Biological and Chemical Physics Commons^™

Fragmentation Properties Of Three-Membered Ring Heterocyclic Molecules By Partial Ion Yield Spectroscopy: C2h4o And C2h4s, Wayne C. Stolte, I. Dumitriu, S-W Yu, Gunnar Ohrwall, Maria Novella Piancastelli, Dennis W. Lindle

Chemistry and Biochemistry Faculty Research

We investigated the photofragmentation properties of two three-membered ring heterocyclic molecules, C₂H₄O and C₂H₄S, by total and partial ion yield spectroscopy. Positive and negative ions have been collected as a function of photon energy around the C 1s and O 1s ionization thresholds in C₂H₄O, and around the S 2p and C 1s thresholds in C₂H₄S. We underline similarities and differences between these two analogous systems. We present a new assignment of the spectral features around the C K-edge and the sulfur L_{2 …}

Effect Of Surfactants On The Structure And Morphology Of Magnesium Borate Hydroxide Nanowhiskers Synthesized By Hydrothermal Route, Latha Kumari, Wz Li, Shrinivas Kulkarni, Kh Wu, Wei Chen, Chunlei Wang, Charles H. Vannoy, Roger M. Leblanc

Department of Physics

Magnesium borate hydroxide (MBH) nanowhiskers were synthesized using a one step hydrothermal process with different surfactants. The effect surfactants have on the structure and morphology of the MBH nanowhiskers has been investigated. The X-ray diffraction profile confirms that the as-synthesized material is of single phase, monoclinic MgBO₂(OH). The variations in the size and shape of the different MBH nanowhiskers have been discussed based on the surface morphology analysis. The annealing of MBH nanowhiskers at 500 °C for 4 h has significant effect on the crystal structure and surface morphology. The UV–vis absorption spectra of the MBH nanowhiskers synthesized …

A Comparison Of New Methods For Generating Energy-Minimizing Configurations Of Patchy Particles, Eric Jankowski, Sharon C. Glotzer

Eric Jankowski

Increasingly complex particles are pushing the limits of traditional simulation techniques used to study self-assembly. In this work, we test the use of a learning-augmented Monte Carlo method for predicting low energy configurations of patchy particles shaped like “Tetris®” pieces. We extend this method to compare it against Monte Carlo simulations with cluster moves and introduce a new algorithm—bottom-up building block assembly—for quickly generating ordered configurations of particles with a hierarchy of interaction energies.

Metal-Induced Bystander Effects: Mechanism And Implicationis., Nicola Cogan

Doctoral

The radiation-induced bystander effect is a phenomenon known to occur post irradiation, characterised by the induction of biological effects in unirradiated cells as a result of receiving signals from irradiated cells or their culture medium. Chemicalinduced bystander effects are poorly characterised and there are no reports of a bystander effect induced by metals. Heavy metals and in particular chromium (VI) are known to cause persistent genomic instability. For the first time, this study provides evidence that a short, low-dose exposure of human fibroblasts to chromium (VI) causes a bystander effect in human fibroblasts that persists for at least thirty days …

Experimental And Theoretical Investigation Of Molecular Field Effects By Polarization-Resolved Resonant Inelastic X-Ray Scattering, Stephane Carniato, Renaud Guillemin, Wayne C. Stolte, Loic Journel, Richard Taieb, Dennis W. Lindle, Marc Simon

Chemistry and Biochemistry Faculty Research

We present a combined theoretical and experimental study of molecular field effects on molecular core levels. Polarization-dependent resonant inelastic x-ray scattering is observed experimentally after resonant K-shell excitation of CF₃Cl and HCl. We explain the linear dichroism observed in spin-orbit level intensities as due to molecular field effects, including singlet-triplet exchange, and interpret this behavior in terms of population differences in the 2p_x,y,z inner-shell orbitals. We investigate theoretically the different factors that can affect the electronic populations and the dynamical R dependence of the spin-orbit ratio. Finally, the results obtained are used to interpret the L-shell …

