Physics Commons^™

Dinitrogen Functionalization Using A Molybdenum Atom: Bridging The Gap Between Small And Coordination Complexes Via Quantum Mechanical Methods, Maria Virginia White

Doctoral Dissertations

Chemistry devotes a significant amount of its research to understanding small molecule activation from an electronic structure perspective to help with the investigation of the reaction pathways of catalytically active substances that can promote biomimetic catalysis. A large portion of the energy used annually in our planet is used for the artificial nitrogen fixation (Haber-Bosch process), which renders dinitrogen activation a subject of study. Molybdenum, a fourth row transitional metal, has demonstrated its effectiveness as an essential component of the dinitrogen reduction catalytic process. To better understand the multiple dinitrogen molybdenum binding modes, the work described herein combines wave function …

Synthetic Heterosynaptic Plasticity Enhances The Versatility Of Memristive Systems Emulating Bio-Synapse Structure And Function, William T. Mcclintic

Doctoral Dissertations

Memristive systems occur in nature and are hallmarked via pinched hysteresis, the difference in the forward and reverse pathways for a given phenomenon. For example, neurons of the human brain are composed of synapses which apply the properties of memristance for neuronal communication, learning, and memory consolidation. Modern technology has much to gain from the characteristics of memristive systems, including lower power operation, on-chip memory, and bio-inspired computing. What is more, a relationship between memristive systems and synaptic plasticity exists and can be investigated focusing on homosynaptic and heterosynaptic plasticity. Where homosynaptic plasticity applies to interactions between neurons at a …

Approaches To Studying Bacterial Biofilms In The Bioeconomy With Nanofabrication Techniques And Engineered Platforms., Michelle Caroline Halsted

Doctoral Dissertations

Studies that estimate more than 90% of bacteria subsist in a biofilm state to survive environmental stressors. These biofilms persist on man-made and natural surfaces, and examples of the rich biofilm diversity extends from the roots of bioenergy crops to electroactive biofilms in bioelectrochemical reactors. Efforts to optimize microbial systems in the bioeconomy will benefit from an improved fundamental understanding of bacterial biofilms. An understanding of these microbial systems shows promise to increase crop yields with precision agriculture (e.g. biosynthetic fertilizer, microbial pesticides, and soil remediation) and increase commodity production yields in bioreactors. Yet conventional laboratory methods investigate these micron-scale …

Probing Structure, Function And Dynamics In Bacterial Primary And Secondary Transporter-Associated Binding Proteins, Shantanu Shukla

Doctoral Dissertations

Substrate binding proteins (SBPs) are ubiquitous in all life forms and have evolved to perform diverse physiological functions, such as in membrane transport, gene regulation, neurotransmission, and quorum sensing. It is quite astounding to observe such functional diversity among the SBPs even when they are restricted by their fold space. Therefore, the SBPs are an excellent set of proteins that can reveal how proteins evolution novel function in a structurally conserved/constrained fold. This study attempts to understand the phenomenon of affinity and specificity evolution in SBPs by combining a set of biochemical, biophysical, and structural studies on the SBPs involved …

Understanding The Fundamentals Of Ionic Conductivity In Polymer Electrolytes, Eric Wayne Stacy

Doctoral Dissertations

The rate of advancement for mobilized electronic technologies is outpacing the development of small efficient batteries. Lithium-ion batteries are currently the most widely used energy storage device for consumer electronics. Traditional lithium-ion batteries use a liquid electrolyte to separate the cathodes and anodes; however, conventional liquid electrolytes have inherent problems, such as consisting of flammable carbonate components, hazardous material, and have a significant cost/weight in the battery. In addition, the liquid electrolyte cannot prevent the growth of lithium dendrites during the charge/discharge cycle of the lithium-ion battery. These dendrites can connect the anode to the cathode of the battery cell …

Transport Of Water And Ions Through Single-Walled Armchair Carbon Nanotubes: A Molecular Dynamics Study, Michelle Patricia Aranha

