Biological and Chemical Physics Commons^™

Cloning And Characterization Of Sas0754, A Hypothetical Protein From Community Associated Staphylococcus Aureus, Unknown Unknown

Symposium 2012

Community associated Staphylococcus aureus (strain MSSA476) is a gram positive cocci capable of infecting many different parts of the body and known to cause serious infections that can be fatal, such as bacterial arthritis and acute endocarditis. To find effective ways of fighting against CA-MRSA strains we must learn more about their ability to infect. The focus of this study was cloning and characterization of a protein referred to as SAS0754. The size of SAS0754 is 340 amino acids and the gene sequence is 1023 nucleotides. The hypothetical function of this protein is that it is an extracellular matrix binding …

A Convenient Synthesis Of 2,6-Dichlorohomonicotinic Acid, Chase Buchanan, Richard W. Fitch

Symposium 2012

In our synthetic efforts toward the alkaloid phantasmidine, we required a convenient source of the title compound. Herein, we describe a short synthesis of 2,6-dichlorohomonicotinic acid by direct allylation of 2,6-dichloropyridine with LDA/allyl chloride, followed by permanganate oxidation of the side chain [figure1]. Yields for the allylation are high, while permanganate oxidation required more adjustment. Successful conditions require the modest acidification of the mixture with acetic acid and cleanup by acid base workup. No chromatography is needed.

Convenient Parallel Synthesis Of Alkyl- And Aryl-S-Tert-Butyl Thiothers, Rebecca Norcross, Jessica Stanfield, Richard W. Fitch

Symposium 2012

While preparing novel cysteine derivatives as oxidation catalysts, we needed S-tert-butylcysteine. We also examined acid-promoted tert-butylation of thiols using tert-butanol as reagent and solvent. While cysteine and aminoethanethiol work well using tBuOH in 4M HCl, other thiols fail in the aqueous environment and aerobic conditions. We examined a variety of aliphatic and aromatic thiols in tBuOH with H2SO4 catalysis and found that argon sparging and the use of 1 eq of acid led to good yields in a parallel format.

Use Of Second Harmonic Generation (Shg) Imaging For 3-Dimensional Ultrastructural Visualization Of Muscle Repair Mechanisms, Matthew Dufner

Honors Scholar Theses

In this study, we have combined SHG imaging with various fluorescent dyes which are designed to stain nuclei and used a skeletal muscle injury and regeneration model to establish the ability of this approach to reliably and reproducibly evaluate the above nuclear parameters. By using the cobra cardiotoxin (CTX-1), which creates acute well defined injuries within the muscle, on the tibialis anterior (TA) and gastrocnemius hind limb muscles of mice, predictable and reproducible regenerative patterns (in response to acute injury) can be observed by harvesting muscle samples at specific time points during recovery. Through SHG imaging, we endeavor to document …

Delphi: A Comprehensive Suite For Delphi Software And Associated Resources, Lin Li, Chuan Li, Subhra Sarkar, Jie Zhang, Shawn Witham, Zhe Zhang, Lin Wang, Nicholas Smith, Marharyta Petukh, Emil Alexov

Publications

Background

Accurate modeling of electrostatic potential and corresponding energies becomes increasingly important for understanding properties of biological macromolecules and their complexes. However, this is not an easy task due to the irregular shape of biological entities and the presence of water and mobile ions.

Results

Here we report a comprehensive suite for the well-known Poisson-Boltzmann solver, DelPhi, enriched with additional features to facilitate DelPhi usage. The suite allows for easy download of both DelPhi executable files and source code along with a makefile for local installations. The users can obtain the DelPhi manual and parameter files required for the corresponding …

Multi-State Analysis Of The Ocs Ultraviolet Absorption Including Vibrational Structure, Johan A. Schmidt, M. S. Johnson, George C. Mcbane, Reinhard Schinke

Peer Reviewed Articles

The first absorption band of OCS (carbonyl sulfide) is analyzed using potential energy surfaces and transition dipole moment functions of the lowest four singlet and the lowest four triplet states. Excitation of the 2¹A' state is predominant except at very low photon energies. It is shown that the vibrational structures in the center of the band are due to excitation of the 2³A" triplet state, whereas the structures at the very low energies are caused by bending excitation in the potential wells of states 2¹A' and 1¹A".

