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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 2017 Chapman University

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 ...


Resin Monoterpene Defenses Decline Within Three Widespread Species Of Pine (Pinus) Along A 1530-M Elevational Gradient, Scott Ferrenberg, Joseph M. Langenhan, Jeffry B. Mitton 2017 New Mexico State University - Main Campus

Resin Monoterpene Defenses Decline Within Three Widespread Species Of Pine (Pinus) Along A 1530-M Elevational Gradient, Scott Ferrenberg, Joseph M. Langenhan, Jeffry B. Mitton

University Libraries Open Access Fund Supported Publications

The elevational gradient in plant defense (EGPD) hypothesis posits that natural enemy pressures increase alongside temperature across elevational climatic gradients, thereby selecting for enhanced defenses at lower elevations while leaving plants less defended at higher elevations. Phylogenetically constrained tests of this hypothesis are uncommon, with tests focused on defenses of mature trees in natural settings being exceedingly rare. In the absence of this information, predicting the spatiotemporal dynamics of forest pests that preferentially attack mature trees is rendered more difficult. Tree properties such as age, growth rate, and size have all been correlated with levels of tree defenses against insect ...


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 2017 Paul Scherrer Institut

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 ...


Modification Of An Implant Material, Emily Leung, Nina A. Reger, Ashley Blystone, Ellen S. Gawalt PhD 2017 Duquesne University

Modification Of An Implant Material, Emily Leung, Nina A. Reger, Ashley Blystone, Ellen S. Gawalt Phd

Undergraduate Research and Scholarship Symposium

Titanium metal is a commonly used implant material which can be colonized by bacteria. Biofilms are formed when bacteria colonizes, attaches to a surface, and immobilizes. Bacterial infections or biofilms are hard to treat once formed on the surface of a metal implant. Coating the material may minimize bacteria attachment. Self-assembled monolayers are comprised of molecules that contain both a head and tail group, and can be used to coat metal to prevent biofilm formation and bacteria growth. 12-mercaptododecylphosphonic acid self-assembled monolayers have a phosphonic acid head group and a thiol tail group. A solution of
12-mercaptododecylphosphonic acid in tetrahydrofuran ...


Nonlinear Oscillatory Dynamics Of The Hardening Of Calcium Phosphate Bone Cements, Vuk Uskoković, Julietta V. Rau 2017 Chapman University

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 2017 Purdue University

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 ...


Functionalization Of Indium-Based Quantum Dots For Use As A Non-Viral Gene Therapy Vector, Nicholas A. Mundt 2017 Missouri State University

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 2017 University of Louisville

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 negative ...


Cellular And Molecular Targets Of Menthol Actions, Murat Oz, Eslam El Nebrisi, Keun-Hang Susan Yang, Frank Christopher Howarth, Lina T. Al Kury 2017 UAE University

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 2017 Georgia Institute of Technology

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 ...


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 2017 CUNY John Jay College

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 ...


Catalytic Conversion Reactions In Nanoporous Systems With Concentration-Dependent Selectivity: Statistical Mechanical Modeling, Andrés García, Jing Wang, Theresa L. Windus, Aaron D. Sadow, James W. Evans 2017 Iowa State University

Catalytic Conversion Reactions In Nanoporous Systems With Concentration-Dependent Selectivity: Statistical Mechanical Modeling, Andrés García, Jing Wang, Theresa L. Windus, Aaron D. Sadow, James W. Evans

Theresa Windus

Statistical mechanical modeling is developed to describe a catalytic conversion reaction A→Bc or Bt with concentration-dependent selectivity of the products, Bc or Bt, where reaction occurs inside catalytic particles traversed by narrow linear nanopores. The associated restricted diffusive transport, which in the extreme case is described by single-file diffusion, naturally induces strong concentration gradients. Furthermore, by comparing kinetic Monte Carlo simulation results with analytic treatments, selectivity is shown to be impacted by strong spatial correlations induced by restricted diffusivity in the presence of reaction and also by a subtle clustering of reactants, A.


Autophagy And Protein Turnover Responses To Exercise-Nutrient Interactions In Human Skeletal Muscle, William J. Smiles 2017 Australian Catholic University

Autophagy And Protein Turnover Responses To Exercise-Nutrient Interactions In Human Skeletal Muscle, William J. Smiles

Theses

Skeletal muscle is a dynamic tissue comprising the largest protein reservoir of the human body with a rate of turnover of ~1-2% per day. Protein turnover is regulated by the coordination of intracellular systems regulating protein synthesis and breakdown that converge in a spatiotemporal manner on lysosomal organelles responsible for integrating a variety of contractile and nutritional stimuli. One such system, autophagy, which literally means to ‘self-eat,’ involves capturing of cellular material for deliver to, and disintegration by, the lysosome. The autophagic ‘cargo’ is subsequently recycled for use in synthetic reactions and thus maintenance of protein balance. As a dynamic ...


