fullerene-containing materials have the ability to store and release electrical energy. Therefore, fullerenes may ultimately find use in high-voltage equipment devices or as super capacitors for high electric energy storage due to this ease of manipulating their excellent dielectric properties and their high volume resistivity. A series of structured fullerene (C₆₀) polymer nanocomposites were assembled using the thiol-ene click reaction, between alkyl thiols and allyl functionalized C₆₀ derivatives. The resulting high-density C₆₀-urethane-thiol-ene (C₆₀-Thiol-Ene) networks possessed excellent mechanical properties. These novel networks were characterized using standard techniques, including infrared spectroscopy (FTIR), differential scanning calorimetry …

New Transitions And Feeding Of The JΠ=(8+) Isomer In 186Re, David A. Matters, Nikolaos Fotiades, James J. Carroll, Christopher J. Chiara, John W. Mcclory, Toshihiko Kawano, Ronald O. Nelson, Matthew Devlin

Faculty Publications

The spallation neutron source at the Los Alamos Neutron Science Center Weapons Neutron Research facility was used to populate excited states in ¹⁸⁶Re via (n,2nγ) reactions on an enriched ¹⁸⁷Re target. Gamma rays were detected with the GErmanium Array for Neutron Induced Excitations spectrometer, a Compton-suppressed array of 18 HPGe detectors. Incident neutron energies were determined by the time-of-flight technique and used to obtain γ-ray excitation functions for the purpose of identifying γ rays by reaction channel. Analysis of the singles γ-ray spectrum gated on the neutron energy range 10≤E_n≤25MeV resulted in five transitions and one …

Force-Enhanced Atomic Refinement: Structural Modeling With Interatomic Forces In A Reverse Monte Carlo Approach Applied To Amorphous Si And Sio2, A. Pandey, Parthapratim Biswas, D. A. Drabold

Faculty Publications

We introduce a structural modeling technique, called force-enhanced atomic refinement (FEAR). The technique incorporates interatomic forces in reverse Monte Carlo (RMC) simulations for structural refinement by fitting experimental diffraction data using the conventional RMC algorithm, and minimizes the total energy and forces from an interatomic potential. We illustrate the usefulness of the approach by studying a−SiO₂ and a−Si. The structural and electronic properties of the FEAR models agree well with experimental neutron and x-ray diffraction data and the results obtained from previous molecular dynamics simulations of a−SiO₂ and a−Si. We have shown that the method is more efficient …

Changes In Litter Quality Caused By Simulated Nitrogen Deposition Reinforce The N-Induced Suppression Of Litter Decay, Linda T. A. Van Diepen, Serita D. Frey, Christopher M. Sthultz, Eric W. Morrison, Rakesh Minocha, Anne Pringle

Faculty Publications

Rates of nitrogen (N) deposition are increasing in industrialized and rapidly developing nations. Simulated N deposition suppresses plant litter decay rates, in particular for low quality (high lignin) litter. Litter quality is a primary driver of litter decomposition; however, it is not clear how changes in litter quality caused by long-term ecosystem exposure to chronic N additions interact with altered soil N-availability to influence litter decay dynamics. To document the effects of simulated N deposition on litter quality, we conducted a meta-analysis of available litter nutrient data from simulated N deposition experiments in temperate forests. To directly test whether changes …

A Nonlinear Splitting Algorithm For Systems Of Partial Differential Equations With Self-Diffusion, Matthew Beauregard, Joshua L. Padgett, Rana D. Parshad

Faculty Publications

Systems of reaction-diffusion equations are commonly used in biological models of food chains. The populations and their complicated interactions present numerous challenges in theory and in numerical approximation. In particular, self-diffusion is a nonlinear term that models overcrowding of a particular species. The nonlinearity complicates attempts to construct efficient and accurate numerical approximations of the underlying systems of equations. In this paper, a new nonlinear splitting algorithm is designed for a partial differential equation that incorporates self diffusion. We present a general model that incorporates self-diffusion and develop a numerical approximation. The numerical analysis of the approximation provides criteria for …

Sculpting The Band Gap: A Computational Approach, Kiran Prasai, Parthapratim Biswas, D.A. Drabold

Faculty Publications

Materials with optimized band gap are needed in many specialized applications. In this work, we demonstrate that Hellmann-Feynman forces associated with the gap states can be used to find atomic coordinates that yield desired electronic density of states. Using tight-binding models, we show that this approach may be used to arrive at electronically designed models of amorphous silicon and carbon. We provide a simple recipe to include a priori electronic information in the formation of computer models of materials, and prove that this information may have profound structural consequences. The models are validated with plane-wave density functional calculations.

No Vacuum Cerenkov Radiation Losses In The Timelike Lorentz-Violating Chern-Simons Theory, Karl Schober, Brett David Altschul

Faculty Publications

In a Lorentz- and CPT-violating modification of electrodynamics that includes a timelike Chern-Simons term, there are no energy losss through vacuum Cerenkov radiation. A charge moving with a constant velocity does not lose energy, because of an unusual cancellation. Higher frequency modes of the electromagnetic field carry away positive energy, but lower frequency modes carry away a compensating negative amount of energy.

