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Design Of Collagen-Mimetic Peptides, Parminder Jeet Kaur 2017 The Graduate Center, City University of New York

Design Of Collagen-Mimetic Peptides, Parminder Jeet Kaur

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

Collagen is the major component of the extracellular matrix and is involved in a wide range of cellular functions during tissue development and action. At the core of the diverse functions of this versatile protein is its remarkable ability to form supramolecular structures through self-assembly and/or through interactions with other biomolecules. One typical example of such supramolecular structure is the fibrils of collagen types I, II and III of the connective tissues. These fibrils have staggered arrangement of the laterally associated collagen triple helices – the structural unit of collagen – to form long, smooth fibrils with a characteristic 67 nm ...


Safer Chemicals Design Diagrams, Longzhu Shen, Fjodor Melnikov, John Roethle, Aditya Gudibanda, Richard Judson, Julie Zimmerman, Paul Anastas 2017 Yale University

Safer Chemicals Design Diagrams, Longzhu Shen, Fjodor Melnikov, John Roethle, Aditya Gudibanda, Richard Judson, Julie Zimmerman, Paul Anastas

Yale Day of Data

The NRF2-ARE antioxidant pathway is an important biological sensing and regulating system that responds to chemical insults. At minute level, it protects a living species to go through hard environmental conditions. However, when the external disruption exceeds the inherent resilience, cellular damage can occur, eventually leading to cytotoxicity. Therefore, studying the likelihood of a chemical activating the NRF2-ARE pathway is interesting to discovering therapeutic agents and designing safer chemicals. In this research, we engaged a combination of computational chemistry, statistical learning and mechanistic toxicology to estimate the likelihood of a chemical to perturb this critical toxicological pathway and derive a ...


Using Atto Dyes To Probe The Photocatalytic Activity Of Au−Cds Nanoparticles, Ujjal Bhattacharjee, Long Men, Bryan A. Rosales, Samuel R. Alvarado, Javier Vela, Jacob W. Petrich 2017 Iowa State University

Using Atto Dyes To Probe The Photocatalytic Activity Of Au−Cds Nanoparticles, Ujjal Bhattacharjee, Long Men, Bryan A. Rosales, Samuel R. Alvarado, Javier Vela, Jacob W. Petrich

Chemistry Publications

Metal−semiconductor nanohybrids (or heterostructures), such as Au−CdS, have become an important class of materials because of their role in photochemical hydrogen production and in other catalytic reactions. Here we report the results of photophysical studies of the interactions of these particles with ATTO dyes (ATTO 590 and 655), which are used as fluorescent probes in a wide range of spectroscopic techniques, most notably super-resolution microscopies. The most important feature of the Au−CdS particles is that they provide the possibility of selective excitation at either their CdS or their Au domains, which absorb preferentially at wavelengths shorter or ...


Phage Display To Identify Functional Resistance Mutations To Rigosertib, Nedim Filipovic 2017 Claremont McKenna College

Phage Display To Identify Functional Resistance Mutations To Rigosertib, Nedim Filipovic

CMC Senior Theses

In vitro protein selection has had major impacts in the field of protein engineering. Traditional screens assay individual proteins for specific function. Selection, however, analyzes a pool of mutants and yields the best variants. Phage display, a successful selection technique, also provides a reliable link between variant phenotype and genotype. It can also be coupled with high throughput sequencing to map protein mutations; potentially highlighting vital mutations in variants. We propose to apply this technique to cancer therapy. RAF, a serine/threonine kinase, is critical for cell regulation in mammals. RAF can be activated by oncogenic RAS, found in over ...


Polyol Induced Partitioning Of Essential Oils In Aqueous Organic Solvent Mixtures, Thomas DelMastro 2016 Seton Hall University

Polyol Induced Partitioning Of Essential Oils In Aqueous Organic Solvent Mixtures, Thomas Delmastro

Seton Hall University Dissertations and Theses (ETDs)

Polyol Induced Extraction (PIE) was developed and patented at Seton Hall University by Drs. John R. Sowa Jr., Wyatt R. Murphy, and Mithilesh Deshpande. It was originally discovered and implemented as a method to recycle and reuse waste acetonitrile during the production shortage in 2008. Through the use of PIE, a solvent mixture containing acetonitrile and water can be separated by employing a polyol mass separating agent, which induces a phase separation. The system is separated into its corresponding aqueous and organic phases, with the organic phase being a highly purified organic liquid. Based on the successful experimental results that ...