Superspin Relaxation Times In Fe3o4 / Hexane Magnetic Fluids Measured By Frequency-Resolved Ac Susceptibility, Joshua L. Morris ^, Michael P. Eastman, Cristian E. Botez *

COURI Symposium Abstracts, Spring 2012

A properly formatted abstract has been uploaded below. The pasted version is here

Superspin relaxation times in Fe₃O₄ / hexane magnetic fluids measured by frequency-resolved ac susceptibility

Joshua Morris^ and Cristian E. Botez*

Department of Physics, University of Texas at El Paso, 500 W. University Avenue,

El Paso, TX 79968, U.S.A

Michael P. Eastman

Department of Chemistry, University of Texas at El Paso, 500 W. University Avenue,

El Paso, TX 79968, U.S.A

We have used frequency-resolved (100 Hz < f < 10,000 Hz) ac magnetic susceptibility measurements to directly determine the Néel and Brown relaxation times in 30-nm-size Fe₃O₄ / hexane magnetic fluids at temperatures between 200 and 300 K. Our data collected on both …

K-Shell X-Ray Spectroscopy Of Atomic Nitrogen, M. M. Sant'anna, Gunnar Ohrwall, Wayne C. Stolte, Alfred S. Schlachter, Dennis W. Lindle, B. M. Mclaughlin

Chemistry and Biochemistry Faculty Research

Absolute K-shell photoionization cross sections for atomic nitrogen have been obtained from both experiment and state-of-the-art theoretical techniques. Because of the difficulty of creating a target of neutral atomic nitrogen, no high-resolution K-edge spectroscopy measurements have been reported for this important atom. Interplay between theory and experiment enabled identification and characterization of the strong 1s → np resonance features throughout the threshold region. An experimental value of 409.64 ± 0.02 eV was determined for the K-shell binding energy.

Analyzing Effects Of Naturally Occurring Missense Mutations, Zhe Zhang, Maria A. Miteva, Lin Wang, Emil Alexov

Publications

Single-point mutation in genome, for example, single-nucleotide polymorphism (SNP) or rare genetic mutation, is the change of a single nucleotide for another in the genome sequence. Some of them will produce an amino acid substitution in the corresponding protein sequence (missense mutations); others will not. This paper focuses on genetic mutations resulting in a change in the amino acid sequence of the corresponding protein and how to assess their effects on protein wild-type characteristics. The existing methods and approaches for predicting the effects of mutation on protein stability, structure, and dynamics are outlined and discussed with respect to their underlying …

Product Angular Distributions In The Ultraviolet Photodissociation Of N2O, George C. Mcbane, Reinhard Schinke

Peer Reviewed Articles

The angular distribution of products from the ultraviolet photodissociation of nitrous oxide yielding O(¹D) and N₂(X¹Σ⁺_g) was investigated using classical trajectory calculations. The calculations modeled absorption only to the 2¹A'electronic state but used surface-hopping techniques to model nonadiabatic transitions to the ground electronic state late in the dissociation. Observed values of the anisotrophy parameter β, which decrease as the product N₂ rotational quantum number jincreases, could be well reproduced. The relatively low observed βvalues arise principally from nonaxial recoil due to the very …

Α−Α Cross-Links Increase Fibrin Fiber Elasticity And Stiffness, Christine C. Helms, Robert A.S. Ariens, S. Uitte De Willige, Kristina F. Standeven, Martin Guthold

Physics Faculty Publications

Fibrin fibers, which are ∼100 nm in diameter, are the major structural component of a blood clot. The mechanical properties of single fibrin fibers determine the behavior of a blood clot and, thus, have a critical influence on heart attacks, strokes, and embolisms. Cross-linking is thought to fortify blood clots; though, the role of α–α cross-links in fibrin fiber assembly and their effect on the mechanical properties of single fibrin fibers are poorly understood. To address this knowledge gap, we used a combined fluorescence and atomic force microscope technique to determine the stiffness (modulus), extensibility, and elasticity of …

Experimental Studies Of The Nacs 53Π0 And A3Σ+ States, Seth T. Ashman, B. Mcgeehan, C. M. Wolfe, C. Faust, K. Richter

Engineering & Physics Faculty Publications

We report high resolution measurements of 372 NaCs 53Π0(v, J) ro-vibrational level energies in the range 0 ≤ v ≤ 22. The data have been used to construct NaCs 53Π0 potential energy curves using the Rydberg–Klein-Rees and inverted perturbation approximation methods. Bound-free 53Π0(v, J) → 1(a)3Σ+ emission has also been measured, and is used to determine the repulsive wall of the 1(a)3Σ+ state and the 53Π0 → 1(a)3Σ+ relative transition dipole moment function. Hyperfine structure in the 53Π0 state has not been observed in this experiment. This null result is explained using a simple vector coupling model.

Modeling Of Growth Kinetics And Characterization Of Membrane Mechanics, Antonio Nava

Electronic Theses and Dissertations

One growing field in alternative energy is biofuel production through microorganisms. These fields of research include hydrogen and biofuel production through the cultivation of algae. We've selected 2 different algae, Anabaena sp. cpcc 387 and Tetraselmis to study. Through mathematical modeling of Anabaena we investigate the complex multicellular relationships and colony stability when noise is introduced. In conjunction with researchers at NREL, we've set out to characterize Tetraselmis cells' membrane elasticity.

