Physical Sciences and Mathematics Commons^™

(Mu-Ctl-01-14) Simsys Game Specification, Hemalochane Jayaraj, Riddhi Raiker, Kendra Cooper, C. Shaun Longstreet

Center for Teaching and Learning Technical Reports

No abstract provided.

Dioxygen Reactivity Of Biomimetic Fe(Ii) Complexes With Noninnocent Catecholate, O-Aminophenolate, And O-Phenylenediamine Ligands, Michael M. Bittner, Sergey Lindeman, Cordina V. Popescu, Adam T. Fiedler

Chemistry Faculty Research and Publications

This study describes the O₂ reactivity of a series of high-spin mononuclear Fe(II) complexes each containing the facially coordinating tris(4,5-diphenyl-1-methylimidazol-2-yl)phosphine (^Ph2TIP) ligand and one of the following bidentate, redox-active ligands: 4-tert-butylcatecholate (^tBuCatH^–), 4,6-di-tert-butyl-2-aminophenolate (^tBu2APH^–), or 4-tert-butyl-1,2-phenylenediamine (^tBuPDA). The preparation and X-ray structural characterization of [Fe²⁺(^Ph2TIP)(^tBuCatH)]OTf, [3]OTf and [Fe²⁺(^Ph2TIP)(^tBuPDA)](OTf)₂, [4](OTf)₂ are described here, whereas [Fe²⁺(^{Ph2 …}

Shewanella Oneidensis Cytochrome C Nitrite Reductase (Ccnir) Does Not Disproportionate Hydroxylamine To Ammonia And Nitrite, Despite A Strongly Favorable Driving Force, Matthew Youngblut, Daniel J. Pauly, Natalia Stein, Daniel Walters, John A. Conrad, Graham R. Moran, Brian Bennett, A. Andrew Pacheco

Physics Faculty Research and Publications

Cytochrome c nitrite reductase (ccNiR) from Shewanella oneidensis, which catalyzes the six-electron reduction of nitrite to ammonia in vivo, was shown to oxidize hydroxylamine in the presence of large quantities of this substrate, yielding nitrite as the sole free nitrogenous product. UV–visible stopped-flow and rapid-freeze-quench electron paramagnetic resonance data, along with product analysis, showed that the equilibrium between hydroxylamine and nitrite is fairly rapidly established in the presence of high initial concentrations of hydroxylamine, despite said equilibrium lying far to the left. By contrast, reduction of hydroxylamine to ammonia did not occur, even though disproportionation of hydroxylamine to …

Micro-Environment Causes Reversible Changes In Dna Methylation And Mrna Expression Profiles In Patient-Derived Glioma Stem Cells, Mehmet Baysan, Kevin Woolard, Serdar Bozdag, Gregory Riddick, Svetlana Kotliarova, Margaret C. Cam, Galina I. Belova, Susie Ahn, Wei Zhang, Hua Song, Jennifer Walling, Holly Stevenson, Paul Meltzer, Howard A. Fine

Mathematics, Statistics and Computer Science Faculty Research and Publications

In vitro and in vivo models are widely used in cancer research. Characterizing the similarities and differences between a patient's tumor and corresponding in vitro and in vivo models is important for understanding the potential clinical relevance of experimental data generated with these models. Towards this aim, we analyzed the genomic aberrations, DNA methylation and transcriptome profiles of five parental tumors and their matched in vitro isolated glioma stem cell (GSC) lines and xenografts generated from these same GSCs using high-resolution platforms. We observed that the methylation and transcriptome profiles of in vitro GSCs were significantly different from their corresponding …

Highly Sensitive Noninvasive Cardiac Transplant Rejection Monitoring Using Targeted Quantification Of Donor-Specific Cell-Free Deoxyribonucleic Acid, Mats Hidestrand, Aoy Tomita-Mitchell, Pip M. Hidestrand, Arnold Oliphant, Mary Goetsch, Karl D. Stamm, Huan-Ling Liang, Chesney Castleberry, D. Woodrow Benson, Gail Stendahl, Pippa Simpson, Stuart Berger, James S. Tweddell, Steven Zangwill, Michael E. Mitchell

Mathematics, Statistics and Computer Science Faculty Research and Publications

No abstract provided.

