Physical Sciences and Mathematics Commons^™

Integrative Modeling Of Macromolecular Assemblies From Low To Near-Atomic Resolution, Xiaojun Xu, Chunli Yan, Robert Wohlhueter, Ivaylo Ivanov

Chemistry Faculty Publications

While conventional high-resolution techniques in structural biology are challenged by the size and flexibility of many biological assemblies, recent advances in low-resolution techniques such as cryo-electron microscopy (cryo-EM) and small angle X-ray scattering (SAXS) have opened up new avenues to define the structures of such assemblies. By systematically combining various sources of structural, biochemical and biophysical information, integrativemodeling approaches aimto provide a unified structural description of such assemblies, starting from high-resolution structures of the individual components and integrating all available information from low-resolution experimental methods. In this review, we describe integrative modeling approaches, which use complementary data from either cryo-EM …

Pancreas-Targeted Nir Fluorophores For Dual-Channel Image-Guided Abdominal Surgery, Hideyuki Wada, Hoon Hyun, Christina Vargas, Julien Gravier, Gwangli Park, Sylvain Gioux, John V. Frangioni, Maged Henary, Hak Soo Choi

Chemistry Faculty Publications

Objective: Pancreas-related complications are some of the most serious ones in abdominal surgery. The goal of this study was to develop and validate novel near-infrared (NIR) fluorophores that would enable real-time pancreas imaging to avoid the intraoperative pancreatic injury. Design: After initial screening of a large NIR fluorophore library, the performance of 3 selected pancreas-targeted 700 nm NIR fluorophores, T700-H, T700-F, and MB, were quantified in mice, rats, and pigs. Dose ranging using 25 and 100 nmol, and 2.5 μmol of T700-F, and its imaging kinetics over a 4 h period were tested in each species. Three different 800 nm …

Crystallographic And Spectroscopic Snapshots Reveal A Dehydrogenase In Action, Lu Huo, Ian Davis, Fange Liu, Babak Andi, Shingo Esaki, Hiroaki Iwaki, Yoshie Hasegawa, Allen M. Orville, Aimin Liu

Chemistry Faculty Publications

Aldehydes are ubiquitous intermediates in metabolic pathways and their innate reactivity can often make them quite unstable. There are several aldehydic intermediates in the metabolic pathway for tryptophan degradation that can decay into neuroactive compounds that have been associated with numerous neurological diseases. An enzyme of this pathway, 2-aminomuconate-6-semialdehyde dehydrogenase, is responsible for ‘disarming’ the final aldehydic intermediate. Here we show the crystal structures of a bacterial analogue enzyme in five catalytically relevant forms: resting state, one binary and two ternary complexes, and a covalent, thioacyl intermediate. We also report the crystal structures of a tetrahedral, thiohemiacetal intermediate, a thioacyl …

A Bayesian Model For Detection Of Highorder Interactions Among Genetic Variants In Genome-Wide Association Studies, Juexin Wang, Trupti Joshi, Babu Valliyodan, Haiying Shi, Yanchun Liang, Henry T. Nguyen, Jing Zhang, Dong Xu

Mathematics and Statistics Faculty Publications

Background: A central question for disease studies and crop improvements is how genetics variants drive phenotypes. Genome Wide Association Study (GWAS) provides a powerful tool for characterizing the genotypephenotype relationships in complex traits and diseases. Epistasis (gene-gene interaction), including high-order interaction among more than two genes, often plays important roles in complex traits and diseases, but current GWAS analysis usually just focuses on additive effects of single nucleotide polymorphisms (SNPs). The lack of effective computational modelling of high-order functional interactions often leads to significant under-utilization of GWAS data. Results: We have developed a novel Bayesian computational method with a Markov …

Effectiveness Of Nutrient Management Plans On Vermont Dairy Farms, Heather Darby, Philip Halteman, Debra Heleba

College of Agriculture and Life Sciences Faculty Publications

A nutrient management plan (NMP) is a tool that helps livestock farmers optimize crop nutrient use. A survey of Vermont dairy farmers was conducted to learn about farmers' implementation of and perceptions about the effects of NMPs. Results showed that 46% of the 301 respondents had NMPs, particularly large and medium size operations. The majority followed the plans most of the time (barring weather and other constraints). The study revealed that NMPs affected total perceived fertilizer use and adoption of conservation practices. It showed that the person(s) updating the NMP affected the frequency to which the plan's recommendations were consulted.

Nonlinear Optical Response Of Simple Molecules And Two-Photon Semiconductor Lasers, Matthew Reichert

Electronic Theses and Dissertations

This dissertation investigates two long standing issues in nonlinear optics: complete characterization of the ultrafast dynamics of simple molecules, and the potential of a two-photon laser using a bulk semiconductor gain medium. Within the Born-Oppenheimer approximation, nonlinear refraction in molecular liquids and gases can arise from both bound-electronic and nuclear origins. Knowledge of the magnitudes, temporal dynamics, polarization and spectral dependences of each of these mechanisms is important for many applications including filamentation, white-light continuum generation, all-optical switching, and nonlinear spectroscopy. In this work the nonlinear dynamics of molecules are investigated in both liquid and gas phase with the recently …

Data Privacy Preservation In Collaborative Filtering Based Recommender Systems, Xiwei Wang

Theses and Dissertations--Computer Science

This dissertation studies data privacy preservation in collaborative filtering based recommender systems and proposes several collaborative filtering models that aim at preserving user privacy from different perspectives.