Simulated Associating Polymer Networks, Joris Billen

CGU Theses & Dissertations

Telechelic associating polymer networks consist of polymer chains terminated by endgroups that have a different chemical composition than the polymer backbone. When dissolved in a solution, the endgroups cluster together to form aggregates. At low temperature, a strongly connected reversible network is formed and the system behaves like a gel. Telechelic networks are of interest since they are representative for biopolymer networks (e.g. F-actin) and are widely used in medical applications (e.g. hydrogels for tissue engineering, wound dressings) and consumer products (e.g. contact lenses, paint thickeners).

In this thesis such systems are studied by means of a molecular dynamics/Monte Carlo …

Electrochemical Polymerization Of Ppy-Mwcnt Composite As A Counter Electrode For Dye-Sensitized Solar Cells, S. Abdulalmohsin, S. M. Al-Mutoki, Z. Li

Journal of the Arkansas Academy of Science

Polypyrrole (PPy) - multi wall carbon nanotube (MWCNT) nanocomposites were synthesized by using in situ electrochemical polymerization with different COOH-functionalized MWCNTs. The PPY-MWCNT composites were used as counter electrode in the fabrication of dye sensitized solar cells (DSCs). Compared to the DSC device with PPy counter electrode, the devices with PPY/MWCNT composite electrode offer much higher total photovoltaic conversion efficiency due to the reduced series resistance. These PPY/MWCNT nanocomposite materials proved to be a good alternate to the expensive Pt as counter electrode in DSC.

Current Range In Lightning Return Strokes, M. Hemmati, W. P. Childs, D. C. Waters, J. R. Christensen, B. C. Richard

Journal of the Arkansas Academy of Science

In our investigation of breakdown waves, we use a one-dimensional, steady-state, constant velocity fluid model. This investigation involves breakdown waves for which the electric field force on electrons is in the opposite direction of wave propagation. The waves are considered to be shock fronted and the electron gas partial pressure is large enough to sustain the wave propagation. Our basic set of electron fluid-dynamical equations is composed of the equations for conservation of mass, momentum and energy, coupled with Poisson’s equation. This investigation involves breakdown waves for which a large current exists behind the shock front. The current behind the …

A New Method To Derive Electronegativity From Resonant Inelastic X-Ray Scattering, Stephane Carniato, Loic Journel, Renaud Guillemin, Maria Novella Piancastelli, Wayne C. Stolte, Dennis W. Lindle, Marc Simon

Chemistry and Biochemistry Faculty Research

Electronegativity is a well-known property of atoms and substituent groups. Because there is no direct way to measure it, establishing a useful scale for electronegativity often entails correlating it to another chemical parameter; a wide variety of methods have been proposed over the past 80 years to do just that. This work reports a new approach that connects electronegativity to a spectroscopic parameter derived from resonant inelastic x-ray scattering. The new method is demonstrated using a series of chlorine-containing compounds, focusing on the Cl 2p−1LUMO1 electronic states reached after Cl 1s→LUMO core excitation and subsequent KL radiative decay. Based on …

Quantitative Reagent-Free Detection Of Fibrinogen Levels In Human Blood Plasma Using Raman Spectroscopy, Kelvin Poon, Fiona Lyng, Peter Knief, Orla L. Howe, Aidan Meade, James Curtin, Hugh Byrne, Joseph Vaughan

Articles

Fibrinogen assays are commonly used as part of clinical screening tests to investigate haemorrhagic states, for detection of disseminated intravascular coagulation and as a predictor of a variety of cardiovascular events. The Clauss assay, which measures thrombin clotting time, is the most commonly used method for measuring fibrinogen levels. Nevertheless, inconsistencies are present in inter-manufacturer reagent sources, calibration standards and methodologies. Automated coagulation analysers, which measure changes in optical density during the prothrombin time (PT-Fg), have found use in many hospitals. However, the PT-Fg method is found to give falsely elevated values due to varying choices of calibrants, reagents and …

Fabrication And Characterization Of Aluminum-Doped Zno/Pani Hybrid Solar Cells, S. Abdulalmohsin, S. M. Al-Mutoki, Z. Li

Journal of the Arkansas Academy of Science

We report a facile method to fabricate an AZO/PANI heterostructure by a sandwiching technique. Aluminum-doped ZnO (AZO) films were deposited onto indium tin oxide (ITO) glass using the sputtering technique while PANI films were deposited onto ITO glass using electropolymerization. The optoelectric properties of the inorganic/organic device were characterized

Al/Pani-Mwnt/Au-Plastic Schottky Diode Solar Cells, S. Abdulalmohsin, S. M. Al-Mutoki, Z. Li

Journal of the Arkansas Academy of Science

Al/PANI-MWNT/Au-Plastic Schottky diode solar cells were fabricated by the electrochemical polymerization technique to make polyaniline films on the top of gold nanoparticles film. The aluminum contact was deposited by thermal evaporation. The electro-optical characteristics of these devices produced at the different polymerization time were compared. Here, we achieved the highest ever reported open-circuit voltage of 0.8 V with the electrochemical polymerization technique. The polymerization of polyaniline films was thought to be a major factor in the enhanced performance. The effects of varying the polyaniline thickness on the device performance were investigated