Mcdonald Log-Logistic Distribution With An Application To Breast Cancer Data, M. H. Tahir, Muhammad Mansoor, Muhammad Zubair, Gholamhossein Hamedani

Mathematics, Statistics and Computer Science Faculty Research and Publications

We introduce a five-parameter continuous model, called the McDonald log-logistic distribution, to extend the two-parameter log-logistic distribution. Some structural properties of this new distribution such as reliability measures and entropies are obtained. The model parameters are estimated by the method of maximum likelihood using L-BFGS-B algorithm. A useful characterization of the distribution is proposed which does not require explicit closed form of the cumulative distribution function and also connects the probability density function with a solution of a first order differential equation. An application of the new model to real data set shows that it can give consistently better fit …

Electron Cooling In A Young Radio Supernova: Sn 2012aw, Naveen Yadav, Alak Ray, Christopher Stockdale, Poonam Chandrasiri, Randall Smith, Rupak Roy, Vikram Dwarkadas, Firoza Sutaria, David Pooley

Physics Faculty Research and Publications

We present the radio observations and modeling of an optically bright Type II-P supernova (SN), SN 2012aw which exploded in the nearby galaxy Messier 95 (M95) at a distance of 10 Mpc. The spectral index values calculated using C, X, and K bands are smaller than the expected values for the optically thin regime. During this time, the optical bolometric light curve stays in the plateau phase. We interpret the low spectral-index values to be a result of electron cooling. On the basis of comparison between the Compton cooling timescale and the synchrotron cooling timescale, we find that …

Quantifying The Statistical Impact Of Grappa In Fcmri Data With A Real-Valued Isomorphism, Iain P. Bruce, Daniel B. Rowe

Mathematics, Statistics and Computer Science Faculty Research and Publications

The interpolation of missing spatial frequencies through the generalized auto-calibrating partially parallel acquisitions (GRAPPA) parallel magnetic resonance imaging (MRI) model implies a correlation is induced between the acquired and reconstructed frequency measurements. As the parallel image reconstruction algorithms in many medical MRI scanners are based on the GRAPPA model, this study aims to quantify the statistical implications that the GRAPPA model has in functional connectivity studies. The linear mathematical framework derived in the work of Rowe , 2007, is adapted to represent the complex-valued GRAPPA image reconstruction operation in terms of a real-valued isomorphism, and a statistical analysis is performed …

Acrylamide Production Using Encapsulated Nitrile Hydratase From Pseudonocardia Thermophila In A Sol–Gel Matrix, Salette Martinez, Misty L. Kuhn, James T. Russell, Richard C. Holz, Timothy E. Elgren

Chemistry Faculty Research and Publications

The cobalt-type nitrile hydratase from Pseudonocardia thermophila JCM 3095 (PtNHase) was successfully encapsulated in tetramethyl orthosilicate sol–gel matrices to produce a PtNHase:sol–gel biomaterial. The PtNHase:sol–gel biomaterial catalyzed the conversion of 600 mM acrylonitrile to acrylamide in 60 min at 35 °C with a yields of >90%. Treatment of the biomaterial with proteases confirmed that the catalytic activity is due to the encapsulated enzyme and not surface bound NHase. The biomaterial retained 50% of its activity after being used for a total of 13 consecutive reactions for the conversion of acrylonitrile to acrylamide. The thermostability and long-term …

When Semi-Monotone Implies Monotone, Paul Bankston

Mathematics, Statistics and Computer Science Faculty Research and Publications

The basic theme of this talk is the extrinsic description of objects by means of morphisms. One way to do this is to say that all monomorphisms from the object are “special” in some way; the dual of this is to single out epimorphisms to the object.