The empirical study on multiple classical recommendation algorithms presents the basic idea of the models and explores their performance on real world datasets. The algorithms that are investigated in this study include a popularity based model, an item similarity based model, a singular value decomposition based model, and a bipartite graph model. Top-N recommendations are evaluated to examine the prediction accuracy.

It is apparent that with more customers' preference data, recommender systems …

Integral Representations Of Positive Linear Functionals, Angela Siple

Electronic Theses and Dissertations

In this dissertation we obtain integral representations for positive linear functionals on commutative algebras with involution and semigroups with involution. We prove Bochner and Plancherel type theorems for representations of positive functionals and show that, under some conditions, the Bochner and Plancherel representations are equivalent. We also consider the extension of positive linear functionals on a Banach algebra into a space of pseudoquotients and give under conditions in which the space of pseudoquotients can be identified with all Radon measures on the structure space. In the final chapter we consider a system of integrated Cauchy functional equations on a semigroup, …

Translocation Of A Semiflexible Polymer Through A Nanopore, Ramesh Adhikari

Electronic Theses and Dissertations

The transport of a biomolecule through a nanopore occurs in many biological functions such as, DNA or RNA transport across nuclear pores and the translocation of proteins across the eukaryotic endoplasmic reticulum. In addition to the biological processes, it has potential applications in technology such as, drug delivery, gene therapy, and single molecule sensing. The DNA translocation through a synthetic nanopore device is considered as the basis for cheap and fast sequencing technology. Motivated by the experimental advances, many theoretical models have been developed. In this thesis, we explore the dynamics of driven translocation of a semiflexible polymer through a …

Mahalanobis Kernel-Based Support Vector Data Description For Detection Of Large Shifts In Mean Vector, Vu Nguyen

Electronic Theses and Dissertations

Statistical process control (SPC) applies the science of statistics to various process control in order to provide higher-quality products and better services. The K chart is one among the many important tools that SPC offers. Creation of the K chart is based on Support Vector Data Description (SVDD), a popular data classifier method inspired by Support Vector Machine (SVM). As any methods associated with SVM, SVDD benefits from a wide variety of choices of kernel, which determines the effectiveness of the whole model. Among the most popular choices is the Euclidean distance-based Gaussian kernel, which enables SVDD to obtain a …

Research On Improving Reliability, Energy Efficiency And Scalability In Distributed And Parallel File Systems, Junyao Zhang

Electronic Theses and Dissertations

With the increasing popularity of cloud computing and "Big data" applications, current data centers are often required to manage petabytes or exabytes of data. To store this huge amount of data, thousands or tens of thousands storage nodes are required at a single site. This imposes three major challenges for storage system designers: (1) Reliability---node failure in these datacenters is a normal occurrence rather than a rare situation. This makes data reliability a great concern. (2) Energy efficiency---a data center can consume up to 100 times more energy than a standard office building. More than 10% of this energy consumption …

Physics 121 General Physics I Fall 2015 Online, Curtis Shoaf

Physics Courses

No abstract provided.

Physics 120 How Things Work Spring 2015 Online, Tim Kosiek

Physics Courses

No abstract provided.

Physics 143 Modern Physics Spring 2015, Matthew Brenner

Physics Courses

No abstract provided.

Physics 143 Modern Physics Spring 2015, Michael Roedelbronn

Physics Courses

No abstract provided.

Physics 121 General Physics I, Jeremy Jang

Physics Courses

No abstract provided.

Chemistry 106 Chemistry For Health Professions Online Fall 2015, Laura B. Sonnichsen

Chemistry Courses

No abstract provided.

Chemistry 101-007 General Chemistry I Fall 2015, C. Britt Carlson

Chemistry Courses

No abstract provided.

Chemistry 102-003 General Chemistry Ii Spring 2015, Steven L. Mullen

Chemistry Courses

No abstract provided.

Physics 142 Electricity And Magnetism Fall 2015, Michael Roedelbronn

Physics Courses

No abstract provided.

Chemistry 101-004 General Chemistry I Fall 2015, Amy Nicely

Chemistry Courses

No abstract provided.

Chemistry 101-005 General Chemistry Spring 2015, Amy Nicely

Chemistry Courses

No abstract provided.

The Link Between Adhd And Chemical Exposures, Lily Rong

Natural Sciences Student Research Presentations

A part of the Natural Sciences Poster Session at Parkland College, this poster investigates the relationship of Attention Deficit Hyperactivity Disorder to exposures to perfluorinated compounds (PFCs) and polychlorinated biphenyls (PCBs).