Three Body Interactions Of Rare Gas Solids Calculated Within The Einstein Model, Dan D'Andrea 2016 University of Tennessee, Knoxville

Three Body Interactions Of Rare Gas Solids Calculated Within The Einstein Model, Dan D'Andrea

Masters Theses

Three body interactions can become important in solids at higher pressures and densities as the molecules can come into close contact. At low temperatures, accurate studies of three body interactions in solids require averaging the three-body terms over the molecules' zero point motions. An efficient, but approximate, averaging approach is based on a polynomial approximation of the three-body term. The polynomial approximation can be developed as a function of the symmetry coordinates of a triangle displaced from its average geometry and also as a function of the Cartesian zero point displacements from each atom’s average position. The polynomial approximation ...


Synthetic Development Of Low Dimensional Materials, Long Men, Miles A. White, Himashi P. Andaraarachchi, Bryan A. Rosales, Javier Vela 2016 Iowa State University

Synthetic Development Of Low Dimensional Materials, Long Men, Miles A. White, Himashi P. Andaraarachchi, Bryan A. Rosales, Javier Vela

Chemistry Publications

In this invited paper, we highlight some of our most recent work on the synthesis of low dimensional nanomaterials. Current graduate students and members of our group present four specific case systems: Nowotny–Juza phases, nickel phosphides, germanium-based core/shells, and organolead mixed-halide perovskites. Each system is accompanied by commentary from the student involved, which explains the motivation behind their work, as well as a protocol detailing the key experimental considerations involved in their synthesis. We trust these and similar efforts will help further advance our understanding of the broader field of synthetic nanomaterials chemistry, while, at the same time ...


Polytypism And Unique Site Preference In Liznsb: A Superior Thermoelectric Reveals Its True Colors, Miles A. White, Gordon J. Miller, Javier Vela 2016 Iowa State University

Polytypism And Unique Site Preference In Liznsb: A Superior Thermoelectric Reveals Its True Colors, Miles A. White, Gordon J. Miller, Javier Vela

Chemistry Publications

The first example of polytypism in the I–II–V semiconductors has been demonstrated with the synthesis of cubic LiZnSb by a low-temperature solution-phase method. This phase exhibits a unique coloring pattern that is novel for this class of compounds. The choice of site configuration has a considerable impact on the band structure of these materials, which in turn affects the transport properties. While the hexagonal polytype has been suggested as a promising n-type and extremely poor p-type thermoelectric material, the cubic analogue is calculated to have high efficiencies for both the n- and p-type derivatives (1.64 and 1 ...


Persistent Dopants And Phase Segregation In Organolead Mixed-Halide Perovskites, Bryan A. Rosales, Long Men, Sarah D. Cady, Michael P. Hanrahan, Aaron J. Rossini, Javier Vela 2016 Iowa State University

Persistent Dopants And Phase Segregation In Organolead Mixed-Halide Perovskites, Bryan A. Rosales, Long Men, Sarah D. Cady, Michael P. Hanrahan, Aaron J. Rossini, Javier Vela

Chemistry Publications

Organolead mixed-halide perovskites such as CH3NH3PbX3–aX′a (X, X′ = I, Br, Cl) are interesting semiconductors because of their low cost, high photovoltaic power conversion efficiencies, enhanced moisture stability, and band gap tunability. Using a combination of optical absorption spectroscopy, powder X-ray diffraction (XRD), and, for the first time, 207Pb solid state nuclear magnetic resonance (ssNMR), we probe the extent of alloying and phase segregation in these materials. Because 207Pb ssNMR chemical shifts are highly sensitive to local coordination and electronic structure, and vary linearly with halogen electronegativity and band gap, this technique can provide the true chemical speciation and ...


The Investigation Of The Electrical Control Of Hemimicelles And Admicelles On Gold For Analyte Preconcentration, Dheyaa Hussein Al-Karawi 2016 Western Kentucky University

The Investigation Of The Electrical Control Of Hemimicelles And Admicelles On Gold For Analyte Preconcentration, Dheyaa Hussein Al-Karawi

Masters Theses & Specialist Projects

Hemimicelles and admicelles are well-investigated wonders in modern science; they are surfactant monolayers and surface adsorbed micelles, respectively. Capacitance measurements for monitoring the formation of dodecyl sulfate (DS) surfactant monolayer on positively charged gold substrates (planar gold) and the adsorbance of 2-naphthol onto DS surfactant monolayer were performed. The investigation of the electrical control of DS at various concentrations (4, 6, 16, and 32 mM) below and above the critical micelle concentration (CMC= 8 mM) on gold surfaces for analyte preconcentration, prior to chromatographic analysis, is presented. Charged ionic surfactants, such as DS, drawn to a surface of opposite charge ...