Synergistic Adsorption Of Heavy Metal Ions And Organic Pollutants By Supramolecular Polysaccharide Composite Materials From Cellulose, Chitosan And Crown Ether, Tamutsiwa M. Mututuvari, Chieu D. Tran

Chemistry Faculty Research and Publications

We have developed a simple one-step method to synthesize novel supramolecular polysaccharide composites from cellulose (CEL), chitosan (CS) and benzo-15-crown 5 (B15C5). Butylmethylimidazolium chloride [BMIm⁺Cl⁻], an ionic liquid (IL), was used as a sole solvent for dissolution and preparation of the composites. Since majority of [BMIm⁺Cl⁻] used was recovered for reuse, the method is recyclable. The [CEL/CS + B15C5] composites obtained retain properties of their components, namely superior mechanical strength (from CEL), excellent adsorption capability for heavy metal ions and organic pollutants (from B15C5 and CS). More importantly, the [CEL/CS + B15C5] …

Resonance Raman Spectroscopy Reveals That Substrate Structure Selectively Impacts The Heme-Bound Diatomic Ligands Of Cyp17, Piotr J. Mak, Michael C. Gregory, Stephen G. Sligar, James R. Kincaid

Chemistry Faculty Research and Publications

An important function of steroidogenic cytochromes P450 is the transformation of cholesterol to produce androgens, estrogens, and the corticosteroids. The activities of cytochrome P450c17 (CYP17) are essential in sex hormone biosynthesis, with severe developmental defects being a consequence of deficiency or mutations. The first reaction catalyzed by this multifunctional P450 is the 17α-hydroxylation of pregnenolone (PREG) to 17α-hydroxypregnenolone (17-OH PREG) and progesterone (PROG) to 17α-hydroxyprogesterone (17-OH PROG). The hydroxylated products then either are used for production of corticoids or undergo a second CYP17 catalyzed transformation, representing the first committed step of androgen formation. While the hydroxylation reactions are catalyzed by …

Recurrence Relations For Moments Of Dual Generalized Order Statistics From Weibull Gamma Distribution And Its Characterizations, M. A. W. Mahmoud, Y. Abdel-Aty, N. M. Mohamed, Gholamhossein Hamedani

Mathematics, Statistics and Computer Science Faculty Research and Publications

In this paper, we establish explicit forms and new recurrence relations satisfied by the single and product moments of dual generalized order statistics from Weibull gamma distribution (WGD). The results include as particular cases the relations for moments of reversed order statistics and lower records. We present characterizations of WGD based on (i) recurrence relation for single moments, (ii) truncated moments of certain function of the variable and (iii) hazard function.

Spectral Data For "Probing The Human Estrogen Receptor-Alpha Binding Requirements For Phenolic Mono- And Do-Hydroxyl Compounds: A Combined Synthesis, Binding And Docking Study", Christopher Mccullough, Terrence S. Neumann, Jayapal Reddy Gone, Zhengjie He, Julie Lukesh, Rajesh K. Pandey, William A. Donaldson, Daniel S. Sem

Natural Products Synthesis via Organoiron Methodology

Spectral data used in the course of researching "Probing the human estrogen receptor-alpha binding requirements for phenolic mono- and do-hydroxyl compounds: A combined synthesis, binding and docking study".

Various estrogen analogs were synthesized and tested for binding to human ERα using a fluorescence polarization displacement assay. Binding affinity and orientation were also predicted using docking calculations. Docking was able to accurately predict relative binding affinity and orientation for estradiol, but only if a tightly bound water molecule bridging Arg394/Glu353 is present. Di-hydroxyl compounds sometimes bind in two orientations, which are flipped in terms of relative positioning of their hydroxyl groups. …

Homoleptic Nickel(Ii) Complexes Of Redox-Tunable Pincer-Type Ligands, Jeewantha S. Hewage, Sarath Wanniarachchi, Tyler James Morin, Brendan J Liddle, Megan Banaszynski, Sergey V. Lindeman, Brian Bennett, James R. Gardinier

Physics Faculty Research and Publications

Different synthetic methods have been developed to prepare eight new redox-active pincer-type ligands, H(X,Y), that have pyrazol-1-yl flanking donors attached to an ortho-position of each ring of a diarylamine anchor and that have different groups, X and Y, at the para-aryl positions. Together with four previously known H(X,Y) ligands, a series of 12 Ni(X,Y)₂ complexes were prepared in high yields by a simple one-pot reaction. Six of the 12 derivatives were characterized by single-crystal X-ray diffraction, which showed tetragonally distorted hexacoordinate nickel(II) centers. The nickel(II) complexes exhibit two quasi-reversible one-electron oxidation waves in their cyclic voltammograms, with …

