Biological and Chemical Physics Commons^™

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 …

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

Resonant Inelastic X-Ray Scattering Of Methyl Chloride At The Chlorine K Edge, L. El Khoury, Loic Journel, Renaud Guillemin, Stephane Carniato, Wayne C. Stolte, T. Marin, Dennis W. Lindle, Marc Simon

Chemistry and Biochemistry Faculty Research

We present a combined experimental and theoretical study of isolated CH3Cl molecules using resonant inelastic x-ray scattering (RIXS). The high-resolution spectra allow extraction of information about nuclear dynamics in the core-excited molecule. Polarization-resolved RIXS spectra exhibit linear dichroism in the spin-orbit intensities, a result interpreted as due to chemical environment and singlet-triplet exchange in the molecular core levels. From analysis of the polarization-resolved data, Cl 2px, y and 2pz electronic populations can be determined.

Thomson-Resonant Interference Effects In Elastic X-Ray Scattering Near The Cl K Edge Of Hcl, Stephane Carniato, P. Selles, Loic Journel, Renaud Guillemin, Wayne C. Stolte, L. El Khoury, T. Marin, Faris Gel'mukhanov, Dennis W. Lindle, Marc Simon

Chemistry and Biochemistry Faculty Research

We experimentally observed interference effects in elastic x-ray scattering from gas-phase HCl in the vicinity of the Cl K edge. Comparison to theory identifies these effects as interference effects between non-resonant elastic Thomson scattering and resonant Raman scattering. The results indicate the non-resonant Thomson and resonant Raman contributions are of comparable strength. The measurements also exhibit strong polarization dependence, allowing an easy identification of the resonant and non-resonant contributions.

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 …

Shaping The Future Past: Finding History, Creating Identity In The Kwan Hsu Papers, Lisa Chere' Donnelly

Dissertations and Theses

Dr. Kwan Hsu was neither a superstar nor a celebrity. Her name does not come up in conversations about important contributors to her field of biophysics nor is she instantly recognizable for her contributions to Portland State University's international program or the state of Oregon's business ties with China. Yet she was a contributor, a cog-in-the-wheel, at the very least, in all of these areas and more. She was a peripheral member of a well-known Chinese family, but few in the United States know of or perhaps have interest in, but otherwise, she had no great connections or family ties …

Viscoelastic Transition And Yield Strain Of The Folded Protein, Yong Wang, Giovanni Zocchi

Physics Faculty Publications and Presentations

For proteins, the mechanical properties of the folded state are directly related to function, which generally entails conformational motion. Through sub-Angstrom resolution measurements of the AC mechanical susceptibility of a globular protein we describe a new fundamental materials property of the folded state. For increasing amplitude of the forcing, there is a reversible transition from elastic to viscoelastic response. At fixed frequency, the amplitude of the deformation is piecewise linear in the force, with different slopes in the elastic and viscoelastic regimes. Effectively, the protein softens beyond a yield point defined by this transition. We propose that ligand induced conformational …

Developing Hybrid Approaches To Predict Pka Values Of Ionizable Groups, Shawn Witham, Kemper Talley, Lin Wang, Zhe Zhang, Daquan Gao, Wei Yang, Emil Alexov

Publications

Accurate predictions of pKa values of titratable groups require taking into account all relevant processes associated with the ionization/deionization. Frequently, however, the ionization does not involve significant structural changes and the dominating effects are purely electrostatic in origin allowing accurate predictions to be made based on the electrostatic energy difference between ionized and neutral forms alone using a static structure. On another hand, if the change of the charge state is accompanied by a structural reorganization of the target protein, then the relevant conformational changes have to be taken into account in the pKa calculations. Here we report a hybrid …

Progress In The Prediction Of Pka Values In Proteins, Emil Alexov, Ernest L. Mehler, Nathan Baker, Antonio Baptista, Yong Huang, Francesca Milletti, Jens Erik Nielsen, Damien Farrell, Tommy Carstensen, Mats H.M. Olsson, Jana K. Shen, Jim Warwicker, Sarah Williams, J Michael Word

Publications

The pK_a-cooperative aims to provide a forum for experimental and theoretical researchers interested in protein pK_a values and protein electrostatics in general. The first round of the pK_a-cooperative, which challenged computational labs to carry out blind predictions against pK_as experimentally determined in the laboratory of Bertrand Garcia-Moreno, was completed and results discussed at the Telluride meeting (July 6–10, 2009). This article serves as an introduction to the reports submitted by the blind prediction participants that will be published in a special issue of PROTEINS: Structure, Function and Bioinformatics. …

Spectroscopic Studies Of Melamine At High Pressure, Martin Donald Galley

UNLV Theses, Dissertations, Professional Papers, and Capstones

We have performed mid- and far- Infra Red (IR) absorption, Raman spectroscopy, and angular dispersive x-ray diffraction (XRD) studies on melamine under high pressure and room temperature. We have verified the presence of two prior reported phase transitions, the first between 1-2 GPa, and the second between 7-9 GPa. We have also found evidence of a third unreported phase transition between 14-16 GPa, during which, there was a sudden disappearance of all low energy peaks (^-1 ) in both the Raman and IR spectra. The far-IR peak movement experiences a discontinuity as the rate of peak movement suddenly changes. …

Critical Torque For Kink Formation In Double-Stranded Dna, Hao Qu, Yong Wang, Chiao-Yu Tseng, Giovanni Zocchi

Physics Faculty Publications and Presentations

We measure the bending energy of double-stranded DNA in the nonlinear (sharply bent) regime. The measurements are obtained from the melting curves of stressed DNA ring molecules. The nonlinear elastic behavior is captured by a single parameter: the critical torque τc at which the molecule develops a kink. In this regime, the elastic energy is linear in the kink angle. This phenomenology is the same as for the previously reported case of nicked DNA. For the sequences examined, we find τc=31 pN×nm. This critical torque corresponds to a characteristic energy scale (π/2)τc=12 kT room relevant for molecular biology processes associated …