Continued Development Of An Empirical Function For Predicting And Rationalizing Protein–Protein Binding Affinities, Joseph Audie

Chemistry & Physics Faculty Publications

Here we summarize recent work on the continued development of our fast and simple empirical equation for predicting and structurally rationalizing protein–protein and protein–peptide binding affinities. Our empirical expression consists of six regression-weighted physical descriptors and derives from two key simplifying assumptions: (1) the assumption of rigid-body association and (2) the assumption that all contributions not explicitly considered in the equation make a net contribution to binding of ≈0 kcal. Within the strict framework of rigid-body association, we tested relative binding affinity predictions using our empirical equation against the corresponding experimental binding free energy data for 197 interface alanine mutants. …

High-Sensitivity Spectral Fluorescence Lifetime Imaging For Resolving Spectroscopically Overlapping Species, Justin Lee Crawford

Masters Theses

The capability to resolve the contributions from spectroscopically overlapping fluorophores has enabled significant breakthroughs in cellular imaging. However, commercial microscopes for this purpose use analog light detection with least squares curve-fitting analysis and improvements in sensitivity are needed. To this end, a microscope has been constructed with high throughput and single-photon detection capability. The fluorescence is separated through use of a prism spectrometer or a series of dichroic mirrors into four spectral bands and detected using four single-photon avalanche diode (SPAD) detectors, which provide high-quantum efficiency in the red spectral region. The detectors are connected to a time-correlated single photon …

Charge Transfer Assisted By Collective H-Bonding Network Dynamics, Omar F. Mohammed, Christina M. Othon, Oh-Hoon Kwon, Ahmed H. Zewail

Christina M Othon

Although there have been numerous studies of solvation, the role of solvent specific and collective interactions, especially for charge-transfer processes, remains difficult to unravel. Here, we report, using femtosecond fluorescence up-conversion and steady-state spectroscopic measurements, studies of well-designed single-sited formylperylene (FPe) in binary solvents. One of the solvents (methanol, MOH) can selectively hydrogen (H) bond to the carbonyl (C=O) site, while the other (acetonitrile, ACN) cannot, but both have similar polarity ( for MOH and for ACN). The results reveal that ultrafast charge transfer from the perylene unit to the carbonyl group of FPe is facilitated by site-specific H-bonding interactions …

Production Of O2 Herzberg States In The Deep Uv Photodissociation Of Ozone, Reinhard Schinke, George C. Mcbane, L. Shen, P. C. Singh, A. G. Suits

Peer Reviewed Articles

High-resolution imaging experiments combined with new electronic structure and dynamics calculations strongly indicate that the O(³P)+O₂ products with very low kinetic energy release (E_tr2: A' ³Δ_u(v=0, 1, 2) and A ³Σ⁺_u(v=0, 1). This interpretation contradicts the earlier assignment to very high (v≥26) vibrational states of O²(³Σ^-_g).

An Exchange-Coulomb Model Potential Energy Surface For The Ne-Co Interaction. I. Calculation Of Ne-Co Van Der Waals Spectra, Ashok K. Dham, Frederick R. W. Mccourt, William J. Meath, George C. Mcbane

Peer Reviewed Articles

Exchange-Coulomb model potential energy surfaces have been developed for the Ne–CO interaction. The initial model is a three-dimensional potential energy surface based upon computed Heitler–London interaction energies and literature results for the long-range induction and dispersion energies, all as functions of interspecies distance, the orientation of CO relative to the interspecies axis, and the bond length of the CO molecule. Both a rigid-rotor model potential energy surface, obtained by setting the CO bond length equal to its experimental spectroscopic equilibrium value, and a vibrationally averaged model potential energy surface, obtained by averaging the stretching dependence over the ground vibrational motion …