Doctoral Dissertations

The narrow hydrophobic interior of a carbon nanotube (CNT) poses a barrier to the transport of water and ions, and yet, unexpectedly, numerous experimental and simulation studies have confirmed fast water transport rates comparable to those seen in biological aquaporin channels. These outstanding features of high water permeability and high solute rejection of even dissolved ions that would typically require a lot of energy for separation in commercial processes makes carbon nanotubes an exciting candidate for desalination membranes. Extending ion exclusion beyond simple mechanical sieving by the inclusion of electrostatics via added functionality to the nanotube bears promise to not …

Development Of Microfluidic Platforms For Studies Of Cellular Organization In Escherichia Coli, Anna Dawn Jennings

Masters Theses

Traditionally, bacteria cells have been imaged on agarose pads allowing them to grow in steady conditions for only a few doubling times. To understand the cellular organization in bacteria, tools are needed that allow the observation of log-phase cells for many generations. In recent years, several microfluidic platforms have been designed that allow microscopic imaging of bacteria for over one hundred generations. One of the most promising approaches has been the so-called mother machine design where bacteria grow in small dead-end channels all connected to a large main channel, which is used to flow fresh nutrients to the cells and …

Biophysical Studies Of Cell Division Protein Localization Mechanisms In Escherichia Coli, Matthew Wayne Bailey

Doctoral Dissertations

How nanometer-scale proteins position accurately within micron-scale bacteria has intrigued both biologists and physicists alike. A critical process requiring precise protein localization is cell division. In most bacteria, cell division starts with the self-assembly of the FtsZ proteins into filaments that form a ring-like structure encircling the cell at its middle, the Z-ring. The Z-ring is a scaffold for additional proteins that synthesize the lateral cell wall which separates the two daughter cells. If division planes are misplaced relative to bacterial chromosomes, also called nucleoids, daughter cells with incomplete genetic material can be produced. In Escherichia coli, research carried out …

Hi-Fidelity Simulation Of The Self-Assembly And Dynamics Of Colloids And Polymeric Solutions With Long Range Interactions, Mahdy Malekzadeh Moghani

Doctoral Dissertations

Modeling the equilibrium properties and dynamic response of the colloidal and polymeric solutions provides valuable insight into numerous biological and industrial processes and facilitates development of novel technologies. To this end, the centerpiece of this research is to incorporate the long range electrostatic or hydrodynamic interactions via computationally efficient algorithms and to investigate the effect of these interactions on the self-assembly of colloidal particles and dynamic properties of polymeric solutions. Specifically, self-assembly of a new class of materials, namely bipolar Janus nano-particles, is investigated via molecular dynamic simulation in order to establish the relationship between individual particle characteristics, such as …

Experimental And Statistical Techniques To Probe Extraordinary Electronic Properties Of Molecules, Byron Hager Smith

Doctoral Dissertations

The existence of an additional electron or hole in the presence of an electric monopole is a well understood physical system, but this ideality is far from the true physical properties of many molecules. Examples of such irregular electronic states include the attachment of an excess charge to a molecule's dipole moment, electronic correlation spanning a molecule, or attachment of multiple excess charges. Current theoretical and experimental interpretations widely vary for these states and further elucidation of the nature of irregular electronic structure may provide solutions to unexplained observations and the impetus for industrial application. For example, in the case …

Three-Dimensional Electrokinetic Trapping Of A Single Fluorescent Nanoparticle In Solution, Jason Keith King

Doctoral Dissertations

This dissertation presents the development of an instrument for effectively trapping a single fluorescent nanoparticle that is freely diffusing in solution in all three dimensions. The instrument is expected to have applications for studies of single nanoparticles or molecules for which prolonged observations are required, but without immobilization or proximity to a surface, which may alter behavior. The trapping technique depends on rapid three-dimensional position measurements of the nanoparticle with sub-micron precision, which are used for real-time control of induced electrokinetic motion, so as to counteract Brownian motion. While anti-Brownian electrokinetic trapping experiments in one and two dimensions have previously …

Application Of Computational Molecular Biophysics To Problems In Bacterial Chemotaxis, Davi Ortega

Doctoral Dissertations

The combination of physics, biology, chemistry, and computer science constitutes the promising field of computational molecular biophysics. This field studies the molecular properties of DNA, protein lipids and biomolecules using computational methods. For this dissertation, I approached four problems involving the chemotaxis pathway, the set of proteins that function as the navigation system of bacteria and lower eukaryotes.