Evolution Of Spur-Length Diversity In Aquilegia Petals Is Achieved Solely Through Cell-Shape Anisotropy, Joshua R. Puzey, Sharon J. Gerbode, Scott A. Hodges, Elena M. Kramer, L. Mahadevan

All HMC Faculty Publications and Research

The role of petal spurs and specialized pollinator interactions has been studied since Darwin. Aquilegia petal spurs exhibit striking size and shape diversity, correlated with specialized pollinators ranging from bees to hawkmoths in a textbook example of adaptive radiation. Despite the evolutionary significance of spur length, remarkably little is known about Aquilegia spur morphogenesis and its evolution. Using experimental measurements, both at tissue and cellular levels, combined with numerical modelling, we have investigated the relative roles of cell divisions and cell shape in determining the morphology of the Aquilegia petal spur. Contrary to decades-old hypotheses implicating a discrete meristematic zone …

Understanding The Molecular Information Contained In Principal Component Analysis Of Vibrational Spectra Of Biological Systems, Franck Bonnier, Hugh Byrne

Articles

K-means clustering followed by Principal Component Analysis (PCA) is employed to analyse Raman spectroscopic maps of single biological cells. K-means clustering successfully identifies regions of cellular cytoplasm, nucleus and nucleoli, but the mean spectra do not differentiate their biochemical composition. The loadings of the principal components identified by PCA shed further light on the spectral basis for differentiation but they are complex and, as the number of spectra per cluster is imbalanced, particularly in the case of the nucleoli, the loadings under-represent the basis for differentiation of some cellular regions. Analysis of pure bio-molecules, both structurally and spectrally distinct, in …

Toward High-Performance Nanostructured Thermoelectric Materials: The Progress Of Bottom-Up Solution Chemistry Approaches, Yixin Zhao, Jeffrey S. Dyck, Clemens Burda

Physics

Significant research effort has recently gone into the synthesis of thermoelectric nanomaterials through different chemical approaches since nanomaterials chemistry became a promising strategy for improving thermoelectric performance. Different thermoelectric nanocrystals, especially PbTe, Bi₂Te₃ and CoSb₃, with various compositions and morphologies have been successfully prepared by solvo/hydrothermal, electrochemical, and ligand-based synthesis methods. Such nanoscale materials show not only substantial reduction in thermal conductivity due to increased phonon scattering at nanoscale grain boundaries and lower densities of phonon states but possibly also an enhancement in thermopower due to electronic quantum size effects. More recently, the notoriously low …

Region-Of-Interest Material Decomposition From Truncated Energy-Resolved Ct, Taly Gilat Schmidt

Biomedical Engineering Faculty Research and Publications

Purpose: Energy-resolved CT using photon-counting detectors has the potential to provide improved material decomposition compared to dual-kVp approaches. However, available photon-counting detectors are susceptible to pulse-pileup artifacts, especially at the periphery of the field of view (FOV) where the object attenuation is low compared to the center of the FOV. Pulse pileup may be avoided by imaging a region-of-interest (ROI) where the dynamic range is expected to be limited. This work investigated performing material decomposition and reconstructing ROI basis images from truncated energy-resolved data.

Methods: A method is proposed to reconstructimages of basis functions primarily contained within the ROI, such …

High Pressure Structural Studies On Nb5si3 Up To 26.2 Gpa, Brandon Stewart, Ravhi S. Kumar

Undergraduate Research Opportunities Program (UROP)

With the use of synchrotron techniques, we can better understand how crystalline structures behave under extreme conditions. This yields the opportunity to resolve complex crystal structures [1]. Here, we focus on the high pressure crystal structure of Nb5Si3. Refractory metal silicides are an important class of materials as they are used in high temperature applications such as turbines and aerospace modules. As an example, the performance of a jet engine is highly influenced by the maximum internal pressure and temperature possible. Obtaining higher levels of thrust is dependent upon the material's ability to remain structurally sound under extreme temperatures and …

Crystal Structural Behavior Of Cocu₂O₃ At High Temperatures, April Jeffries, Ravhi S. Kumar, Andrew L. Cornelius

Undergraduate Research Opportunities Program (UROP)

High temperature structure of CoCu₂O₃ The spin ladder compounds have received much attention recently due to their relation to the high transition temperature superconductivity. Also the study of spin ladder compounds is of great interest to explore the specific characteristics that result in their behavior. The CoCu₂O₃ spin ladder crystal structure is similar to SrCu₂O₃, which is apparent composition for many high temperature superconductors. The effects of temperature on structural change are investigated for this system. High temperature x-ray diffraction patterns were collected up to 1000⁰C and the variation of lattice parameters as a function of temperature up to decomposition …

A Missense Mutation In Clic2 Associated With Intellectual Disability Is Predicted By In Silico Modeling To Affect Protein Stability And Dynamics, Shawn Witham, Kyoko Takano, Charles Schwartz, Emil Alexov

Publications

Large-scale next generation resequencing of X chromosome genes identified a missense mutation in the CLIC2 gene on Xq28 in a male with X-linked intellectual disability (XLID) and not found in healthy individuals. At the same time, numerous nsSNPs (nonsynonomous SNP) have been reported in the CLIC2 gene in healthy individuals indicating that the CLIC2 protein can tolerate amino acid substitutions and be fully functional. To test the possibility that p.H101Q is a disease-causing mutation, we performed in silico simulations to calculate the effects of the p.H101Q mutation on CLIC2 stability, dynamics, and ionization states while comparing the effects obtained for …