Mesoporous silica nanoparticles (MSNs) have attracted great interest for last two decades due to their unique and advantageous structural properties, such as high surface area, pore volume, stable mesostructure, tunable pore size and controllable particle morphology. The robust silica framework provides sites for organic modifications, making MSNs ideal platforms for adsorbents and supported organocatalysts. In addition, the pores of MSNs provide cavities/ channels for incorporation of metal and metal oxide nanoparticle catalysts. These supported metal nanoparticle catalysts benefit from confined local environments to enhance their activity and selectivity for various reactions. Biomass is considered as a sustainable feedstock with potential to replace diminishing fossil fuels for the production of biofuels. Among several strategies, one of the promising methods of biofuel production from biomass is to reduce the oxygen content of the feedstock in order to improve the energy density. This can be achieved by creating C-C bonds between biomass derived intermediates to increase the molecular weight of the final hydrocarbon molecules. In this context, pore size and organic functionality of MSNs are varied to obtain the ideal catalyst for a C-C bond forming reaction: the aldol condensation. The mechanistic aspects of this reaction in supported heterogeneous catalysts are explored. The …

This study focused on creating a new tristructural isotropic (TRISO) coated particle fuel performance model and demonstrating the integration of this model into an existing system of neutronics and heat transfer codes, creating a user-friendly option for including fuel performance analysis within system design optimization and system-level trade-off studies. The end product enables both a deeper understanding and better overall system performance of nuclear energy systems limited or greatly impacted by TRISO fuel performance. A thorium-fueled hybrid fusion-fission Laser Inertial Fusion Energy (LIFE) blanket design was used for illustrating the application of this new capability and demonstrated both the importance of integrating fuel performance calculations into mainstream design studies and the impact that this new integrated analysis had on system-level design decisions. A new TRISO fuel performance model named TRIUNE was developed and verified and validated during this work with a novel methodology established for simulating the actual lifetime of a TRISO particle during repeated passes through a pebble bed. In addition, integrated self-consistent calculations were performed for neutronics depletion analysis, heat transfer calculations, and then fuel performance modeling for a full parametric study that encompassed over 80 different design options that went through all three phases of analysis. Lastly, …

As the National Ignition Facility continues its campaign to achieve ignition, new methods and tools will be required to measure the quality of the targets used to achieve this goal. Techniques have been developed to measure target surface features using a phase-shifting diffraction interferometer and Leica Microsystems confocal microscope. Using these techniques we are able to produce a detailed view of the shell surface, which in turn allows us to refine target manufacturing and cleaning processes. However, the volume of data produced limits the methods by which this data can be effectively viewed by a user. This paper introduces an image-based visualization system for data exploration of target shells at the National Ignition Facility (NIF) at Lawrence Livermore National Laboratory. It aims to combine multiple image sets into a single visualization to provide a method of navigating the data in ways that are not possible with existing tools.

Experimental evidence has established that neutrino flavor states evolve over time. A neutrino of a particular flavor that travels some distance can be detected in a different neutrino flavor state. The Main Injector Neutrino Oscillation Search (MINOS) is a long-baseline experiment that is designed to study this phenomenon, called neutrino oscillations. MINOS is based at Fermilab near Chicago, IL, and consists of two detectors: the Near Detector located at Fermilab, and the Far Detector, which is located in an old iron mine in Soudan, MN. Both detectors are exposed to a beam of muon neutrinos from the NuMI beamline, and MINOS measures the fraction of muon neutrinos that disappear after traveling the 734 km between the two detectors. One can measure the atmospheric neutrino mass splitting and mixing angle by observing the energy-dependence of this muon neutrino disappearance. MINOS has made several prior measurements of these parameters. Here I describe recently-developed techniques used to enhance our sensitivity to the oscillation parameters, and I present the results obtained when they are applied to a dataset that is twice as large as has been previously analyzed. We measure the mass splitting {Delta}m{sub 23}{sup 2} = (2.32{sub -0.08}{sup +0.12}) x 10{sup -3} eV{sup …

