A detailed study was done of the neomycin-B RNA aptamer for determining its selectivity and binding ability to both neomycin– and kanamycin-class aminoglycosides. A novel method to increase drug concentrations in cells for more efficiently killing is described. To test the method, a bacterial model system was adopted and several small RNA molecules interacting with aminoglycosides were cloned downstream of T7 RNA polymerase promoter in an expression vector. Then, the growth analysis of E. coli expressing aptamers was observed for 12-hour period. Our analysis indicated that aptamers helped to increase the intracellular concentration of aminoglycosides thereby increasing their efficacy.

The energies arising from the rotation of free hydroxyl groups in the central glucose residue of a cellulose crystalline assembly, calculated using RHF, DFT, and FMO2/MP2 methods, will be presented. In addition, interactions of this central glucose residue with some of the surrounding residues (selected on the basis of the interaction strengths) are analyzed. The mechanism of acid-catalyzed hydrolysis of cellobiose, which is the repeating unit of cellulose. Energies corresponding to the different steps of this mechanism calculated using RHF and DFT are compared with those previously reported using molecular dynamics calculations and with experimental data.

This work presents explorations of the potential energy surface of clusters of atoms and of the interactions between molecules. First, structures of small aluminum clusters are examined and classified as ground states, transition states, or higher-order saddle points. Subsequently, the focus shifts to dispersion-dominated π-π interactions when the potential energy surfaces of benzene, substituted benzene, and pyridine dimers are explored. Because DNA nucleotide bases can be thought of as substituted heterocycles, a natural extension of the substituted benzene and pyridine investigations is to model paired nucleotide bases. Finally, the success of the dispersion studies inspires the development of an extension to the computational method used, which will enable the dispersion energy to be modeled – and the potential energy surface explored – in additional chemical systems. The effective fragment potential (EFP) method is described, as well as various quantum mechanical methods. An ab inito quantum mechanical study of 13-atom aluminum clusters is described. EFP studies of aromatic dimers are reported in which dispersion energy makes a significant contribution to the attraction between monomers. Theory and code development toward a means of computing dispersion energy in mixed ab inito-EFP systems are described.

In 2009, a National Academy of Sciences report called for investigation into the scienti#12;c basis behind tool mark comparisons (National Academy of Sciences, 2009). Answering this call, Chumbley et al. (2010) attempted to prove or disprove the hypothesis that tool marks are unique to a single tool. They developed a statistical algorithm that could, in most cases, discern matching and non-matching tool marks made at di#11;erent angles by sequentially numbered screwdriver tips. Moreover, in the cases where the algorithm misinterpreted a pair of marks, an experienced forensics examiner could discern the correct outcome. While this research served to con#12;rm the basic assumptions behind tool mark analysis, it also suggested that statistical analysis software could help to reduce the examiner's workload. This led to a new tool mark analysis approach, introduced in this thesis, that relies on 3D scans of screwdriver tip and marked plate surfaces at the micrometer scale from an optical microscope. These scans are carefully cleaned to remove noise from the data acquisition process and assigned a coordinate system that mathematically de#12;nes angles and twists in a natural way. The marking process is then simulated by using a 3D graphics software package to impart rotations to the tip …

The goal of this work is to characterize surfaces of intermetallics, including quasicrystals. In this work, surface characterization is primarily focused on composition and structure using X-ray photoelectron spectroscopy (XPS) and scanning tunneling microscopy (STM) performed under ultrahigh vacuum (UHV) conditions.

It was hypothesized that the variations in time to solution are driven by the competing mechanisms of exploration and exploitation.This thesis explores this hypothesis by examining two contrasting problems that embody the hypothesized tradeoff between exploration and exploitation. Plus one recall store (PORS) is an optimization problem based on the idea of a simple calculator with four buttons: plus, one, store, and recall. Integer addition and store are classified as operations, and one and memory recall are classified as terminals. The goal is to arrange a fixed number of keystrokes in a way that maximizes the numerical result. PORS 15 (15 keystrokes) represents the subset of difficult PORS problems and PORS 16 (16 keystrokes) represents the subset of PORS problems that are easiest to optimize. The goal of this work is to examine the tradeoff between exploitation and exploration in graph based evolutionary algorithm (GBEA) optimization. To do this, computational experiments are used to examine how solutions evolve in PORS 15 and 16 problems when solved using GBEAs. The experiment is comprised of three components; the graphs and the population, the evolutionary algorithm rule set, and the example problems. The complete, hypercube, and cycle graphs were used for this experiment. …