In the first chapter, I used a special-purpose machine for molecular dynamics simulations, Anton, to simulate the signaling domain of the chemoreceptor in different signaling states for a total of 6 microseconds. Among other findings, this study provides enough evidence to propose …

Confinement Effects Of Solvation On A Molecule Physisorbed On A Metal Particle, Jacob Fosso Tande

Doctoral Dissertations

We describe and present results of the implementation of the surface and volume polarization for electrostatics~(SVPE) and the iso-density surface solvation models. Unlike most other implementation of the solvation models where the solute and the solvent are described with multiple numerical representation, our implementation uses a multiresolution, adaptive multiwavelet basis to describe both solute and the solvent. This requires reformulation to use integral equations throughout as well as a conscious management of numerical properties of the basis.

Likewise, we investigate the effects of solvation on the static properties of a molecule physisorbed on a spherical particle, modeled as a polarizable …

Spatially Resolved Laser And Thermal Desorption/Ionization Coupled With Mass Spectrometry, Olga Sergeevna Ovchinnikova

Doctoral Dissertations

The work discussed in this dissertation is aimed at creating novel approaches to chemical imaging that ultimately allow for submicron resolution. This goal has been approached from two direction using laser based desorption and coupling it with an AFM using apertureless tip-enhanced laser ablation/ionization. The second direction was through the development a new approach to thermal desorption based mass spectrometry experiments by using a proximal probe to spatially desorb the surface and ionizing the plume of neutrals using a secondary ionization source at atmospheric pressure. The thermal desorption approach allows for the easy scaling of the technique all the way …

Quantitative Binocular Assessment Using Infrared Video Photoscreening, Lei Shi

Doctoral Dissertations

Photorefraction is a technique that has been used in the past two decades for pediatric vision screening. The technique uses a digital or photographic camera to capture the examinee‟s retinal reflex from a light source that is located near the camera‟s lens. It has the advantages of being objective, binocular and low cost, which make it a good candidate for pediatric screening when compared to other methods. Although many children have been screened using this technique in the U.S., its sensitivity and other disadvantages make it unacceptable for continued use. The Adaptive Photorefraction system (APS) was developed at the Center …

Adaptation And Stochasticity Of Natural Complex Systems, Roy David Dar

Doctoral Dissertations

The methods that fueled the microscale revolution (top-down design/fabrication, combined with application of forces large enough to overpower stochasticity) constitute an approach that will not scale down to nanoscale systems. In contrast, in nanotechnology, we strive to embrace nature’s quite different paradigms to create functional systems, such as self-assembly to create structures, exploiting stochasticity, rather than overwhelming it, in order to create deterministic, yet highly adaptable, behavior. Nature’s approach, through billions of years of evolutionary development, has achieved self-assembling, self-duplicating, self-healing, adaptive systems. Compared to microprocessors, nature’s approach has achieved eight orders of magnitude higher memory density and three orders …

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 …

Environmental Analysis And White Cell Applications Ftir Spectroscopy, Maria Gabriela Oliveros

Masters Theses

The research is concerned with atmospheric chemistry & physics, and analyzing the environment with respect to the quantity of molecules is in the air we breathe. Fourier Transform Infrared Spectroscopy is used to identify the IR active molecules in our atmosphere. FTIR Spectrometer determines the intensity loss for molecules that have absorbed IR light. The FTIR spectroscopy is performed using the light from the sun or a carbon rod light source in the lab. A Sun-tracking device was employed to direct the sunlight into the spectrometer. Open-path measurements were made using multiple mirror reflections of the carbon rod light source …

Direct Observation Of H2 Binding To A Metal Oxide Surface, J. Z. Larese, T. Arnold, L. Frazier, R. J. Hinde, A. J. Ramirez-Cuesta

Chemistry Publications and Other Works

Inelastic neutron scattering is used to probe the dynamical response of H₂ films adsorbed on MgO(100) as a function of film thickness. Concomitant diffraction measurements and a reduced-dimensionality quantum dynamical model provide insight into the molecule-surface interaction potential. At monolayer thickness, the rotational motion is strongly influenced by the surface, so that the molecules behave like quasiplanar rotors. These findings have a direct impact on understanding how molecular hydrogen binds to the surface of materials used in catalytic and storage applications.