Solvation In Protein (Un)Folding: Effect Of Local And Bulk Dynamics In The Melittin Tetramer-Monomer Transition, Christina M. Othon, Oh-Hoon Kwon, Milo M. Lin, Ahmed H. Zewail

Christina M Othon

Protein structural integrity and flexibility are intimately tied to solvation. Here we examine the effect that changes in bulk and local solvent properties have on protein structure and stability. We observe the change in solvation of an unfolding of the protein model, melittin, in the presence of a denaturant, trifluoroethanol. The peptide system displays a well defined transition in that the tetramer unfolds without disrupting the secondary or tertiary structure. In the absence of local structural perturbation, we are able to reveal exclusively the role of solvation dynamics in protein structure stabilization and the (un)folding pathway. A sudden retardation in …

The Conformational Gymnastics Of The Escherichia Coli Seca Molecular Machine And Its Interactions With Signal Sequences, Jenny Lynn Maki

Open Access Dissertations

Protein secretion is a selective and regulated process that is essential in all organisms. In bacteria the preprotein translocase SecA, either free in the cytosol or associated with the SecYEG translocon, recognizes and binds most post-translational secretory proteins containing an N-terminal signal sequence. In Gram-negative bacteria, the molecular chaperone SecB binds many of the preproteins to keep them in a translocation-competent state. Subsequently, SecB delivers the preproteins to the translocon-associated SecA, which binds the signal sequence and also interacts with mature regions of the preprotein. After the preprotein/SecA/SecYEG complex has formed, the energy derived from ATP hydrolysis by SecA coupled …

Measuring Dose To Small Animals In Micro-Ct, Avi Hameroff

Honors Capstone Projects - All

An important application of William Röntgen’s discovery of x-rays is computed tomography (CT). First developed in the 1970’s, CT scanners of today are able to provide a detailed image of a patient’s body with minimal risk to patient and a very short turnaround time from scan to reconstructed image. This powerful tool provides physicians another way to diagnose patients while simultaneously allowing for researchers to learn about the human body.

Scientists soon became interested in using the technology on small animals but practical issues plagued the widespread use of CT in preclinical research. The scale of the scanners was simply …

Magnetic Sensors For Biodetection, Pranjali Vineet Sneha Deshpande

UNLV Theses, Dissertations, Professional Papers, and Capstones

The objective of thesis is to design magnetic sensor for detection of nanoparticles. Recently integrating the standard laboratory techniques into integrated system on chip is growing attention. Recent development is to combine magnetic markers and magnetoresistive sensors together in magnetic chip. In this thesis two magnetoresistive sensors were studied and designed.

By applying magnetic fields, magnetic nanoparticles can be manipulated on-chip, which can be utilized to pull the molecules to specific binding sites or to test the binding strength and distinguish between specifically and non-specifically bound molecules

Magnetoresistive sensors are compatible with the semiconductor industry which provides electronic signal directly …

The Rotational Spectrum Of The Fed Radical In Its X4Δ State, Measured By Far-Infrared Laser Magnetic Resonance, Michael Jackson, Lyndon R. Zink, Jonathan P. Towle, Neil Riley, John M. Brown

All Faculty Scholarship for the College of the Sciences

Transitions between the spin-rotational levels of the FeD radical in the v = 0level of the X ⁴Δ ground state have been detected by the technique of laser magnetic resonance at far-infrared wavelengths. Pure-rotational transitions have been observed for the three lowest spin components. Lambda-type doubling is resolved on all the observed transitions; nuclear hyperfine structure is not observed. The energy levels of FeD are strongly affected by the breakdown of the Born–Oppenheimer approximation and cannot be modeled accurately by an effective Hamiltonian. The data are therefore fitted to an empirical formula to yield term values and g-factors for …

Periodic And Dynamic 3-D Gold Nanoparticle− Dna Network Structures For Surface-Enhanced Raman Spectroscopy-Based Quantification, Kyuwan Lee