Probing The Structure And Photophysics Of Porphyrinoid Systems For Functional Materials, Christopher D. Farley 2016 The Graduate Center, City University of New York

Probing The Structure And Photophysics Of Porphyrinoid Systems For Functional Materials, Christopher D. Farley

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

Porphyrins (Pors) and their many cousins, including phthalocyanines (Pcs), corroles (Cors), subphthalocyanines (SubPcs), porphyrazines (Pzs), and naphthalocyanines (NPcs), play amazingly diverse roles in biological and non-biological systems because of their unique and tunable physical and chemical properties. These compounds, collectively known as porphyrinoids, can be employed in any number of functional devices that have the potential to address the challenges of modern society. Their incorporation into such devices, however, depends on many structural factors that must be well understood and carefully controlled in order to achieve the desired behavior. Self-assembly and self-organization are key processes for developing these new technologies ...


Large Scale Nanoparticle Screening For Small Molecule Analysis In Laser Desorption Ionization Mass Spectrometry, Gargey B. Yagnik, Rebecca L. Hansen, Andrew R. Korte, Malinda D. Reichert, Javier Vela, Young-Jin Lee 2016 Iowa State University

Large Scale Nanoparticle Screening For Small Molecule Analysis In Laser Desorption Ionization Mass Spectrometry, Gargey B. Yagnik, Rebecca L. Hansen, Andrew R. Korte, Malinda D. Reichert, Javier Vela, Young-Jin Lee

Chemistry Publications

Nanoparticles (NPs) have been suggested as efficient matrixes for small molecule profiling and imaging by laser-desorption ionization mass spectrometry (LDI-MS), but so far there has been no systematic study comparing different NPs in the analysis of various classes of small molecules. Here, we present a large scale screening of 13 NPs for the analysis of two dozen small metabolite molecules. Many NPs showed much higher LDI efficiency than organic matrixes in positive mode and some NPs showed comparable efficiencies for selected analytes in negative mode. Our results suggest that a thermally driven desorption process is a key factor for metal ...


Gc Verification Of The Spacecraft Atmosphere Monitor, Jessica S. Castro, Richard D. Kidd, Jeffrey D. Hein 2016 California Polytechnic State University, San Luis Obispo

Gc Verification Of The Spacecraft Atmosphere Monitor, Jessica S. Castro, Richard D. Kidd, Jeffrey D. Hein

STAR (STEM Teacher and Researcher) Presentations

International Space Station crew members face the unique challenge of maintaining air quality due to the volatile organic compounds (VOCs) that have the potential to accumulate at unsafe levels. The Spacecraft Atmosphere Monitor (SAM) is a miniature gas chromatograph/mass spectrometer (GCMS) designed to measure major constituents (such as N2, O2 and CO2) and trace VOCs within the cabin of the spacecraft. The gas chromatograph is responsible for separating the sample into its components in order to be characterized. The oven of the gas chromatograph must reach a temperature of 150°C in order to heat constituents ...


Directed Self-Assembly Of Block Copolymer, No1, Hiromichi Yamamoto 2016 Singh Center

Directed Self-Assembly Of Block Copolymer, No1, Hiromichi Yamamoto

Protocols and Reports

The PS-rich and neutral PS-b-PMMA block copolymer (BCP) films were spin coated on the neutral random copolymer hydroxyl-terminated PS-r-PMMA layers grafted on the native oxide and 50 nm thick PECVD amorphous silicon oxide layers. Relationship between the grafting density of BCP and surface density of hydroxyl moiety on silicon oxide is discussed. Furthermore, optimization of annealing BCP films is reported, and wetted and de-wetted BCP films are shown in optical microscope images. In addition, finger print and nanopore structures of BCP films are also indicated in SEM images.


Qualitative Detection Of Selected Designer Drugs And Relevant Metabolites In Environmental Water Samples, Marley Pruyn 2016 Florida International University

Qualitative Detection Of Selected Designer Drugs And Relevant Metabolites In Environmental Water Samples, Marley Pruyn

FIU Electronic Theses and Dissertations

Designer drugs are compounds which have been synthetically derived from illicit drugs. After consumption, drugs and their metabolites are introduced into the sewage water which is treated and disposed into the environment. A combined target, suspect and non-target workflow was created to detect designer drugs in environmental water samples. Multiple water samples were spiked with an unknown mixture of drugs and metabolites to assess the efficiency of the method. Samples were collected from sewage influent and effluent pipes, downstream from a sewage outfall and reclaimed water. Analysis was conducted with high resolution MS using the QExactive Orbitrap. Screening was performed ...