A Six-Dimensional H2–H2 Potential Energy Surface For Bound State Spectroscopy, Robert Hinde

Chemistry Publications and Other Works

We present a six-dimensional potential energy surface for the (H₂)₂ dimer based on coupled-cluster electronic structure calculations employing large atom-centered Gaussian basis sets and a small set of midbond functions at the dimer’s center of mass. The surface is intended to describe accurately the bound and quasibound states of the dimers (H₂)₂, (D₂)₂, and H₂–D₂ that correlate with H₂ or D₂ monomers in the rovibrational levels (v, j) =(0,0), (0,2), (1,0), and (1,2). We employ a close-coupled approach to compute the …

Population Size Bias In Descendant-Weighted Diffusion Quantum Monte Carlo Simulations, G. Lee Warren, Robert J. Hinde

Chemistry Publications and Other Works

We consider the influence of population size on the accuracy of diffusion quantum Monte Carlo simulations that employ descendant weighting or forward walking techniques to compute expectation values of observables that do not commute with the Hamiltonian. We show that for a simple model system, the d-dimensional isotropic harmonic oscillator, the population size must increase rapidly with d in order to ensure that the simulations produce accurate results. When the population size is too small, expectation values computed using descendant-weighted diffusion quantum Monte Carlo simulations exhibit significant systematic biases.

Interaction-Induced Dipole Moment Of The Ar–H2 Dimer: Dependence On The H2 Bond Length, Robert J. Hinde

Chemistry Publications and Other Works

We present ab initio calculations of the interaction-induced dipole moment of the Ar–H₂ van der Waals dimer. The primary focus of our calculations is on the H₂ bond length dependence of the dipole moment, which determines the intensities of both the collision-induced H₂ = 1 ← 0 fundamental band in gaseous Ar–H₂ mixtures and the dopant-induced H₂ = 1 ← 0 absorption feature in Ar-doped solid H₂ matrices. Our calculations employ large atom-centered basis sets, diffuse bond functions positioned between the two monomers, and a coupled cluster treatment of valence electron correlation; core-valence correlation …

Vibrational Dependence Of The H2–H2 C6 Coefficients, Robert Hinde

Chemistry Publications and Other Works

We use the sum-over-states formalism to compute the imaginary-frequency dipole polarizabilities for H₂, as a function of the H–H bond length, at the full configuration interaction level of theory using atom-centered d-aug-cc-pVQZ basis sets. From these polarizabilities, we obtain isotropic and anisotropic C₆ dispersion coefficients for a pair of H₂ molecules as functions of the two molecules’ bond lengths.

Infrared-Active Vibron Bands Associated With Substitutional Impurities In Solid Parahydrogen, Robert Hinde

Chemistry Publications and Other Works

We present a model for the line shapes of infrared-active Q₁(0) vibron bands observed in solid parahydrogen doped with low concentrations of spherical substitutional impurities. The line shapes are highly sensitive to the H₂ vibrational dependence of the dopant–H₂ interaction. When this vibrational dependence is strong, the dopant can trap the infrared-active vibron in its first solvation shell; in this case, the trapped vibron manifests itself in the absorption spectrum as a narrow feature to the red of the pure solid’s vibron band.

The He-Lih Potential Energy Surface Revisited. I. An Interpolated Rigid Rotor Surface, Robert Hinde

Chemistry Publications and Other Works

We reconsider the potential energy surface of the He–LiH system recently examined by Gianturco and co-workers [F. A. Gianturco et al., Chem. Phys. 215, 227 (1997)]. We compute the He–LiH interaction energy at the CCSD(T) level using large correlation consistent atomic basis sets supplemented with bond functions. To capture the severe anisotropy of the He–LiH potential, we interpolate our ab initio points in the angular direction with cubic splines, then expand the splines in terms of Legendre polynomials. The resulting smooth potential surface differs substantially from that of Gianturco et al.; in particular, our attractive He–LiH well is more …