Indemics: An Interactive High-Performance Computing Framework For Data Intensive Epidemic Modeling, Keith R. Bisset, Jiangzhuo Chen, Suruchi Deodhar, Xizhou Feng, Yifei Ma, Madhav V. Marathe

Mathematics, Statistics and Computer Science Faculty Research and Publications

We describe the design and prototype implementation of Indemics (_Interactive; Epi_demic; _Simulation;)—a modeling environment utilizing high-performance computing technologies for supporting complex epidemic simulations. Indemics can support policy analysts and epidemiologists interested in planning and control of pandemics. Indemics goes beyond traditional epidemic simulations by providing a simple and powerful way to represent and analyze policy-based as well as individual-based adaptive interventions. Users can also stop the simulation at any point, assess the state of the simulated system, and add additional interventions. Indemics is available to end-users via a web-based interface.

Detailed performance analysis shows that Indemics greatly enhances the …

Characterizations Of New Modified Weibull Distribution, Gholamhossein Hamedani

Mathematics, Statistics and Computer Science Faculty Research and Publications

Several characterizations of a New Modified Weibull distribution, introduced by Doostmoradi et al. (2014), are presented. These characterizations are based on: (i) truncated moment of a function of the random variable; (ii) the hazard function; (iii) a single function of the random variable; (iv) truncated moment of certain function of the 1st order statistic.

Varieties Of P-Restriction Semigroups, Peter R. Jones

Mathematics, Statistics and Computer Science Faculty Research and Publications

The restriction semigroups, in both their one-sided and two-sided versions, have arisen in various fashions, meriting study for their own sake. From one historical perspective, as “weakly E-ample” semigroups, the definition revolves around a “designated set” of commuting idempotents, better thought of as projections. This class includes the inverse semigroups in a natural fashion. In a recent paper, the author introduced P-restriction semigroups in order to broaden the notion of “projection” (thereby encompassing the regular *-semigroups). That study is continued here from the varietal perspective introduced for restriction semigroups by V. Gould. The relationship between varieties of regular …

Accurate Calculations Of Rotationally Inelastic Scattering Cross Sections Using Mixed Quantum/Classical Theory, Alexander Semenov, Dmitri Babikov

Chemistry Faculty Research and Publications

For computational treatment of rotationally inelastic scattering of molecules, we propose to use the mixed quantum/classical theory, MQCT. The old idea of treating translational motion classically, while quantum mechanics is used for rotational degrees of freedom, is developed to the new level and is applied to Na + N₂ collisions in a broad range of energies. Comparison with full-quantum calculations shows that MQCT accurately reproduces all, even minor, features of energy dependence of cross sections, except scattering resonances at very low energies. The remarkable success of MQCT opens up wide opportunities for computational predictions of inelastic scattering cross sections …

Rotational Quenching Of H2O By He: Mixed Quantum/Classical Theory And Comparison With Quantum Results, Mikhail V. Ivanov, Marie-Lise Dubernet, Dmitri Babikov

Chemistry Faculty Research and Publications

The mixed quantum/classical theory (MQCT) formulated in the space-fixed reference frame is used to compute quenching cross sections of several rotationally excited states of water molecule by impact of He atom in a broad range of collision energies, and is tested against the full-quantum calculations on the same potential energy surface. In current implementation of MQCT method, there are two major sources of errors: one affects results at energies below 10 cm⁻¹, while the other shows up at energies above 500 cm⁻¹. Namely, when the collision energy E is below the state-to-state transition energy ΔE the …

Isomer Dependence In The Assembly And Lability Of Silver(I) Trifluoromethanesulfonate Complexes Of The Heteroditopic Ligands, 2-, 3-, And 4-[Di(1H-Pyrazolyl)Methyl]Phenyl(Di-P-Tolyl)Phosphine, James R. Gardinier, Jeewantha S. Hewage, Sergey V. Lindeman