Ketoconozole, Jeremy M. Wood

Natural Sciences Student Research Presentations

This is a poster presented at the Natural Sciences Poster Session at Parkland College, which provides the chemical makeup, dosage, and the body's response to Ketoconazole, or Nizoral, an antifungal medication used in the treatment of animals.

Mid-Infrared Plasmonics, Farnood Khalilzadeh Rezaie

Electronic Theses and Dissertations

This dissertation reports investigations into materials for, and applications of, infrared surface plasmon polaritons (SPP). SPPs are inhomogeneous electromagnetic waves that are bound to the surface of a conductor. Tight confinement of electromagnetic energy, the primary virtue of SPPs for so-called "plasmonic" applications, requires plasma frequencies for the conductor near the intended infrared operational frequencies. This requires carrier concentrations that are much less than those of usual metals such as gold and silver. I have investigated the optical properties and SPP excitation resonances of two materials having infrared plasma frequencies, namely the semimetal bismuth and the transparent conducting fluorine-doped tin-oxide …

Scaling Of Geochemical Reaction Rates Via Advective Solute Transport, Allen Hunt, B. Ghanbarian-Alavijeh, Thomas E. Skinner, R. P. Ewing

Physics Faculty Publications

Transport in porous media is quite complex, and still yields occasional surprises. In geological porous media, the rate at which chemical reactions (e.g., weathering and dissolution) occur is found to diminish by orders of magnitude with increasing time or distance. The temporal rates of laboratory experiments and field observations differ, and extrapolating from laboratory experiments (in months) to field rates (in millions of years) can lead to order-of-magnitude errors. The reactions are transport-limited, but characterizing them using standard solute transport expressions can yield results in agreement with experiment only if spurious assumptions and parameters are introduced. We previously developed a …

Characterization Of Gold Black And Its Application In Un-Cooled Infrared Detectors, Deep Panjwani

Electronic Theses and Dissertations

Gold black porous coatings were thermally evaporated in the chamber backfilled with inert gas pressure and their optical properties were studied in near-far-IR wavelengths. The porosities of coatings were found to be extremely high around ~ 99%. Different approaches of effective medium theories such as Maxwell-Garnett, Bruggeman, Landau-Lifshitz-Looyenga and Bergman Formalism were utilized to calculate refractive index (n) and extinction coefficient (k). The aging induced changes on electrical and optical properties were studied in regular laboratory conditions using transmission electron microscopy, Fourier transform infrared spectroscopy, and fore-probe electrical measurements. A significant decrease in electrical resistance in as deposited coating was …

Growth Of Sparingly-Soluble Ab-Type Minerals As A Function Of Their A:B Ratio, Jacquelyn N. Bracco

Browse all Theses and Dissertations

A fundamental understanding of mineral growth kinetics is necessary to predict mineral reactivity in geologic environments. We use hydrothermal atomic force microscopy (HAFM) to measure step advance speeds and morphological evolution of the sparingly-soluble minerals magnesite (MgCO3), barite (BaSO4) and celestite (SrSO4) while systematically varying the concentrations of their constituent cations and anions in solution. For all three minerals, a maximum step velocity is reached at an aqueous cation:anion concentration (r) near unity and decreases with extreme r despite order of magnitude differences in the water exchange rate for the cations comprising the minerals. Affinity based models fail to reproduce …

Accelerated Degradation Of Chlorinated Solvents By Nanoscale Zero-Valent Iron Coated With Iron Monosulfide And Stabilized With Carboxymethyl Cellulose, Shirin Ghahghaei Nezamabadi

Browse all Theses and Dissertations

Nanoscale zero-valent iron (nZVI) injections have proven to be a promising approach for the remediation of aquifers contaminated by chlorinated organic pollutants. This study compares the efficacy of nZVI in sulfidated and unamended forms in degrading selected chlorinated hyrocarbons (CHCs). Results show that nZVI amended with iron monosulfide (FeS) increases the rate of dechlorination of CT, CF and 1,1,1-TCA compared to that by unamended nZVI. The focus of this research was to characterize degradation kinetics and degradation byproduct distributions of CT, CF and 1,1,1-TCA by nZVI coated by iron monosulfide, which is represented as nZVI/FeS. To prevent nZVI particles from …

Optical Propagation Of Self-Sustaining Wavefronts And Nonlinear Dynamics In Parabolic Multimode Fibers, Matthew Mills

Electronic Theses and Dissertations

The aim of this thesis is to introduce my work which has generally been focused on optical wavefronts that have the unusual property of resisting commonplace phenomena such as diffraction and dispersion. Interestingly, these special beams are found both in linear and nonlinear situations. For example, in the linear regime, localized spatio-temporal waves which resemble the spherical harmonic symmetries of the hydrogen quantum orbitals can simultaneously negotiate both diffractive and dispersive effects. In the nonlinear regime, dressed optical filaments can be arranged to propagate multi-photon produced plasma channels orders of magnitude longer than expected. The first portion of this dissertation …