This thesis describes the measurement of the branching fractions of the suppressed charmed B{sup 0} {yields} D{sup (*)-} a{sub 0}{sup +} decays and the non-resonant B{sup 0} {yields} D{sup (*)-} {eta}{pi}{sup +} decays in approximately 230 million {Upsilon}(4S) {yields} B{bar B} events. The data have been collected with the BABAR detector at the PEP-II B factory at the Stanford Linear Accelerator Center in California. Theoretical predictions of the branching fraction of the B{sup 0} {yields} D{sup (*)-} a{sub 0}{sup +} decays show large QCD model dependent uncertainties. Non-factorizing terms, in the naive factorization model, that can be calculated by QCD factorizing models have a large impact on the branching fraction of these decay modes. The predictions of the branching fractions are of the order of 10{sup -6}. The measurement of the branching fraction gives more insight into the theoretical models. In general a better understanding of QCD models will be necessary to conduct weak interaction physics at the next level. The presence of CP violation in electroweak interactions allows the differentiation between matter and antimatter in the laws of physics. In the Standard Model, CP violation is incorporated in the CKM matrix that describes the weak interaction between quarks. Relations …

Here we report structural and functional studies of Mms6, a biomineralization protein that can promote the formation in vitro of magnetic nanoparticles with sizes and morphologies similar to the magnetites synthesized by magnetotactic bacteria. We found the binding pattern of Mms6 to ferric ion to be two-phase and multivalent. We quantatively determined that Mms6 binds one Fe{sup 3+} with a very high affinity (K{sub d} = 10{sup -16} M). The second phase of iron binding is multivalent and cooperative with respect to iron with a K{sub d} in the {mu}M range and a stoichiometry of about 20 ferric ion per protein molecule. We found that Mms6 exists in large particles of two sizes, one consisting of 20-40 monomeric units and the other of 200 units. From proteolytic digestion, ultracentrifugation and liposome fusion studies, we found that Mms6 forms a large micellar quaternary structure with the N-terminal domain self-assembling into a uniformly sized micelle and the C-terminal domain on the surface. The two-phase iron-binding pattern may be relevant to iron crystal formation. We propose that the first high affinity phase may stabilize a new conformation of the C-terminal domain that allows interaction with other C-terminal domains leading to a structural change …

Stimuli-responsive end-capped MSN materials are promising drug carriers that securely deliver a large payload of drug molecules without degradation or premature release. A general review of the recent progress in this field is presented, including a summary of a series of hard and soft caps for drug encapsulation and a variety of internal and external stimuli for controlled release of different therapeutics, a discussion of the biocompatibility of MSN both in vitro and in vivo, and a description of the sophisticated stimuli-responsive systems with novel capping agents and controlled release mechanism. The unique internal and external surfaces of MSN were utilized for the development of a glucose-responsive double delivery system end-capped with insulin. This unique system consists of functionalized MSNs capable of releasing insulin when the concentration of sugar in blood exceeds healthy levels. The insulin-free nanoparticles are then up taken by pancreatic cells, and release inside of them another biomolecule that stimulates the production of more insulin. The in vivo application of this system for the treatment of diabetes requires further understanding on the biological behaviors of these nanoparticles in blood vessels. The research presented in this dissertation demonstrated the size and surface effects on the interaction of MSNs …

We report on the search for heavy metastable particles that decay into quark pairs with a macroscopic lifetime (c{tau} {approx} 1 cm) using data taken with the CDF II detector at Fermilab. We use a data driven background approach, where they build probability density functions to model Standard Model secondary vertices from known processes in order to estimate the background contribution from the Standard Model. No statistically significant excess is observed above the background. Limits on the production cross section in a Hidden Valley benchmark phenomenology are set for various Higgs boson masses as well as metastable particle masses and lifetimes.

This dissertation presents the first search for the standard model Higgs boson (H) in decay topologies containing a muon, an imbalance in transverse momentum (E{sub T}) and jets, using p{bar p} collisions at {radical}s = 1.96 TeV with an integrated luminosity of 4.3 fb{sup -1} recorded with the D0 detector at the Fermilab Tevatron Collider. This analysis is sensitive primary to contributions from Higgs bosons produced through gluon fusion, with subsequent decay H {yields} WW {yields} {mu}{nu}jj where W represents a real or virtual W boson. In the absence of signal, limits are set at 95% confidence on the production and decay of the standard model Higgs boson for M{sub H} in the range of 115-200 GeV. For M{sub H} = 165 GeV, the observed and expected limits are factors of 11.2 larger than the standard model value. Combining this channel with e{nu}jj final states and including earlier data to increase the integrated luminosity to 5.4 fb{sup -1} produces observed(expected) limits of 5.5(3.8) times the standard model value.