Asymmetry measurements were conducted in Jefferson Lab's experimental Hall A through electron scattering from a polarized {sup 3}He target in the quasi-elastic polarized-{sup 3}He(e,e'n) reaction. Measurements were made with the target polarized in the longitudinal direction with respect to the incoming electrons A_L, in a transverse direction that was orthogonal to the beam-line and parallel to the q-vector A_T, and in a vertical direction that was orthogonal to both the beam-line and the q-vector (A_y^0). The experiment measured $A_y^0$ at four-momentum transfer squared Q^2 of 0.127 (GeV/c)^2, 0.456 (GeV/c)^2, and 0.953 (GeV/c)^2. The A_T and A_L asymmetries were both measured at Q^2 of 0.505 (GeV/c)^2 and 0.953 (GeV/c)^2. This is the first time that three orthogonal asymmetries have been measured simultaneously. Results from this experiment are compared with the plane wave impulse approximation (PWIA) and Faddeev calculations. These results provide important tests of models that use 3He as an effective neutron target and show that the PWIA holds above Q^2 of 0.953 (GeV/c)^2.

Organic photovoltaic (OPV) technology is an attractive solar-electric conversion paradigm due to the promise of low cost roll-to-roll production and amenability to flexible substrates. Power conversion efficiency (PCE) exceeding 7% has recently been achieved. OPV cells suffer from low charge carrier mobilities of polymers, leading to recombination losses, higher series resistances and lower fill-factors. Thus, it is imperative to develop fabrication methodologies that can enable efficient optical absorption in films thinner than optical absorption length. Active layers conformally deposited on light-trapping, microscale textured, grating-type surfaces is one possible approach to achieve this objective. In this study, 40% theoretical increase in photonic absorption over flat OPVs is shown for devices with textured geometry by the simulation results. For verifying this theoretical result and improving the efficiency of OPVs by light trapping, OPVs were fabricated on grating-type textured substrates possessing t pitch and -coat PV active-layer on these textured substrates led to over filling of the valleys and shunts at the crest, which severely affected the performance of the resultant PV devices. Thus, it is established that although the optical design is important for OPV performance but the potential of light trapping can only be effectively tapped if the textures are amenable …

Deuteron photodisintegration is a benchmark process for the investigation of the role of quarks and gluons in nuclei. Existing theoretical models of this process describe the available cross sections with the same degree of success. Therefore, spin-dependent observables are crucial for a better understanding of the underlying dynamical mechanisms. However, data on the induced polarization (P{sub y}), along with the polarization transfers (C{sub x'} and C{sub z'} ), have been shown to be insensitive to differences between theoretical models. On the other hand, the beam-spin asymmetry {Sigma} is predicted to have a large sensitivity and is expected to help in identifying the energy at which the transition from the hadronic to the quark-gluon picture of the deuteron takes place. Here, the work done to determine the experimental values of the beam-spin asymmetry in deuteron photodisintegration for photon energies between 1.1 – 2.3 GeV is presented. The data were taken with the CLAS at the Thomas Jefferson National Accelerator Facility during the g13 experiment. Photons with linear polarization of ~80% were produced using the coherent bremsstrahlung facility in Hall B. The work done by the author to calibrate a specific detector system, select deuteron photodisintegration events, study the degree of photon …

This thesis is dedicated to a study of a spin-isospin structure of the polarized {sup 3}He. First, an introduction to the spin structure of {sup 3}He is given, followed by a brief overview of past experiments. The main focus of the thesis is the E05-102 experiment at Jefferson Lab, in which the reactions {sup 3}{ovr He} ({rvec e}, e'd) and {sup 3}{ovr He} ({rvec e}, e'p) in the quasi-elastic region were studied. The purpose of this experiment was to better understand the effects of the S'- and D-state contributions to the {sup 3}He ground-state wave-functions by a precise measurement of beam-target asymmetries A{sub x} and A{sub z} in the range of recoil momenta from 0 to about 300 MeV/c. The experimental equipment utilized in these measurements is described, with special attention devoted to the calibration of the hadron spectrometer, BigBite. Results on the measured asymmetries are presented, together with first attempts at their comparison to the state-of-the art Faddeev calculations. The remaining open problems and challenges for future work are also discussed.