Chemistry Faculty Research and Publications

Three isomers of a new heteroditopic ligand that contains a di(1H-pyrazolyl)methyl (−CHpz₂) moiety connected to a di(p-tolyl)phosphine group via a para-, meta-, or ortho-phenylene spacer (pL, mL, and oL, respectively) have been synthesized by using a palladium(0)-catalyzed coupling reaction between HP(p-tolyl)₂ and the appropriate isomer of (IC₆H₄)CHpz₂. The 1:1 complexes of silver(I) trifluoromethanesulfonate, Ag(OTf), were prepared to examine the nature of ligand coordination and the type of supramolecular isomer (monomeric, cyclic oligomeric, or polymeric) that would be obtained. …

Assembly, Structure, And Reactivity Of Cu4S And Cu3S Models For The Nitrous Oxide Reductase Active Site, CuZ*, Brittany J. Johnson, Sergey V. Lindeman, Neal P. Mankad

Chemistry Faculty Research and Publications

Bridging diphosphine ligands were used to facilitate the assembly of copper clusters with single sulfur atom bridges that model the structure of the Cu_Z* active site of nitrous oxide reductase. Using bis(diphenylphosphino)amine (dppa), a [Cu^I₄(μ₄-S)] cluster with N–H hydrogen bond donors in the secondary coordination sphere was assembled. Solvent and anion guests were found docking to the N–H sites in the solid state and in the solution phase, highlighting a kinetically viable pathway for substrate introduction to the inorganic core. Using bis(dicyclohexylphosphino)methane (dcpm), a [Cu^I₃(μ₃-S)] cluster was assembled …

Mixed Quantum/Classical Theory For Inelastic Scattering Of Asymmetric-Top-Rotor + Atom In The Body-Fixed Reference Frame And Application To The H2O + He System, Alexander Semenov, Marie-Lise Dubernet, Dmitri Babikov

Chemistry Faculty Research and Publications

The mixed quantum/classical theory (MQCT) for inelastic molecule-atom scattering developed recently [A. Semenov and D. Babikov, J. Chem. Phys.139, 174108 (2013)] is extended to treat a general case of an asymmetric-top-rotor molecule in the body-fixed reference frame. This complements a similar theory formulated in the space-fixed reference-frame [M. Ivanov, M.-L. Dubernet, and D. Babikov, J. Chem. Phys.140, 134301 (2014)]. Here, the goal was to develop an approximate computationally affordable treatment of the rotationally inelastic scattering and apply it to H₂O + He. We found that MQCT is somewhat less accurate at lower scattering energies. For example, below E …

Probing The Human Estrogen Receptor-Α Binding Requirements For Phenolic Mono- And Di-Hydroxyl Compounds: A Combined Synthesis, Binding And Docking Study, Christopher Mccullough, Terrence S. Neumann, Jayapal Reddy Gone, Zhengjie He, Christian Herrild, Julie Lukesh, Rajesh K. Pandey, William A. Donaldson, Daniel S. Sem

Chemistry Faculty Research and Publications

Various estrogen analogs were synthesized and tested for binding to human ERα using a fluorescence polarization displacement assay. Binding affinity and orientation were also predicted using docking calculations. Docking was able to accurately predict relative binding affinity and orientation for estradiol, but only if a tightly bound water molecule bridging Arg394/Glu353 is present. Di-hydroxyl compounds sometimes bind in two orientations, which are flipped in terms of relative positioning of their hydroxyl groups. Di-hydroxyl compounds were predicted to bind with their aliphatic hydroxyl group interacting with His524 in ERα. One nonsteroid-based dihdroxyl compound was 1000-fold specific for ERβ over ERα, and …

On Readout Of Vibrational Qubits Using Quantum Beats, Dmytro Shyshlov, Eduardo Berrios, Martin Gruebele, Dmitri Babikov

Chemistry Faculty Research and Publications

Readout of the final states of qubits is a crucial step towards implementing quantum computation in experiment. Although not scalable to large numbers of qubits per molecule, computational studies show that molecular vibrations could provide a significant (factor 2–5 in the literature) increase in the number of qubits compared to two-level systems. In this theoretical work, we explore the process of readout from vibrational qubits in thiophosgene molecule, SCCl₂, using quantum beat oscillations. The quantum beats are measured by first exciting the superposition of the qubit-encoding vibrational states to the electronically excited readout state with variable time-delay pulses. …

