Other Chemistry Commons^™

Eigenstate–Specific Temperatures In Two–Level Paramagnetic Spin Lattices, Mark Masthay, Calley N. Eads, Amber N. Johnson, R. Gerald Keil, Phillip Miller, Ross E. Jones, Joe D. Mashburn, Harry B. Fannin

Chemistry Faculty Publications

Increasing interest in the thermodynamics of small and/or isolated systems, in combination with recent observations of negative temperatures of atoms in ultracold optical lattices, has stimulated the need for estimating the conventional, canonical temperature Tconvc of systems in equilibrium with heat baths using eigenstate-specific temperatures (ESTs). Four distinct ESTs—continuous canonical, discrete canonical, continuous microcanonical, and discrete microcanonical—are accordingly derived for two-level paramagnetic spin lattices (PSLs) in external magnetic fields. At large N, the four ESTs are intensive, equal to Tconvc, and obey all four laws of thermodynamics. In contrast, for N < 1000, the ESTs of most PSL eigenstates are non-intensive, differ from Tconvc, and violate each of the thermodynamic laws. Hence, in spite of their similarities to Tconvc at large N, the ESTs …

Applying The Diffusion Of Innovation Theory To Characterize Stem Faculty Attending Professional Development Programs, Dihua Xue

Department of Chemistry: Dissertations, Theses, and Student Research

Instructional practices in undergraduate STEM courses have been static for decades, with a primary focus on lecture. Over the last twenty years, extensive research on how people learn science has led to the development of innovative instructional strategies that have been shown to enhance students’ learning and interest. These in turn have led to calls to reform instructional practices in STEM fields at the undergraduate level. However, evidence shows that these research-based instructional strategies have largely not been incorporated into classes. The promotion of these new strategies has been mostly conducted through workshops. Although numerous studies have evaluated the impact …

The Autophagy-Related Beclin-1 Protein Requires The Coiled-Coil And Bara Domains To Form A Homodimer With Submicromolar Affinity, Matthew J. Ranaghan, Michael A. Durney, Michael F. Mesleh, Patrick R. Mccarren, Colin W. Garvie, Douglas S. Daniels, Kimberly L. Carey, Adam P. Skepner, Beth Levine, Jose R. Perez

Chemistry Faculty Publications

Beclin-1 (BECN1) is an essential component of macroautophagy. This process is a highly conserved survival mechanism that recycles damaged cellular components or pathogens by encasing them in a bilayer vesicle that fuses with a lysosome to allow degradation of the vesicular contents. Mutations or altered expression profiles of BECN1 have been linked to various cancers and neurodegenerative diseases. Viruses, including HIV and herpes simplex virus 1 (HSV-1), are also known to specifically target BECN1 as a means of evading host defense mechanisms. Autophagy is regulated by the interaction between BECN1 and Bcl-2, a pro-survival protein in the apoptotic pathway that …

No Evidence For Trace Metal Limitation On Anaerobic Carbon Mineralization In Three Peatland Soils, Jason K. Keller, Jillian Wade

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Peatlands store roughly one-third of the terrestrial soil carbon and release the potent greenhouse gas methane (CH₄) to the atmosphere, making these wetlands among the most important ecosystems in the global carbon cycle. Despite their importance, the controls of anaerobic decomposition of organic matter to carbon dioxide (CO₂) and CH₄ within peatlands are not well understood. It is known, however, that the enzymes responsible for CH₄ production require cobalt, iron and nickel, and there is a growing appreciation for the potential role of trace metal limitation in anaerobic decomposition. To explore the possibility of …

Interactions Between Amyloid-Beta And Microglial Cells, Lisa Gouwens

Dissertations

Alzheimer’s disease (AD), the most common cause of dementia, is a neurodegenerative condition characterized by loss of memory and intellectual abilities. Intracellular plaques of aggregated amyloid-beta (Ab) protein are a well-known pathology associated with AD. Although symptoms usually appear late in life, the accumulation of Ab begins decades earlier and causes activation of microglia, the brain’s immune cells. The ensuing inflammation contributes significantly to neurodegeneration. Determination of the particular form of Ab that causes the most damage in the brain is one of the major questions in the AD field. My research focused on the interactions of microglia with monomers, …