Kyuwan Lee

The enhancement factor of gold nanoparticles linked by DNA in a three-dimensional (3-D) network structure was evaluated as 1.12 × 107 and shown to be greater than a two-dimensional (2-D) array by a factor of 10, possibly due to the dimensional expansion of resonance and periodicity of the so formed structures. Uniform and higher level of enhancement was possible from these DNA linked gold nanoparticle networks because of the matching of the resonant condition and the excitation wavelength (785 nm) to enable dynamic quantification of analytes by surface-enhanced Raman spectroscopy (SERS). The structure was first validated by obtaining a SERS …

Thermal Inactivation Of Bacillus Anthracis Using Laser Irradiation Of Micro-Etched Platforms, Jeffrey B. Bacon

Theses and Dissertations

The purpose of this research was to determine the probability of kill for a thermal inactivation strategy for use against biological agents; specifically the resilient endospore of Bacillus anthracis (Ba). The effort focused on short durations (milliseconds to several seconds) and temperatures (300 to 1300 K) simulating the periphery effects after an explosion generated by conventional munitions. For an improved statistical counting, applied microlithography techniques were used to produce micro-etched glass platforms consisting of 532 circular sample wells, evenly spaced. Small carbon black radiators, which provide fast heating/cooling rate and confined temperature distribution, were produced by populating the etched wells …

In Vitro Toxicity Of Silver Nanoparticles In Human Lung Epithelial Cells, Christina R. Kearns

Theses and Dissertations

Nanotechnology is quickly becoming incorporated into everyday products and uses. Silver nanoparticles, specifically, are being used in commercial products, to include aerosols. The purpose of this research was to determine whether silver nanoparticles are toxic to human lung epithelial cells. Different types (coated vs. uncoated), concentrations (10, 50, 100, and 200 µg/mL) and sizes (coated 5 and 80nm, uncoated 10 and 80nm) of silver nanoparticles were used during this study. Toxicity measurements were completed through in vitro techniques. Another study was also completed on toxicity mechanisms by measuring the reactive oxygen species (ROS) generated. Results showed that silver nanoparticles induce …

Modeling Effects Of Human Single Nucleotide Polymorphisms On Protein-Protein Interactions, Shaolei Teng, Thomas Madej, Anna Panchenko, Emil Alexov

Publications

A large set of three-dimensional structures of 264 protein-protein complexes with known nonsynonymous single nucleotide polymorphisms (nsSNPs) at the interface was built using homology-based methods. The nsSNPs were mapped on the proteins' structures and their effect on the binding energy was investigated with CHARMM force field and continuum electrostatic calculations. Two sets of nsSNPs were studied: disease annotated Online Mendelian Inheritance in Man (OMIM) and nonannotated (non-OMIM). It was demonstrated that OMIM nsSNPs tend to destabilize the electrostatic component of the binding energy, in contrast with the effect of non-OMIM nsSNPs. In addition, it was shown that the change of …

Swcnt Suppress Inflammatory Mediator Responses In Human Lung Epithelium In Vitro, Eva Herzog, Hugh Byrne, Maria Davoren, Anke-Gabriele Lenz, Albert Duschl, Gertie Janneke Oostingh

Articles

Single walled carbon nanotubes have gained enormous popularity due to a variety of potential applications which will ultimately lead to increased human and environmental exposure to these nanoparticles. This study was carried out in order to evaluate the inflammatory response of immortalised and primary human lung epithelial cells (A549 and NHBE) to single walled carbon nanotube samples (SWCNT). Special focus was placed on the mediating role of lung surfactant on particle toxicity. The toxicity of SWCNT dispersed in cell culture medium was compared to that of nanotubes dispersed in dipalmitoylphosphatidylcholine (DPPC, the main component of lung lining fluid). Exposure was …

The Mechanical Properties Of Individual, Electrospun Fibrinogen Fibers, Christine C. Helms, Corentin Coulais, Manoj Namboothiry, David L. Carroll, Roy R. Hantgan, Martin Guthold