Cellulose-Chitosan-Keratin Composite Materials: Synthesis, Immunological And Antibacterial Properties, Meghann Rosewald, Fang Yao Stephen Hou, Tamutsiwa Moven Mututuvari, April L. Harkins, Chieu D. Tran

Chemistry Faculty Research and Publications

Novel composites were synthesized from keratin (KER), cellulose (CEL) and chitosan (CS). The method is recyclable because majority (>88%) of [BMIm⁺Cl^-], an ionic liquid (IL), used as the sole solvent, was recovered for reuse. Experimentally, it was confirmed that unique properties of each component remain intact in the composites, namely bactericide (from KER and CS) and anti-inflammatory property (from KER). Specifically, the composites were examined for their anti-inflammatory influence on macrophages. The cells were imaged and immunophenotyped to determine the quantity using the macrophage marker CD11b. The 75:25 [KER+CS] composite was found to have the …

Mixed Quantum/Classical Calculations Of Total And Differential Elastic And Rotationally Inelastic Scattering Cross Sections For Light And Heavy Reduced Masses In A Broad Range Of Collision Energies, Alexander Semenov, Dmitri Babikov

Chemistry Faculty Research and Publications

The mixed quantum/classical theory (MQCT) for rotationally inelastic scattering developed recently [A. Semenov and D. Babikov, J. Chem. Phys.139, 174108 (2013)] is benchmarked against the full quantum calculations for two molecular systems: He + H2 and Na + N2. This allows testing new method in the cases of light and reasonably heavy reduced masses, for small and large rotational quanta, in a broad range of collision energies and rotational excitations. The resultant collision cross sections vary through ten-orders of magnitude range of values. Both inelastic and elastic channels are considered, as well as differential (over scattering angle) cross sections. In …

Enantiomeric Selective Adsorption Of Amino Acid By Polysaccharide Composite Materials, Simon Duri, Chieu D. Tran

Chemistry Faculty Research and Publications

A composite containing cellulose (CEL) and chitosan (CS) synthesized by a simple and recyclable method by using butylmethylimmidazolium chloride, an ionic liquid, was found to exhibit remarkable enantiomeric selectivity toward the adsorption of amino acids. The highest adsorption capacity and enantiomeric selectivity are exhibited by 100% CS. A racemic amino acid can be enantiomerically resolved by 100% CS in about 96–120 h. Interestingly, adsorption by 50:50 CEL/CS is more similar to that by 100% CS than to 100% CEL. Specifically, whereas 100% CEL has the lowest adsorption capacity and enantiomeric selectivity, 50:50 CEL/CS has sufficient enantiomeric selectivity to enable it …

Controlled Release Kinetics In Hydroxy Double Salts: Effect Of Host Anion Structure, Stephen Majoni, Jeanne M. Hossenlopp

Chemistry Faculty Research and Publications

Nanodimensional layered metal hydroxides such as layered double hydroxides (LDHs) and hydroxy double salts (HDSs) can undergo anion exchange reactions releasing intercalated anions. Because of this, these metal hydroxides have found applications in controlled release delivery of bioactive species such as drugs and pesticides. In this work, isomers of hydroxycinnamate were used as model compounds to systematically explore the effects of anion structure on the rate and extent of anion release in HDSs. Following intercalation and subsequent release of the isomers, it has been demonstrated that the nature and position of substituent groups on intercalated anions have profound effects on …

Trivial Meet And Join Within The Lattice Of Monotone Triangles, John Engbers, Adam Hammett

Mathematics, Statistics and Computer Science Faculty Research and Publications

The lattice of monotone triangles (�_n, ≼) ordered by entry-wise comparisons is studied. Let τ_min denote the unique minimal element in this lattice, and τ_max the unique maximum. The number of r-tuples of monotone triangles (τ₁...,τ_r) with minimul infimum τ_min (maximul supremum τ_max, resp.) is shown to asymptotically approach r|�_n|^r-1 as n→ ∞. Thus, with high probability this even implies that one of the τ_i is τ_min (τ_max, resp.). Higher-order error terms are also discussed.