Physical Sciences and Mathematics Commons^™

Clustering, Reorientation Dynamics, And Proton Transfer In Glassy Oligomeric Solids, Jacob Allen Harvey

Open Access Dissertations

We have modelled structures and dynamics of hydrogen bond networks that form from imidazoles tethered to oligomeric aliphatic backbones in crystalline and glassy phases. We have studied the behavior of oligomers containing 5 or 10 imidazole groups. These systems have been simulated over the range 100-900 K with constantpressure molecular dynamics using the AMBER 94 force field, which was found to show good agreement with ab initio calculations on hydrogen bond strengths and imidazole rotational barriers. Hypothetical crystalline solids formed from packed 5-mers and 10-mers melt above 600 K, then form glassy solids upon cooling. Viewing hydrogen bond networks as …

Reactive Heterocycles For Examining Polyketide Biosynthesis, Gitanjeli Prasad

Open Access Dissertations

Polyketides are a class of natural products that exhibit remarkable structural and functionally diversity and are highly sought after due to their medicinally important activities. For many decades now, polyketide synthases (PKSs), the mega-enzymes responsible for biosynthesis of polyketides have been the focus of extensive investigation to make new polyketides by polyketide engineering strategies. While there are many established methods to investigate polyketide enzymes and biosynthesis mechanisms, they have substantial shortcomings that have limited the extent of success with polyketide engineering efforts.

This thesis focuses on developing simple, flexible yet powerful tools for examining polyketide biosynthesis by overcoming some deficiencies …

O2 Activation And Allosteric Zn(Ii) Binding On Hif-Prolyl Hydroxylase-2 (Phd2), Serap Pektas

Open Access Dissertations

Oxygen homeostasis is essential to the life of aerobes, which is regulated in humans by Hypoxia Inducible Factor-1α (HIF-1α). Under hypoxic conditions, HIF-1α transactivates over a hundred genes related angiogenesis, erythropoiesis, etc. HIF-1α level and function is regulated by four HIF hydroxylase enzymes: three isoforms of prolyl hydroxylase domain (PHD1, PHD2 and PHD3) and factor inhibiting HIF-1α (FIH). PHD2 is the focus of this research. PHD2 is a non-heme Fe(II) 2-oxoglutarate dependent dioxygenase, which controls HIF-1α levels by hydroxylating two proline residues within the ODD domain of HIF-1α, then the hydroxylated prolines are recognized by pVHL, which targets HIF-1α for …

Development Of Mass Spectrometry-Based Methods For Quantitation And Characterization Of Protein Drugs: Transferrin As A Model Drug Delivery Vehicle, Shunhai Wang

Open Access Dissertations

In the last two decades, protein drugs have enjoyed a rapid growth and achieved a tremendous success in treating human diseases. However, the presence of physiological barriers greatly impedes the efficient delivery of such unconventional large molecule drugs, and therefore limits their clinical utility. An elegant way to address this challenge takes advantage of certain endogenous transporter proteins, such as human transferrin (Tf), whose ability to traverse physiological barriers has been extensively exploited. However, methods to investigate Tf-based drug delivery remained insufficient and unsatisfactory until recent development of quantitative mass spectrometry (MS). Hereby, MS-based methods have been developed and validated …

Evolution Of Hierarchical Structures In Polyelectrolyte–Micelle Coacervates, Ebru Kizilay, Anthony D. Dinsmore, David A. Hoagland, Lianhong Sun, Paul Dubin

Paul Dubin

We investigated the temperature-induced liquid–liquid phase separation (coacervation) of polyelectrolyte (PE)–micelle systems and the structure of the resultant coacervates. Dynamic light scattering, small angle neutron scattering and cryo-transmission electron microscopy (DLS, SANS, Cryo-TEM) were used to examine the evolution of complex structure up to the point of temperature-induced coacervation and beyond. Three diffusional modes, seen in the single phase samples and in the coexisting coacervated supernatant phases were attributed respectively to free micelles, PE–micelle complexes, and aggregates thereof. They corresponded to SANS Guinier region slopes yielding Rg [similar] 4 nm (micelles) and Rg [similar] 50 nm (unresolved complexes and aggregates). …

Enhanced Electrostatic Discrimination Of Proteins On Nanoparticle-Coated Surfaces, Yisheng Xu, Yoni Engel, Yunfeng Yan, Kaimin Chen, Daniel F. Moyano, Paul Dubin, Vincent M. Rotello

Paul Dubin

Two β-lactoglobulin (BLG) isoforms, BLGA and BLGB, were used as a test bed for the differentiation of proteins using electrostatics. In these studies, the BLGA and BLGB binding to a highly charged, cationic gold nanoparticle (GNP) modified surface was investigated by atomic force microscopy (AFM) and surface plasmon resonance (SPR) spectroscopy. The binding affinity, and more importantly, the selectivity of this surface towards these two almost identical protein isoforms were both significantly increased on the cationic GNP surface array relative to the values measured with the same free cationic GNP in solution. While protein recognition is traditionally achieved almost exclusively …

Enhanced Detection Strategies Accomplished Through Metal Binding And Miniature Mass Spectrometry, Adam Graichen

Open Access Dissertations

A multiplexed method for performing MS/MS on multiple ions simultaneously in a miniature rectilinear ion trap (RIT) mass spectrometer has been developed. This method uses an ion encoding procedure that relies on the mass bias that exists when ions are externally injected into an RIT operated with only a single phase RF applied to one pair of electrodes. The ion injection profile under such conditions ions is Gaussian-like over a wide range of RF amplitudes, or low mass cutoff (LMCO) values, during ion accumulation. We show that this distribution is related to ion m/z and is likely caused by ions …

Investigation Of The Orientation Dependence On Chiroptical Properties Of Single Molecules, Austin Joseph Cyphersmith

Open Access Dissertations

Optical activity is the defining property of chiral materials that is essential for characterization in biology, chemistry, and physics. While a substantial body of research has provided a strong theoretical framework of the origin of optical activity, we still know very little by way of experiment about an individual molecule’s contribution to the bulk optical activity. The chiroptical response of a single molecule can depend on molecular orientation and local molecular environment, information which is lost in ensemble averaging.