"Sorbents For Carbon Dioxide Capture.", J. Brannon Gary

Faculty Publications

Provided herein are sorbents for carbon dioxide (CO₂) capture, such as from natural gas and coal-fired power plant flue gases, and uses thereof.

Relativistic Elastic Differential Cross Sections For Equal Mass Nuclei, Charles M. Werneth, Khin M. Maung, W.P. Ford

Faculty Publications

The effects of relativistic kinematics are studied for nuclear collisions of equal mass nuclei. It is found that the relativistic and non-relativistic elastic scattering amplitudes are nearly indistinguishable, and, hence, the relativistic and non-relativistic differential cross sections become indistinguishable. These results are explained by analyzing the Lippmann–Schwinger equation with the first order optical potential that was employed in the calculation.

A Generalized Force-Modified Potential Energy Surface For Mechanochemical Simulations, Gopinath Subramanian, Nithin Mathew, Jeff Leiding

Faculty Publications

We describe the modifications that a spatially varying external load produces on a Born-Oppenheimer potential energy surface (PES) by calculating static quantities of interest. The effects of the external loads are exemplified using electronic structure calculations (at the HF/6-31G- level) of two different molecules: ethane and hexahydro-1,3,5-trinitro-s-triazine (RDX). The calculated transition states and Hessian matrices of stationary points show that spatially varying external loads shift the stationary points and modify the curvature of the PES, thereby affecting the harmonic transition rates by altering both the energy barrier as well as the prefactor. The harmonic spectra of both molecules are blueshifted …

Effects Of Oil-Contaminated Sediments On Submerged Vegetation: An Experimental Assessment Of Ruppia Maritima, Charles W. Martin, Lauris O. Hollis, R. Eugene Turner

Faculty Publications

Oil spills threaten the productivity of ecosystems through the degradation of coastal flora and the ecosystem services these plants provide. While lab and field investigations have quantified the response of numerous species of emergent vegetation to oil, the effects on submerged vegetation remain uncertain. Here, we discuss the implications of oil exposure for Ruppia maritima, one of the most common species of submerged vegetation found in the region affected by the recent Deepwater Horizon oil spill. We grew R. maritima in a range of manipulated sediment oil concentrations: 0, 0.26, 0.53, and 1.05 mL oil /L tank volume, and tracked …

Interannual And Subdecadal Variability In The Nutrient Geochemistry Of The Cariaco Basin, Mary I. Scranton, Gordon T. Taylor, Robert Thunell, Claudia R. Benitez-Nelson, Frank Muller-Karger, Kent Fanning, Laura Lorenzoni, Enrique Montes, Ramon Varela, Yrene Astor

Faculty Publications

The CARIACO Ocean Time Series program has made monthly measurements of oxygen, nutrients, and carbon system parameters (∑CO2, alkalinity, pH) in the Cariaco Basin since 1996. At the same time, sediment traps have collected settling particles at four to five depths ranging from 150 to 1,200 m. The depth of the transition from oxic to anoxic conditions has fluctuated dramatically over the time series due to changes in the occurrence of Caribbean water intrusions into the deep basin. Nutrient concentrations in the deep basin have increased steadily with time in a proportion reflective of the elemental ratios in the settling …

Oxygen Vacancies In Lialo2 Crystals, Maurio S. Holston, I. P. Ferguson, John W. Mcclory, Nancy C. Giles, Larry E. Halliburton

Faculty Publications

Singly ionized oxygen vacancies are produced in LiAlO₂ crystals by direct displacement events during a neutron irradiation. These vacancies, with one trapped electron, are referred to as V+O centers. They are identified and characterized using electron paramagnetic resonance (EPR) and optical absorption. The EPR spectrum from the V+O centers is best monitored near 100 K with low microwave power. When the magnetic field is along the [001] direction, this spectrum has a g value of 2.0030 and well-resolved hyperfine interactions of 310 and 240 MHz with the two 27Al nuclei that are adjacent to the oxygen vacancy. A second …

Modeling Napl Dissolution From Pendular Rings In Idealized Porous Media, Junqi Huang, John A. Christ, Mark N. Goltz, Avery H. Demond

Faculty Publications

The dissolution rate of nonaqueous phase liquid (NAPL) often governs the remediation time frame at subsurface hazardous waste sites. Most formulations for estimating this rate are empirical and assume that the NAPL is the nonwetting fluid. However, field evidence suggests that some waste sites might be organic wet. Thus, formulations that assume the NAPL is nonwetting may be inappropriate for estimating the rates of NAPL dissolution. An exact solution to the Young‐Laplace equation, assuming NAPL resides as pendular rings around the contact points of porous media idealized as spherical particles in a hexagonal close packing arrangement, is presented in this …

Semianalytical Solutions For Transport In Aquifer And Fractured Clay Matrix System, Junqi Huang, Mark N. Goltz