Ensemble-Based Modeling And Rigidity Decomposition Of Allosteric Interaction Networks And Communication Pathways In Cyclin-Dependent Kinases: Differentiating Kinase Clients Of The Hsp90-Cdc37 Chaperone, Gabrielle Stetz, Amanda Tse, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The overarching goal of delineating molecular principles underlying differentiation of protein kinase clients and chaperone-based modulation of kinase activity is fundamental to understanding activity of many oncogenic kinases that require chaperoning of Hsp70 and Hsp90 systems to attain a functionally competent active form. Despite structural similarities and common activation mechanisms shared by cyclin-dependent kinase (CDK) proteins, members of this family can exhibit vastly different chaperone preferences. The molecular determinants underlying chaperone dependencies of protein kinases are not fully understood as structurally similar kinases may often elicit distinct regulatory responses to the chaperone. The regulatory divergences observed for members of CDK …

Single-Reference Coupled Cluster Theory For Multi-Reference Problems, Johannes T. Margraf, Ajith Perera, Jesse J. Lutz, Rodney J. Bartlett

Faculty Publications

Coupled cluster (CC) theory is widely accepted as the most accurate and generally applicable approach in quantum chemistry. CC calculations are usually performed with single Slater-determinant references, e.g., canonical Hartree-Fock (HF) wavefunctions, though any single determinant can be used. This is an attractive feature because typical CC calculations are straightforward to apply, as there is no potentially ambiguous user input required. On the other hand, there can be concern that CC approximations give unreliable results when the reference determinant provides a poor description of the system of interest, i.e., when the HF or any other single determinant ground state has …

How The E. Coli Hsp70 Molecular Chaperone, Dnak, Binds A Client Protein, Joseph Tilitsky

Masters Theses

Protein folding is essential for all cellular life. While some proteins are able to reach their folded state reliably using nothing but their amino acid sequence, a great number of essential proteins are unable to do so without the aid of molecular chaperones. One family of molecular chaperone, the Hsp70 family, is found in virtually all cell types and across all domains of life. Certain to the function of Hsp70s are how they bind their client proteins. Substantial effort has been expended to study how Hsp70s work on model peptides as a substrate mimic, but relatively little work has been …

Phase Behavior Of Binary And Polydisperse Suspensions Of Compressible Microgels Controlled By Selective Particle Deswelling, A. Scotti, U. Gasser, E. S. Herman, Jun Han, A. Menzel, L. Andrew Lyon, A. Fernandez-Nieves

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We investigate the phase behavior of suspensions of poly(N-isopropylacrylamide) (pNIPAM) microgels with either bimodal or polydisperse size distribution. We observe a shift of the fluid-crystal transition to higher concentrations depending on the polydispersity or the fraction of large particles in suspension. Crystallization is observed up to polydispersities as high as 18.5%, and up to a number fraction of large particles of 29% in bidisperse suspensions. The crystal structure is random hexagonal close-packed as in monodisperse pNIPAM microgel suspensions.We explain our experimental results by considering the effect of bound counterions. Above a critical particle concentration, these cause deswelling of the largest …

Nonlinear Oscillatory Dynamics Of The Hardening Of Calcium Phosphate Bone Cements, Vuk Uskoković, Julietta V. Rau

Pharmacy Faculty Articles and Research

Here we report on the nonlinear, oscillatory dynamics detected in the evolution of phase composition during the setting of different calcium phosphate cements, two of which evolved toward brushite and one toward hydroxyapatite as the final product. Whereas both brushite-forming cements contained iondoped b-tricalcium phosphate as the initial phase, the zinc-containing one yielded scholzite as an additional phase during setting and the oscillations between these two products were pronounced throughout the entire 80 h setting period, long after the hardening processes was over from the mechanical standpoint. Oscillations in the copper-containing system involved the amount of brushite as the main …

Parallelization Of Molecular Docking Algorithms Using Cuda For Use In Drug Discovery, Brandon Stewart, Jonathan Fine, Gaurav Chopra Phd

The Summer Undergraduate Research Fellowship (SURF) Symposium

Traditional drug discovery methodology uses a multitude of software packages to design and evaluate new drug-like compounds. While software packages implement a wide variety of methods, the serial (i.e. single core) implementation for many of these algorithms, prohibit large scale docking, such as proteome-wide docking (i.e. thousands of compounds with thousands of proteins). Several docking algorithms can be parallelized, significantly reducing the runtime of the calculations, thus enabling large-scale docking. Implementing algorithms that take advantage of the distributed nature of graphical processing units (GPUs) via the Compute Unified Device Architecture (CUDA) enables us to efficiently implement massively parallel algorithms. Two …

Ab Initio Methyl Linoleate Bond Dissociation Energies: First Principles Fishing For Wise Crack Products, Zachary Ryan Wilson