Physics Faculty Publications

We used a combined atomic force microscope (AFM)/fluorescence microscope technique to study the mechanical properties of individual, electrospun fibrinogen fibers in aqueous buffer. Fibers (average diameter 208 nm) were suspended over 12 μm-wide grooves in a striated, transparent substrate. The AFM, situated above the sample, was used to laterally stretch the fibers and to measure the applied force. The fluorescence microscope, situated below the sample, was used to visualize the stretching process. The fibers could be stretched to 2.3 times their original length before breaking; the breaking stress was 22·10⁶ Pa. We collected incremental stress-strain curves to determine the …

Development And Validation Of An Empirical Free Energy Function For Calculating Protein–Protein Binding Free Energy Surfaces, Joseph Audie

Chemistry & Physics Faculty Publications

In a previous paper, we described a novel empirical free energy function that was used to accurately predict experimental binding free energies for a diverse test set of 31 protein–protein complexes to within ≈1.0 kcal. Here, we extend that work and show that an updated version of the function can be used to (1) accurately predict native binding free energies and (2) rank crystallographic, native-like and non-native binding modes in a physically realistic manner. The modified function includes terms designed to capture some of the unfavorable interactions that characterize non-native interfaces. The function was used to calculate one-dimensional binding free …

Violence On The Brain: A Critique Of Neuroscience In Criminal Law, Amanda C. Pustilnik

Faculty Scholarship

Is there such a thing as a criminally "violent brain"? Does it make sense to speak of "the neurobiology of violence" or the "psychopathology of crime"? Is it possible to answer on a physiological level what makes one person engage in criminal violence and another not, under similar circumstances?

This Article first demonstrates parallels between certain current claims about the neurobiology of criminal violence and past movements that were concerned with the law and neuroscience of violence: phrenology, Lombrosian biological criminology, and lobotomy. It then engages in a substantive review and critique of several current claims about the neurological bases …

Spectroscopic Study Of The Dimerisation Process Of Iron Protoporphyrin Ix, K. Dziedzic-Kocurek, Hugh Byrne, A. Swiderski, J. Stanek

Articles

The commercial protoporphyrin IX, iron-ferriprotoporphyrin IX-chloride and synthesized iron porphyrin μ-oxo-dimers were examined by UV/vis absorption and fluorescence, Fourier transformed infrared spectroscopy, resonance Raman, X-ray absorption, Mössbauer spectroscopy and SQUID. The evidence of Fe-O-Fe antiferromagnetic coupling concluded from SQUID and Mössbauer in the case of samples containing dimerized forms confirmed the presence of the oxo-bridges. In this paper the results of UV/vis, fluorescence, Fourier transform infrared FTIR and Raman spectroscopies are reported and discussed. The study is based on the comparison of the free-base protoporphyrin IX, Fe-PPIX-Cl and the synthesized dimerized specimen. The vibrational modes in two energy regions i.e. …

Partial Ion Yield Sspectroscopy Around The Cl 2p And C 1s Ionization Thresholds In Cf3cl, D. Ceolin, Maria Novella Piancastelli, Wayne C. Stolte, Dennis W. Lindle

Chemistry and Biochemistry Faculty Research

We present a partial ion yield experiment on freon 13, CF₃Cl, excited in the vicinity of the C 1s and Cl 2p ionization thresholds. We have collected a large amount of cationic fragments and a few anionic fragments at both edges. We have observed a strong intensity dependence of Rydberg transitions with ion fragment size for the CF_nCl⁺ and CF_n⁺/F⁺ (n=0–3) series at both the Cl 2p and C 1s ionization edges. Selectivity in the fragmentation processes involving the C–Cl and C–F bonds are highlighted by the intensities of the C …

Yttrium And Hydrogen Superstructure And Correlation Of Lattice Expansion And Proton Conductivity In The Bazr0.9y0.1o2.95 Proton Conductor, A. Braun, A. Ovalle, V. Pomjakushin, A. Cervellino, S. Erat, Wayne C. Stolte, T. Graule