Faculty Publications

A three‐dimensional mathematical model that describes transport of contaminant in a horizontal aquifer with simultaneous diffusion into a fractured clay formation is proposed. A group of semianalytical solutions is derived based on specific initial and boundary conditions as well as various source functions. The analytical model solutions are evaluated by numerical Laplace inverse transformation and analytical Fourier inverse transformation. The model solutions can be used to study the fate and transport in a three‐dimensional spatial domain in which a nonaqueous phase liquid exists as a pool atop a fractured low‐permeability clay layer. The nonaqueous phase liquid gradually dissolves into the …

A Polynomial Time Algorithm For Computing The Area Under A Gdt Curve, Aleksandar Poleksic

Faculty Publications

Background

Progress in the field of protein three-dimensional structure prediction depends on the development of new and improved algorithms for measuring the quality of protein models. Perhaps the best descriptor of the quality of a protein model is the GDT function that maps each distance cutoff θ to the number of atoms in the protein model that can be fit under the distance θ from the corresponding atoms in the experimentally determined structure. It has long been known that the area under the graph of this function (GDT_A) can serve as a reliable, single numerical measure …

Differential Effects Of Munc18s On Multiple Degranulation-Relevant Trans-Snare Complexes, Hao Xu, Matthew Grant Arnold, Sushmitha Vijay Kumar

Faculty Publications

Mast cell exocytosis, which includes compound degranulation and vesicle-associated piecemeal degranulation, requires multiple Q- and R- SNAREs. It is not clear how these SNAREs pair to form functional trans-SNARE complexes and how these trans-SNARE complexes are selectively regulated for fusion. Here we undertake a comprehensive examination of the capacity of two Q-SNARE subcomplexes (syntaxin3/SNAP-23 and syntaxin4/SNAP-23) to form fusogenic trans-SNARE complexes with each of the four granule-borne R-SNAREs (VAMP2, 3, 7, 8). We report the identification of at least six distinct trans-SNARE complexes under enhanced tethering conditions: i) VAMP2/syntaxin3/SNAP-23, ii) VAMP2/syntaxin4/SNAP-23, iii) VAMP3/syntaxin3/SNAP-23, iv) VAMP3/syntaxin4/SNAP-23, v) VAMP8/syntaxin3/SNAP-23, and vi) VAMP8/syntaxin4/SNAP-23. …

Experimentally Generating Any Desired Partially Coherent Schell-Model Source Using Phase-Only Control, Milo W. Hyde Iv, Santasri Basu, David G. Voelz, Xifeng Xiao

Faculty Publications

A technique is presented to produce any desired partially coherent Schell-model source using a single phase-only liquid-crystal spatial light modulator (SLM). Existing methods use SLMs in combination with amplitude filters to manipulate the phase and amplitude of an initially coherent source. The technique presented here controls both the phase and amplitude using a single SLM, thereby making the amplitude filters unnecessary. This simplifies the optical setup and significantly increases the utility and flexibility of the resulting system. The analytical development of the technique is presented and discussed. To validate the proposed approach, experimental results of three partially coherent Schell-model sources …

The Sluggs Survey: Globular Cluster Kinematics In A ‘Double Sigma’ Galaxy – Ngc 4473, Adebusola Alabi, Caroline Foster, Duncan Forbes, Aaron Romanowsky, Nicola Pastorello, Jean Brodie, Lee Spitler, Jay Strader, Christopher Usher

Faculty Publications

NGC 4473 is a so-called double sigma (2σ) galaxy, i.e. a galaxy with rare, double peaks in its 2D stellar velocity dispersion. Here, we present the globular cluster (GC) kinematics in NGC 4473 out to ∼10Re (effective radii) using data from combined Hubble Space Telescope/Advanced Camera for Surveys and Subaru/Suprime-Cam imaging and Keck/Deep Imaging Multi-Object Spectrograph. We find that the 2σ nature of NGC 4473 persists up to 3Re, though it becomes misaligned to the photometric major axis. We also observe a significant offset between the stellar and GC rotation amplitudes. This offset can be understood as a co-addition of …

The Sluggs Survey: Inferring The Formation Epochs Of Metal-Poor And Metal-Rich Globular Clusters, Duncan Forbes, Nicola Pastorello, Aaron Romanowsky, Christopher Usher, Jean Brodie, Jay Strader

Faculty Publications

We present a novel, observationally-based framework for the formation epochs and sites of globular clusters (GCs) in a cosmological context. Measuring directly the mean ages of the metal-poor and metal-rich GC subpopulations in our own Galaxy, and in other galaxies, is observationally challenging. Here we apply an alternative approach utilizing the property that the galaxy mass–metallicity relation is a strong function of redshift (or look-back age) but is relatively insensitive to galaxy mass for massive galaxies. Assuming that GCs follow galaxy mass–metallicity relations that evolve with redshift, one can estimate the mean formation epochs of the two GC subpopulations by …