MSU Graduate Theses

With the prices of petroleum reflecting demand for this finite resource, attention has been turned to alternative sources of energy. Biodiesel, defined as fatty acid methyl esters (FAMEs), exhibits many of the same properties as conventional diesel but is derived from biological sources. FAMEs are subsequently thermally cracked to form more light-weight petrochemical products. I aim to further understand the thermal cracking procedure, at an atomic-level, in hopes that this may aid in future engineering of viable fuels. I studied the effective computational modeling of bond disassociations in the FAME methyl linoleate. Bond dissociation in a 44-reaction database with known …

Functionalization Of Indium-Based Quantum Dots For Use As A Non-Viral Gene Therapy Vector, Nicholas A. Mundt

MSU Graduate Theses

This work aims to develop functionalized, water-soluble indium-based quantum dots (QDs) as a non-viral gene therapy vector. The QDs were solubilized in water by exchanging native hydrophobic surface ligands with 11-mercaptoundecanioc acid (MUA); an amphiphilic ligand providing terminal carboxylate groups that impart water solubility to the QDs. The aqueous QDs were then functionalized with a terminal tertiary amine to impart a positive surface charge, allowing negatively-charged DNA to complex with the nanoparticles. The QDs were characterized via electrophoresis to determine their ability to bind DNA. Results show that further work is needed to optimize DNA binding. In addition, this work …

Controlled Electrochemical Synthesis Of Single One-Dimensional Metal Nanochains Across Microgap Electrodes., Amareshwari Konutham

Electronic Theses and Dissertations

This study mainly focuses on the fabrication of single one dimensional (1D) NP chains across the 5-micron gap of Au two electrode devices (TED). This has been achieved by electrochemical deposition of Ag onto the two electrodes, soaking the TED in 0.1 M Cetyltrimethyl ammonium bromide for 2-3 hours, and then close monitoring of the current as a function of time while a voltage across the two Ag coated Au electrodes in air. One dimensional Ag nanoparticle chain formation occurred by oxidation of Ag to Ag⁺ at the positive electrode followed by movement of Ag⁺ ions to the …

Cellular And Molecular Targets Of Menthol Actions, Murat Oz, Eslam El Nebrisi, Keun-Hang Susan Yang, Frank Christopher Howarth, Lina T. Al Kury

Mathematics, Physics, and Computer Science Faculty Articles and Research

Menthol belongs to monoterpene class of a structurally diverse group of phytochemicals found in plant-derived essential oils. Menthol is widely used in pharmaceuticals, confectionary, oral hygiene products, pesticides, cosmetics, and as a flavoring agent. In addition, menthol is known to have antioxidant, anti-inflammatory, and analgesic effects. Recently, there has been renewed awareness in comprehending the biological and pharmacological effects of menthol. TRP channels have been demonstrated to mediate the cooling actions ofmenthol. There has been new evidence demonstrating thatmenthol can significantly influence the functional characteristics of a number of different kinds of ligand and voltage-gated ion channels, indicating that at …

Oligo(Ethylene Glycol)-Sidechain Microgels Prepared In Absence Of Cross-Linking Agent: Polymerization, Characterization And Variation Of Particle Deformability, Nicole Welsch, L. Andrew Lyon

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We present a systematic study of self-cross-linked microgels formed by precipitation polymerization of oligo ethylene glycol methacrylates. The cross-linking density of these microgels and, thus, the network flexibility can be easily tuned through the modulation of the reaction temperature during polymerization. Microgels prepared in absence of any difunctional monomer, i.e. cross-linker, show enhanced deformability and particle spreading on solid surfaces as compared to microgels cross-linked with varying amounts of poly(ethylene glycol diacrylate) (PEG-DA) in addition to self-crosslinking. Particles prepared at low reaction temperatures exhibit the highest degree of spreading due to the lightly cross-linked and flexible polymer network. Moreover, AFM …

Applications Of Paper Microfluidic Systems In The Field Detection Of Drugs Of Abuse, Ling Wang

FIU Electronic Theses and Dissertations

Over the years, colorimetric reagents and immunology have been widely used in screening tests for illicit drugs; however, the test kits are not always convenient for field use and often require the user to mix and develop a specific set of reagents. In our project, we have been working on alternative platforms based on paper microfluidic devices (uPADs) for field testing. These devices utilize wax channels printed on paper to direct the analyte towards a specific set of chemical reagents. Using the procedure, we have developed a six-channel chip that adapts known colorimetric reagents targeting cocaine, opiates, amphetamines and ketamine …

Understanding The Surface Fouling Mechanism Of Ultrananocrystalline Diamond Microelectrodes Using Microfluidics For Neurochemical Detection, An-Yi Chang

Doctoral Dissertations

Electrochemical methods are widely used for chronic neurochemical sensing, but thus far, the organic solution redox reactions fouled the electrodes' surface. It caused the reduction of sensitivity and the electrodes' lifetime.