The Standard Model of particle physics provides an excellent description of particle interactions at energies up to {approx}1 TeV, but it is expected to fail above that scale. Multiple models developed to describe phenomena above the TeV scale predict the existence of very massive, vector-like quarks. A search for single electroweak production of such particles in p{anti p} collisions at a center-of-mass energy of 1.96 TeV is performed in the W+jets and Z+jets channels. The data were collected by the D0 detector at the Fermilab Tevatron Collider and correspond to an integrated luminosity of 5.4 fb{sup -1}. Events consistent with a heavy object decaying to a vector boson and a jet are selected. We observe no significant excess in comparison to the background prediction and set 95% confidence level upper limits on production cross sections for vector-like quarks decaying to W+jet and Z+jet. Assuming a vector-like quark -- standard model quark coupling parameter {tilde {kappa}}{sub qQ} of unity, we exclude vector-like quarks with mass below 693 GeV for decays to W+jet and mass below 449 GeV for decays to Z+jet. These represent the most sensitive limits to date.

The composition of matter is a topic in which the man has been interested throughout History. Since the introduction of the atom by Democritus in the 5th century BC until the establishment of the Standard Model, our successful theory that contains our current knowledge on the matter and their interactions, it has come a long way trying to solve this fundamental question. The efforts of many of the greatest minds to perform crucial experiments and develop theoretical models have helped to get deeper insight into the origin of the matter. Today we know that indivisible atoms postulated by Democritus are no longer true, and they are actually composed of a nucleus made of protons and neutrons (nucleons) with orbiting electrons through electromagnetic interactions. Also the nucleons are not fundamental particles but are composed of more fundamental ones called quarks. According to the present state of our knowledge, matter is composed of two types of particles: quarks and leptons. Leptons are believed to be fundamental particles and can occur freely in nature. Quarks are also fundamental particles, and there are no free in nature, but are confined to form hadrons. The hadrons may consist of a quark and an antiquark (mesons) …

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.

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The field of metamaterials is driven by fascinating and far-reaching theoretical visions, such as perfect lenses, invisibility cloaking, and enhanced optical nonlinearities. However, losses have become the major obstacle towards real world applications in the optical regime. Reducing the losses of optical metamaterials becomes necessary and extremely important. In this thesis, two approaches are taken to reduce the losses. One is to construct an indefinite medium. Indefinite media are materials where not all the principal components of the permittivity and permeability tensors have the same sign. They do not need the resonances to achieve negative permittivity, {var_epsilon}. So, the losses can be comparatively small. To obtain indefinite media, three-dimensional (3D) optical metallic nanowire media with different structures are designed. They are numerically demonstrated that they are homogeneous effective indefinite anisotropic media by showing that their dispersion relations are hyperbolic. Negative group refraction and pseudo focusing are observed. Another approach is to incorporate gain into metamaterial nanostructures. The nonlinearity of gain is included by a generic four-level atomic model. A computational scheme is presented, which allows for a self-consistent treatment of a dispersive metallic photonic metamaterial coupled to a gain material incorporated into the nanostructure using the finite-difference time-domain (FDTD) method. …

The MINOS experiment is a long-baseline neutrino oscillation experiment in the the NuMI beamline at Fermilab, USA. Using a near detector at 1 km distance from the neutrino production target, and a far detector at 735 km from the target, it is designed primarily to measure the disappearance of muon neutrinos. This thesis presents an analysis using MINOS data of the possibility of oscil- lation of the neutrinos in the NuMI beam to a hypothetical sterile flavour, which would have no Standard Model couplings. Such oscillations would result in a deficit in the neutral current interaction rate in the MINOS far detector relative to the expectation derived from the near detector data. The method used to identify neutral current and charged current events in the MINOS detectors is described and a new method of predicting and fitting the far detector spectrum presented, along with the effects of systematic uncertainties on the sterile neutrino oscillation analysis. Using this analysis, the fraction f{sub s} of the disappearing neutrinos that go to steriles is constrained to be below 0.15 at the 90% confidence level in the absence of electron neutrino appearance in the NuMI beam. With electron appearance at the CHOOZ limit, f{sub …