Chemistry and Biochemistry Faculty Research

Bragg reflections in Y-resonant x-ray diffractograms of BaZr_0.9Y_0.1O_2.95 (BZY10) reveal that Y is organized in a superstructure. Comparison with neutron diffraction superstructure reflections in protonated/deuterated BZY10 suggests that both superstructures are linked, and that protons move in the landscape imposed by the Y. The thermal lattice expansion decreases abruptly for protonated BZY10 at T≥648±20 K, coinciding with the onset of lateral proton diffusion and suggesting a correlation of structural changes and proton conductivity. The chemical shift in the Y L₁-shell x-ray absorption spectra reveals a reduction from Y³⁺ toward Y²⁺ upon …

Characterisation Of Immunosensor Surfaces Using Scanning Force Microscopy, Eva Maria Gil Romero

Theses

The overall aim of this thesis was twofold. Firstly, to evaluate how scanning force microscopy (SFM) could be used to characterise the surfaces of immunosensors. Four aspects of immunosensor characteristics where SFM has particular application potential have been identified: (a) immobilisation chemistry and (b) the surface density, (c) orientation and (d) specificity of the immobilised antibodies. Secondly, to examine experimentally how the Explorer SFM instrument could be used for such characterisation.

The Explorer SFM instrument is of an open-loop actuator design that is exposed to the intrinsic inadequacies of piezoelectric actuators. In this regard, careful calibration has shown that achieving …

Pressure-Driven Transport Of Particles Through A Converging-Diverging Microchannel, Ye Ai, Sang W. Joo, Xiangchun Xuan, Shizhi Qian

Mechanical & Aerospace Engineering Faculty Publications

Pressure-driven transport of particles through a symmetric converging-diverging microchannel is studied by solving a coupled nonlinear system, which is composed of the Navier-Stokes and continuity equations using the arbitrary Lagrangian-Eulerian finite-element technique. The predicted particle translation is in good agreement with existing experimental observations. The effects of pressure gradient, particle size, channel geometry, and a particle's initial location on the particle transport are investigated. The pressure gradient has no effect on the ratio of the translational velocity of particles through a converging-diverging channel to that in the upstream straight channel. Particles are generally accelerated in the converging region and then …

Appearance Of A Fractional Stokes-Einstein Relation In Water And A Structural Interpretation Of Its Onset, L. Xu, F. Mallamace, Z. Yan, Francis W. Starr, S. V. Buldyrev, H. E. Stanley

Francis Starr

The Stokes–Einstein relation has long been regarded as one of the hallmarks of transport in liquids. It predicts that the self-diffusion constant D is proportional to (τ/T)−1, where τ is the structural relaxation time and T is the temperature. Here, we present experimental data on water confirming that, below a crossover temperature T× ≈ 290 K, the Stokes– Einstein relation is replaced by a ‘fractional’ Stokes–Einstein relation D ∼ (τ/T)−ζ with ζ ≈ 3/5 (refs 1–6). We interpret the microscopic origin of this crossover by analysing the OH- stretch region of the Fourier transform infrared spectrum over a temperature range …

Review Of Biocd Physics And Technology, David D. Nolte

David D Nolte

Spinning biodisks have advantages that make them attractive for specialized biochip applications. The two main classes of spinning biodisks are microfluidic disks and bio-optical compact disks BioCD. Microfluidic biodisks take advantage of noninertial pumping for lab-on-a-chip devices using noninertial valves and switches under centrifugal and Coriolis forces to distribute fluids about the disks. BioCDs use spinning-disk interferometry, under the condition of common-path phase quadrature, to perform interferometric label-free detection of molecular recognition and binding. The optical detection of bound molecules on a disk is facilitated by rapid spinning that enables high-speed repetitive sampling to eliminate 1/ f noise through common-mode …