Here, we present the boron-doped nanocrystalline diamond microelectrodes (BDUNCD) as the next generation electrode material for neurochemical sensor development. To aid in long-term chronic monitoring of neurochemicals, they have a wide window of electrochemical potential, extremely low background current, and excellent chemical inertness. The main research goal is to reduce the rate of electrode fouling due to the reaction by-products, and significantly extend their useful lifetime.

We systematically characterize …

Electrochemical Behavior Of Dense Electrodes For Impedancemetric Nox Sensors, Nabamita Pal

Doctoral Dissertations

NOx (NO and NO2) exhaust gas sensors for diesel powered vehicles have traditionally consisted of porous platinum (Pt) electrodes along with a dense ZrO2 based electrolyte. Advancement in diesel engine technology results in lower NOx emissions. Although Pt is chemically and mechanically tolerant to the extreme exhaust gas environment, it is also a strong catalyst for oxygen reduction, which can interfere with the detection of NOx at concentrations below 100 ppm. Countering this behavior can add to the complexity and cost of the conventional NO x sensor design. Recent studies have shown that dense electrodes are less prone to heterogeneous …

The Quantification Of Cocaine From The Erythroxylum Coca Plant And The Comparison On High Performance Liquid Chromatography And Gas Chromatography Mass Spectroscopy As An Analytical Method., Tuesday James

Student Theses

Cocaine is derived from the Erythroxylum coca plant, is a highly addictive stimulant abused all over the world. There are two types of Erythroxylum coca plants that produce cocaine; the E. Coca and E. Novogranatense. Cocaine exists as the salt, and the freebase which is typically referred to as “crack” due to the crackling sound it makes when heated. It is popular because it is inexpensive and easily available on the streets, mainly in poor urban areas. The purpose of this project was to determine the amount of cocaine that can be extracted from E.coca and to assess which analytical …

The Advanced Spectroscopic Analysis Of Organic Gunshot Residue And Explosives, Jennifer M. Leonard

Dissertations, Theses, and Capstone Projects

With the prevalence of shooting cases and terrorist attacks/or threats that plague the current state of the criminal justice system, it is of paramount importance to be able to detect, identify and interpret the presence of gunshot residue or explosives material. This concern is seen in law enforcement agencies and the media throughout the United States and abroad.

Currently, the typical method of analyzing gunshot residue in most crime laboratories serves to identify the inorganic constituents of the primer residue, namely lead, barium and antimony. However, it is possible that the organic matter from the propellant could provide different information …

From The Making To The Tuning To The Use Of Chlorins For Biomedical Applications, Junior Gonzales

Dissertations, Theses, and Capstone Projects

Chlorins are porphyrins missing a double bond. These pigments are optimal platforms for the development of novel dyes that display drug-like attributes such as photodynamic therapy (PDT) agents. More recently, it was demonstrated that chlorins can serve both as a PDT agent and as a modality for fluorescence or PET imaging. Thus, multifunctional chlorins eliminate the differences that may occur in specificity, uptake, and distribution between separate compounds or constructs for imaging and therapy. The overall goal of this dissertation is to take advantage of the reputed intrinsic attributes of chlorins as a viable tool in biomedical applications. In this …

Chelating Ligands And Nanomaterials Based On Graphene Oxide For The Reduction And Sequestration Of Radiometals And Protein Purification, Sam Groveman

Dissertations, Theses, and Capstone Projects

Nuclear waste remediation and protein purification using immobilized metals can benefit enormously from the design and implementation of novel chelating nanomaterials. Available commercial resins capable of sequestering metals are based on bulk materials such as organic polymers, ceramics, and their composites. The use of two-dimensional nanoplatforms with large surface areas expands the horizon for the research and development of new systems with higher efficiency and lower cost. Fundamental science challenges remain in the synthesis and characterization of these nanomaterials and their integration with known or novel coordinating ligands.