Laser wakefield acceleration of electrons holds great promise for producing ultra-compact stages of GeV scale, high quality electron beams for applications such as x-ray free electron lasers and high energy colliders. Ultra-high intensity laser pulses can be self-guided by relativistic plasma waves over tens of vacuum diffraction lengths, to give >1 GeV energy in cm-scale low density plasma using ionization-induced injection to inject charge into the wake at low densities. This thesis describes a series of experiments which investigates the physics of LWFA in the self-guided blowout regime. Beginning with high density gas jet experiments the scaling of the LWFA-produced electron beam energy with plasma electron density is found to be in excellent agreement with both phenomenological theory and with 3-D PIC simulations. It is also determined that self-trapping of background electrons into the wake exhibits a threshold as a function of the electron density, and at the densities required to produce electron beams with energies exceeding 1 GeV a different mechanism is required to trap charge into low density wakes. By introducing small concentrations of high-Z gas to the nominal He background the ionization-induced injection mechanism is enabled. Electron trapping is observed at densities as low as 1.3 x …

The use of the ReaxFF force field to correlate with NMR mobilities of amine catalytic substituents on a mesoporous silica nanosphere surface is considered. The interfacing of the ReaxFF force field within the Surface Integrated Molecular Orbital/Molecular Mechanics (SIMOMM) method, in order to replicate earlier SIMOMM published data and to compare with the ReaxFF data, is discussed. The development of a new correlation consistent Composite Approach (ccCA) is presented, which incorporates the completely renormalized coupled cluster method with singles, doubles and non-iterative triples corrections towards the determination of heats of formations and reaction pathways which contain biradical species.

The study of {Lambda} hypernuclear structure is very interesting in point of the understanding of the interaction between {Lambda} and nucleon ({Lambda}-N interaction) and its ”strange” structure itself due to the containment of a {Lambda} hyperon which has a strangeness as a new degree of freedom. In the several way to study the Lamda hypernuclei, the (e,e'K{sup +}) reaction spectroscopy is a powerful tool for the precise investigation of {Lamda} hypernuclear structure. The purpose of the preset thesis is the establishment of the experimental design with the efficient data analysis method for the (e,e'K{sup +}) hypernuclear spectroscopic experiment in the wide mass region (from A=7 to A=52). It is very challenging to perform the (e,e'K{sup +}) spectroscopic experiment with such a heavy target, because of the huge electron background due to the bremsstrahlung process. In the experiment, it is required to obtain the necessary hypernuclear yield, suppressing the background event ratio. We achieved these requirements by newly constructing the high resolution electron spectrometer (HES) and splitter magnet (SPL) dedicated to the (e,e'K{sup +}) spectroscopic experiment. The HES consists of two quadrupole magnets and a dipole magnets (Q-Q-D) with a momentum resolution of dp/p = 3x10^-4 at p = 0.84 GeV/c. …

After a general introduction to OLEDs and OLED-based PL sensors, the transient emission mechanism of guest-host OLEDs is described both experimentally and theoretically. A monolithic and easy-to-apply process is demonstrated for fabricating multicolor microcavity OLEDs (that improve the sensor platform). The outcoupling issues of OLEDs at the substrate/air interface are addressed by using a microstructured polymer film resulting from a PS and polyethylene glycol (PEG) mixture. Based on the understanding of OLEDs and their improvement, research was done in order to realize integrated all organic-based O{sub 2} and pH sensors with improved signal intensity and sensitivity. The sensor design modification and optimization are summarized