Differential interference contrast (DIC) microscopy is a far-field as well as wide-field optical imaging technique. Since it is non-invasive and requires no sample staining, DIC microscopy is suitable for tracking the motion of target molecules in live cells without interfering their functions. In addition, high numerical aperture objectives and condensers can be used in DIC microscopy. The depth of focus of DIC is shallow, which gives DIC much better optical sectioning ability than those of phase contrast and dark field microscopies. In this work, DIC was utilized to study dynamic biological processes including endocytosis and intracellular transport in live cells. The suitability of DIC microscopy for single particle tracking in live cells was first demonstrated by using DIC to monitor the entire endocytosis process of one mesoporous silica nanoparticle (MSN) into a live mammalian cell. By taking advantage of the optical sectioning ability of DIC, we recorded the depth profile of the MSN during the endocytosis process. The shape change around the nanoparticle due to the formation of a vesicle was also captured. DIC microscopy was further modified that the sample can be illuminated and imaged at two wavelengths simultaneously. By using the new technique, noble metal nanoparticles with different …

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.

The COUPP collaboration has successfully used bubble chambers, a technology previously applied only to high-energy physics experiments, as direct dark matter detectors. It has produced the world's most stringent spin-dependent WIMP limits, and increasingly competitive spin-independent limits. These limits were achieved by capitalizing on an intrinsic rejection of the gamma background that all other direct detection experiments must address through high-density shielding and empirically-determined data cuts. The history of COUPP, including its earliest prototypes and latest results, is briefly discussed in this thesis. The feasibility of a new, windowless bubble chamber concept simpler and more inexpensive in design is discussed here as well. The dark matter limits achieved with a 15 kg windowless chamber, larger than any previous COUPP chamber (2 kg, 4 kg), are presented. Evidence of the greater radiopurity of synthetic quartz compared to natural is presented using the data from this 15 kg device, the first chamber to be made from synthetic quartz. The effective reconstruction of the three-dimensional positions of bubbles in a highly distorted optical field, with ninety-degree bottom lighting similar to cloud chamber lighting, is demonstrated. Another innovation described in this thesis is the use of the sound produced by bubbles recorded by an …

Organic semiconductors have evolved rapidly over the last decades and currently are considered as the next-generation technology for many applications, such as organic light-emitting diodes (OLEDs) in flat-panel displays (FPDs) and solid state lighting (SSL), and organic solar cells (OSCs) in clean renewable energy. This dissertation focuses mainly on OLEDs. Although the commercialization of the OLED technology in FPDs is growing and appears to be just around the corner for SSL, there are still several key issues that need to be addressed: (1) the cost of OLEDs is very high, largely due to the costly current manufacturing process; (2) the efficiency of OLEDs needs to be improved. This is vital to the success of OLEDs in the FPD and SSL industries; (3) the lifetime of OLEDs, especially blue OLEDs, is the biggest technical challenge. All these issues raise the demand for new organic materials, new device structures, and continued lower-cost fabrication methods. In an attempt to address these issues, we used solution-processing methods to fabricate highly efficient small molecule OLEDs (SMOLEDs); this approach is costeffective in comparison to the more common thermal vacuum evaporation. We also successfully made efficient indium tin oxide (ITO)-free SMOLEDs to further improve the efficiency of …

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.

A search for the standard model Higgs boson is performed in 6.4 fb{sup -1} of p{bar p} collisions at {radical}s = 1.96 TeV, collected with the D0 detector during Run II of the Fermilab Tevatron. The final state considered is a pair of jets originating from b quarks and missing transverse energy, as expected from p{bar p} {yields} ZH {yields} {nu}{bar {nu}}b{bar b} production. The search is also sensitive to the WH {yields} {ell}{nu}b{bar b} channel, where the charged lepton is not identified. Boosted decision trees are used to discriminate signal from background. Good agreement is observed between data and expected backgrounds, and a limit is set at 95% C.L. on the section multiplied by branching fraction of (p{bar p} {yields} (Z/W)H) x (H {yields} b{bar b}). For a Higgs boson mass of 115 GeV, the observed limit is a factor of 3.5 larger than the value expected from the standard model.

We present a search for associated production of Z and Higgs bosons in 4.2 fb{sup -1} of {bar p}p collisions at {radical}s = 1.96 TeV, produced in RunII of the Tevatron and recorded by the D0 detector. The search is performed in events containing at least two muons and at least two jets. The ZH signal is distinguished from the expected backgrounds by means of multivariate classifiers known as random forests. Binned random forest output distributions are used in comparing the data to background-only and signal+background hypotheses. No excess is observed in the data, so we set upper limits on ZH production with a 95% confidence level.