Chemical exfoliation of graphite under strong oxidizing conditions yields graphene oxide (GO) …

Application Of Bottlebrush Block Copolymers As Photonic Crystals, Allegra L. Liberman-Martin, Crystal K. Chu, Robert H. Grubbs

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Brush block copolymers are a class of comb polymers that feature polymeric side chains densely grafted to a linear backbone. These polymers display interesting properties due to their dense functionality, low entanglement, and ability to rapidly self-assemble to highly ordered nanostructures. The ability to prepare brush polymers with precise structures has been enabled by advancements in controlled polymerization techniques. This Feature Article highlights the development of brush block copolymers as photonic crystals that can reflect visible to near-infrared wavelengths of light. Fabrication of these materials relies on polymer self-assembly processes to achieve nanoscale ordering, which allows for the rapid preparation …

A Computational Approach To Studying The Properties Of Photosensitizers In Photodynamic Therapy, Keenan Komoto

Graduate Student Symposium

Cancer has long been a significant problem that has affected our world’s population for years and continues to this day. With the number of cases expected to increase annually there is a societal pressure to find effective treatment methods for eliminating cancer. Current forms of cancer treatment tend to cause detrimental effects to the human body and are usually quite expensive and long lasting, some costing upwards of $30,000 over an 8 week period. A more recently established form of cancer treatment known as photodynamic therapy is an effective treatment option for ridding cancers that lie on or just below …

Towards Autonomous Microcystin Detection: Investigating Methods For Automation, Maureen Anne Schneider

Theses and Dissertations

Due to increased anthropogenic activity, severe eutrophication is occurring in bodies of water around the world. Effects include decreased water quality, decreased value of surrounding land and recreational use (estimated loss in revenue of 0.67 and 3.96 U.S. billion dollars per year), and increased occurrence of toxin producing Harmful Algal Blooms (HABs). Microcystins are cyclic peptides made up of 7 amino acids and 800-1100 Daltons in size. They are one of the most predominantly produced of these toxins, and therefore was the focus of this study. Numerous structural variants of microcystin (referred to as congeners) exist, but microcystin-LR is one …

Ab Initio And Semi-Empirical Calculations Of Cyanoligated Rhodium Dimer Complexs, Yazeed Asiri

Electronic Theses and Dissertations

Molecular modeling, using both ab initio and semi-empirical methods has been undertaken for a series of dirhodium complexes in order to improve the understanding of the nature of the chemical bonding in this class of homogeneous catalysts. These complexes, with carboxylamidate and carboxylate ligands, are extremely functional metal catalysts used in the synthesis of pharmaceuticals and agrochemicals. The X-ray crystallography shows anomalies in the bond angles that have potential impact on understanding the catalysis. To resolve these issues, minimum energy structures of several examples (e.g. Rh₂(NHCOCH₃)₄, Rh₂(NHCOCH₃)₄NC, Rh …

Conservative Tryptophan Mutations In Protein Tyrosine Phosphatase Ptp1b And Its Effect On Catalytic Rate And Chemical Reaction, Teisha Richan

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein-tyrosine phosphatases (PTPs) catalyze the hydrolysis of phosphorylated tyrosines by a 2-step mechanism involving nucleophilic attack by cysteine and general acid catalysis by aspartic acid. In most PTPs the aspartic acid resides on a flexible protein loop, consisting of about a dozen residues, called the WPD loop. PTP catalysis rates span several orders of magnitude, and differences in WPD loop dynamics have recently been show to correlate with the rate of enzymatic catalysis. The rate of WPD loop motion could possibly be related to a widely conserved tryptophan residue on the WPD loop. Therefore, point mutants were made in PTP1B …

Analyzing The Kinetics Of A Bromophenol Blue Fading Reaction In Basic Conditions For An Undergraduate Lab, Zeljka Popovic

Georgia College Student Research Events

Bromophenol blue is a common pH indicator and dye used in many different industries. Once a solution of bromophenol blue is placed in a concentrated basic solution, the color fades from a blue/violet color to clear solution with a pH of 4.6 or greater. The rate law of the reaction is analyzed through the use of a small footprint visible-near-infrared spectrometer (Vis-NIR) with a diode array detector. An absorbance wavelength of 590 nm as a function of time was collected using Ocean Optics OceanView software. The results contained in the data collection file are exported to a spreadsheet for further …

Assessing The Efficacy Of Recommended Antiseptics For Killing Bacterial Growth In Neonatal Blue Bulb Syringes: Addressing A Clinical Issue, Linda A. Hanson

Research Horizons Day Posters

No abstract provided.