This thesis reports on two experiments conducted by the HAPPEx (Hall A Proton Parity Experiment) collaboration at the Thomas Je#11;erson National Accelerator Facil- ity. For both, the weak neutral current interaction (WNC, mediated by the Z{sup 0} boson) is used to probe novel properties of hadronic targets. The WNC interaction amplitude is extracted by measuring the parity-violating asymmetry in the elastic scattering of longitudinally polarized electrons o#11; unpolarized target hadrons. HAPPEx-III, con- ducted in the Fall of 2009, used a liquid hydrogen target at a momentum transfer of Q{sup 2} = 0.62 GeV{sup 2}. The measured asymmetry was used to set new constraints on the contribution of strange quark form factors (G{sup s}{sub E,M} ) to the nucleon electromagnetic form factors. A value of A{sub PV} = -23.803{+-}#6; 0.778 (stat){+-}#6; 0.359 (syst) ppm resulted in G{sup s}{sub E} + 0:517G{sup s}{sub M} = 0.003{+-} 0.010 (stat){+-} #6;0.004 (syst){+-}#6; #6;0.009 (FF). PREx, conducted in the Spring of 2010, used a polarized electron beam on a 208Pb target at a momentum transfer of Q{sup 2} = 0.009 GeV{sup 2}. This parity-violating asymmetry can be used to obtain a clean measurement of the root-mean-square radius of the neutrons in the {sup 208}Pb nucleus. …

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This dissertation mainly focuses on the investigation of the cellular membrane trafficking of mesoporous silica nanoparticles. We are interested in the study of endocytosis and exocytosis behaviors of mesoporous silica nanoparticles with desired surface functionality. The relationship between mesoporous silica nanoparticles and membrane trafficking of cells, either cancerous cells or normal cells was examined. Since mesoporous silica nanoparticles were applied in many drug delivery cases, the endocytotic efficiency of mesoporous silica nanoparticles needs to be investigated in more details in order to design the cellular drug delivery system in the controlled way. It is well known that cells can engulf some molecules outside of the cells through a receptor-ligand associated endocytosis. We are interested to determine if those biomolecules binding to cell surface receptors can be utilized on mesoporous silica nanoparticle materials to improve the uptake efficiency or govern the mechanism of endocytosis of mesoporous silica nanoparticles. Arginine-glycine-aspartate (RGD) is a small peptide recognized by cell integrin receptors and it was reported that avidin internalization was highly promoted by tumor lectin. Both RGD and avidin were linked to the surface of mesoporous silica nanoparticle materials to investigate the effect of receptor-associated biomolecule on cellular endocytosis efficiency. The effect of ligand …

Signal transduction pathways are usually activated by external stimuli and are transient. The downstream changes such as transcription of the activated genes are also transient. Real-time detection of promoter activity is useful for understanding changes in gene expression, especially during cell differentiation and in development. A simple and reliable method for viewing gene expression in real time is not yet available. Reporter proteins such as fluorescent proteins and luciferase allow for non-invasive detection of the products of gene expression in living cells. However, current reporter systems do not provide for real-time imaging of promoter activity in living cells. This is because of the long time period after transcription required for fluorescent protein synthesis and maturation. We have developed an RNA reporter system for imaging in real-time to detect changes in promoter activity as they occur. The RNA reporter uses strings of RNA aptamers that constitute IMAGEtags (Intracellular MultiAptamer GEnetic tags), which can be expressed from a promoter of choice. The tobramycin, neomycin and PDC RNA aptamers have been utilized for this system and expressed in yeast from the GAL1 promoter. The IMAGEtag RNA kinetics were quantified by RT-qPCR. In yeast precultured in raffinose containing media the GAL1 promoter responded faster …