Biological Information And Its Origins: The Curious Case Of Rna, Grace E. Andrews 2016 Seattle Pacific University

Biological Information And Its Origins: The Curious Case Of Rna, Grace E. Andrews

Honors Projects

Information is an important pre-requisite for the onset of life, which means that any study of the origins of life must also address the origin of information. Biological information today is generally conceptualized in terms of the Central Dogma of Biology, with DNA as a digitized code within the cell. However, here I propose that biological information - particularly in prebiotic conditions, where information would have first arisen - is better understood in terms of the three-dimensional structure of a molecule. Evidence for information storage in RNA can be seen in a number of ways. One of these is that, instead of ...


Interaction Of Spliceosomal U2 Snrnp Protein P14 With Its Branch Site Rna Target, William Perea Vargas 2016 Graduate Center, City University of New York

Interaction Of Spliceosomal U2 Snrnp Protein P14 With Its Branch Site Rna Target, William Perea Vargas

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

Newly transcribed precursor messenger RNA (pre-mRNA) molecules contain coding sequences (exons) interspersed with non-coding intervening sequences (introns). These introns must be removed in order to generate a continuous coding sequence prior to translation of the message into protein. The mechanism through which these introns are removed is known as pre-mRNA splicing, a two-step reaction catalyzed be a large macromolecular machine, the spliceosome, located in the nucleus of eukaryotic cells. The spliceosome is a protein-directed ribozyme composed of small nuclear RNAs (snRNA) and hundreds of proteins that assemble in a very dynamic process. One of these snRNAs, the U2 snRNA, is ...


Facilitating Conceptual Learning In Quantitative Chemistry, Sarah R. Johnson 2016 East Tennessee State University

Facilitating Conceptual Learning In Quantitative Chemistry, Sarah R. Johnson

Electronic Theses and Dissertations

Traditional chemistry laboratory courses have a manual consisting of “step-by-step” experiments; instructions are given to complete experiments, requiring minimal information/concepts processing to be successful. This experience leaves students unprepared for the real-world, where critical thinking skills are needed to conduct research. This study focused on building analytical techniques, conceptual knowledge, and critical thinking skills used to solve research problems. A new quantitative chemistry laboratory manual was developed to transition students from traditional to inquiry-based experiments, requiring analytical method development. Data showed students having less difficulty using the new manual (0.8281 average difficulty) on method development exam questions and ...


Staphylococcal Nuclease And Ubiquitin Local Folding Energies And Rates Using Peps-Hdx-Esi-Ms, Julie Rhee 2016 University of Arkansas, Fayetteville

Staphylococcal Nuclease And Ubiquitin Local Folding Energies And Rates Using Peps-Hdx-Esi-Ms, Julie Rhee

Chemistry & Biochemistry Undergraduate Honors Theses

In this study, Protein Equilibrium Population Snapshot Hydrogen-Deuterium Exchange Electrospray Ionization Mass Spectrometry (PEPS-HDX-ESI-MS) was applied to study the local regions of model proteins, staphylococcal nuclease and ubiquitin. The hydrogen deuterium exchange (HDX) has become a key technique for studying the structural and dynamic aspects of proteins in solution. This technique creates a rapid exchange between all of the exchangeable hydrogen ions with deuterium when the protein is exposed to a solvent. The PEPS method is an equilibrium-based method used to determine the populations of the closed native and open denatured states of a protein. By combining the applications of ...


Direct Band Gap Gallium Antimonide Phosphide (Gasbxp1-X) For Solar Fuels., Harry Benjamin Russell 2016 University of Louisville

Direct Band Gap Gallium Antimonide Phosphide (Gasbxp1-X) For Solar Fuels., Harry Benjamin Russell

Electronic Theses and Dissertations

Photoelectrochemical water splitting has been identified as a promising route for achieving sustainable energy future. However, semiconductor materials with the appropriate optical, electrical and electrochemical properties have yet to be discovered. In search of an appropriate semiconductor to fill this gap, GaSbP, a semiconductor never tested for PEC performance is proposed here and investigated. Density functional theory (DFT+U) techniques were utilized to predict band gap and band edge energetics for GaSbP alloys with low amount of antimony. The overall objective of this dissertation is to understand the suitability of GaSbxP1-x alloys for photoelectrochemical water splitting application ...


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