This thesis focuses on establishing methods for a priori determination of chiral molecule orientations and refining measurements to probe the chiroptical …

Determination Of Arsenic In Water By Potentially Portable Methodology, Chengbei Li

Open Access Dissertations

Arsenic contamination in groundwater is a worldwide problem. The existing portable field test kits can not provide accurate results when the arsenic concentration is around 10 μg L-1 or lower. This research first was focused on the development and validation of methods in which portable instrumentation, such as electrochemistry instruments or quartz crystal microbalances, could be used to accurately determine arsenic concentrations in water even when the concentration is below 10 μg L-1. A modified anodic stripping voltammetry (ASV) and cathodic stripping voltammetry (CSV) method with measurement at a microarray electrode manufactured by TraceDetect Inc. was developed. When the ASV …

Assembly Of Surface Engineered Nanoparticles For Functional Materials, Xi Yu

Open Access Dissertations

Nanoparticles are regarded as exciting new building blocks for functional materials due to their fascinating physical properties because of the nano-confinement. Organizing nanoparticles into ordered hierarchical structures are highly desired for constructing novel optical and electrical artificial materials that are different from their isolated state or thermodynamics random ensembles. My research integrates the surface chemistry of nanoparticles, interfacial assembly and lithography techniques to construct nanoparticle based functional structures. We designed and synthesized tailor-made ligands for gold, semiconductor and magnetic nanoparticle, to modulate the assembly process and collective properties of the assembled structures, by controlling the key parameters such as particle-interface …

Development And Characterization Of Caspase Activatable Gfp And A Family Of Fluorescent Reporters, Samantha Elizabeth Bernard Nicholls

Open Access Dissertations

The cellular process of programmed cell death, or apoptosis, is critical in homeostasis and development. In addition it's misfunction is implicated in an array of disease states from cancer to neurodegeration, making it an attractive pathway for drug targeting. A family of proteases, known as caspases, plays a central role in the apoptotic cascade resulting in the ultimate destruction of the cell. We report a genetically encoded dark-to-bright reporter of caspase activity used in E.coli, mammalian cells, and whole organisms which can be used to monitor apoptosis. This reporter, caspase activatable green fluorescent protein (CA-GFP) consists of GFP fused through …

Protein–Polyelectrolyte Interactions, A. Basak Kayitmazer, Daniel Seeman, Burcu Baykal Minsky, Paul Dubin, Yisheng Xu

Paul Dubin

The interactions of proteins and polyelectrolytes lead to diverse applications in separations, delivery and wound repair, and are thus of interest to scientists in e.g. (a) glycobiology, (b) tissue engineering, (c) biosensing, and (d) pharmacology. This breadth is accompanied by an assortment of contexts and models in which polyelectrolytes are seen as (a) protein cognates assisting in complex cellular roles, (b) surrogates for the extracellular matrix, mimicking its hydration, mechanical and sequestering properties, (c) benign hosts that gently entrap, deposit and tether protein substrate specificity, and (d) selective but non-specific agents that modify protein solubility. Unsurprisingly, this literature is somewhat …

Resin Volatiles Of Eastern Hemlock Induced By Its Non-Native Herbivores, Joshua D. Pezet

Masters Theses 1911 - February 2014

Eastern hemlock (Tsuga canadensis) is in decline because of infestation by the invasive hemlock woolly adelgid (Adelges tsugae; ‘HWA’) and, to a lesser extent, the elongate hemlock scale (Fiorinia externa; ‘EHS’). Many conifers respond to insect herbivory by inducing oleoresin-based defenses, however it is unknown whether eastern hemlock is capable of this inducible response. We conducted a plantation setting study of artificially infested saplings to determine if feeding by HWA or EHS induces changes in the tree’s volatile chemistry. The induced changes in volatiles we found were unlike the terpenoid-based defenses of related conifers. Only HWA feeding …

Making Solar Cells, D. Venkataraman

Nanotechnology Teacher Summer Institutes

Overview of solar energy and photovoltaic cells. Making a cuprous oxide cell activity.

How Much Arsenic Do We Eat?, Julian Tyson

Science and Engineering Saturday Seminars

No abstract provided.

Trace Determination Of Total Mercury In Rice By Conventional Inductively Coupled Plasma Mass Spectrometry, Lindsay R. Drennan-Harris, Sirinapa Wongwilawan, Julian Tyson

Chemistry Department Faculty Publication Series

No abstract provided.

Determination Of Inorganic Arsenic In Water By A Quartz Crystal Microbalance, C Li, A. E. Basaran, Julian Tyson

Chemistry Department Faculty Publication Series

No abstract provided.

Dispersive Liquid–Liquid Microextraction And Microsample Injection System Coupled With Inductively Coupled Plasma-Mass Spectrometry For Inorganic Arsenic Speciation In Natural Waters, Latif Elci, Aydan Elci, Tiffany Berg, Julian Tyson

Chemistry Department Faculty Publication Series

No abstract provided.

My Relations With Russian Polymer Science, Otto Vogl, Frank T. Traceski, Friderikh Diachekovski

Otto Vogl

No abstract provided.