Organic semiconductors devices, such as, organic solar cells (OSCs), organic light-emitting diodes (OLEDs) and organic field-effect transistors (OFETs) have drawn increasing interest in recent decades. As organic materials are flexible, light weight, and potentially low-cost, organic semiconductor devices are considered to be an alternative to their inorganic counterparts. This dissertation will focus mainly on OSCs and OLEDs. As a clean and renewable energy source, the development of OSCs is very promising. Cells with 9.2% power conversion efficiency (PCE) were reported this year, compared to < 8% two years ago. OSCs belong to the so-called third generation solar cells and are still under development. While OLEDs are a more mature and better studied field, with commercial products already launched in the market, there are still several key issues: (1) the cost of OSCs/OLEDs is still high, largely due to the costly manufacturing processes; (2) the efficiency of OSCs/OLEDs needs to be improved; (3) the lifetime of OSCs/OLEDs is not sufficient compared to their inorganic counterparts; (4) the physics models of the behavior of the devices are not satisfactory. All these limitations invoke the demand for new organic materials, improved device architectures, low-cost fabrication methods, and better understanding of device physics. For …

An experiment was conducted at Jefferson Lab's Continuous Electron Beam Accelerator Facility to develop a beam-based technique for characterizing the extent of the nonlinearity of the magnetic fields of a beam transport system. Horizontally and vertically oriented pairs of air-core kicker magnets were simultaneously driven at two different frequencies to provide a time-dependent transverse modulation of the beam orbit relative to the unperturbed reference orbit. Fourier decomposition of the position data at eight different points along the beamline was then used to measure the amplitude of these frequencies. For a purely linear transport system one expects to find solely the frequencies that were applied to the kickers with amplitudes that depend on the phase advance of the lattice. In the presence of nonlinear fields one expects to also find harmonics of the driving frequencies that depend on the order of the nonlinearity. Chebyshev polynomials and their unique properties allow one to directly quantify the magnitude of the nonlinearity with the minimum error. A calibration standard was developed using one of the sextupole magnets in a CEBAF beamline. The technique was then applied to a pair of Arc 1 dipoles and then to the magnets in the Transport Recombiner beamline to …

This thesis is the culminating project for my participation in the OECD NEA International School of Nuclear Law. This paper will begin by providing a historical background to current disarmament and denuclearization treaties. This paper will discuss the current legal framework based on current and historical activities related to denuclearization and nuclear disarmament. Then, it will propose paths forward for the future efforts, and describe the necessary legal considerations. Each treaty or agreement will be examined in respect to its requirements for: 1) limitations and implementation; 2) and verification and monitoring. Then, lessons learned in each of the two areas (limitations and verification) will be used to construct a proposed path forward at the end of this paper.

The aim of the present thesis is to investigate the local magnetic properties of homometallic Cr{sub 8} antiferromagnetic (AFM) ring and the changes occurring by replacing one Cr{sup 3+} ion with diamagnetic Cd{sup 2+} (Cr{sub 7}Cd) and with Ni{sup 2+} (Cr{sub 7}Ni). In the heterometallic ring a redistribution of the local magnetic moment is expected in the low temperature ground state. We have investigated those changes by both {sup 53}Cr-NMR and {sup 19}F-NMR. We have determined the order of magnitude of the transferred hyperfine coupling constant {sup 19}F - M{sup +} where M{sup +} = Cr{sup 3+}, Ni{sup 2+} in the different rings. This latter result gives useful information about the overlapping of the electronic wavefunctions involved in the coordinative bond.

GdNi is a rare earth intermetallic material that exhibits very interesting magnetic properties. Spontaneous magnetostriction occurs in GdNi at T{sub C}, on the order of 8000ppm strain along the c-axis and only until very recently the mechanism causing this giant magnetostriction was not understood. In order to learn more about the electronic and magnetic structure of GdNi, single crystals are required for anisotropic magnetic property measurements. Single crystal processing is quite challenging for GdNi though since the rare-earth transition-metal composition yields a very reactive intermetallic compound. Many crystal growth methods are pursued in this study including crucible free methods, precipitation growths, and specially developed Bridgman crucibles. A plasma-sprayed Gd{sub 2}O{sub 3} W-backed Bridgman crucible was found to be the best means of GdNi single crystal processing. With a source of high-quality single crystals, many magnetization measurements were collected to reveal the magnetic structure of GdNi. Heat capacity and the magnetocaloric effect are also measured on a single crystal sample. The result is a thorough report on high quality single crystal processing and the magnetic properties of GdNi.