Catalytic Conversion Reactions In Nanoporous Systems With Concentration-Dependent Selectivity: Statistical Mechanical Modeling, Andrés García, Jing Wang, Theresa L. Windus, Aaron D. Sadow, James W. Evans 2017 Iowa State University

Catalytic Conversion Reactions In Nanoporous Systems With Concentration-Dependent Selectivity: Statistical Mechanical Modeling, Andrés García, Jing Wang, Theresa L. Windus, Aaron D. Sadow, James W. Evans

James W. Evans

Statistical mechanical modeling is developed to describe a catalytic conversion reaction A→Bc or Bt with concentration-dependent selectivity of the products, Bc or Bt, where reaction occurs inside catalytic particles traversed by narrow linear nanopores. The associated restricted diffusive transport, which in the extreme case is described by single-file diffusion, naturally induces strong concentration gradients. Furthermore, by comparing kinetic Monte Carlo simulation results with analytic treatments, selectivity is shown to be impacted by strong spatial correlations induced by restricted diffusivity in the presence of reaction and also by a subtle clustering of reactants, A.


Mesoporous Silica Nanoparticles: Structural Design And Applications, Igor I. Slowing, Juan Luis Vivero-escoto, Brian G. Trewyn, Victor S.Y. Lin 2017 Iowa State University

Mesoporous Silica Nanoparticles: Structural Design And Applications, Igor I. Slowing, Juan Luis Vivero-Escoto, Brian G. Trewyn, Victor S.Y. Lin

Igor I. Slowing

The structural properties of mesoporous silica nanoparticles are reviewed. Different strategies for the introduction of functional groups are considered. Based on the architectural features of the material, the functionalization at defined regions of the particles is described, along with the properties emerging from the corresponding site-specific modifications of their chemistry. Many applications derived from the unique architecture and chemistry of these nanostructured composite materials are shown.


Role Of Co2 As A Soft Oxidant For Dehydrogenation Of Ethylbenzene To Styrene Over A High-Surface-Area Ceria Catalyst, Li Zhang, Zili Wu, Nicholas C. Nelson, Aaron D. Sadow, Igor I. Slowing 2017 Oak Ridge National Laboratory

Role Of Co2 As A Soft Oxidant For Dehydrogenation Of Ethylbenzene To Styrene Over A High-Surface-Area Ceria Catalyst, Li Zhang, Zili Wu, Nicholas C. Nelson, Aaron D. Sadow, Igor I. Slowing

Igor I. Slowing

Catalytic performance and the nature of surface adsorbates were investigated for high-surface-area ceria during the ethylbenzene oxidative dehydrogenation (ODH) reaction using CO2 as a soft oxidant. The high surface area ceria material was synthesized using a template-assisted method. The interactions among ethylbenzene, styrene, and CO2 on the surface of ceria and the role of CO2 for the ethylbenzene ODH reaction have been investigated in detail by using activity test, in situ diffuse reflectance infrared and Raman spectroscopy. CO2 as an oxidant not only favored the higher yield of styrene but also inhibited the deposition of coke during the ethylbenzene ODH ...


Heterogeneous Multicatalytic System For Single-Pot Oxidation And C–C Coupling Reaction Sequences, Nicholas C. Nelson, Umesh Chaudhary, Kapil Kandel, Igor I. Slowing 2017 Iowa State University

Heterogeneous Multicatalytic System For Single-Pot Oxidation And C–C Coupling Reaction Sequences, Nicholas C. Nelson, Umesh Chaudhary, Kapil Kandel, Igor I. Slowing

Igor I. Slowing

A system comprising two catalysts supported on mesoporous silica nanoparticles (MSNs) was employed to perform a sequence of two reactions in a single pot. Palladium nanoparticles catalyzed the oxidation of furfuryl alcohol with molecular oxygen at atmospheric pressure. The oxidation product, furfural, was then reacted with acetone via an aldol condensation catalyzed by amines supported on MSNs. Each reaction was first tested individually to establish optimal conditions. Both catalysts were then introduced into the same reactor under the proven conditions, and the entire reaction sequence was performed giving the desired product with high selectivity. The overall yield of the reaction ...


Supported Iron Nanoparticles For The Hydrodeoxygenation Of Microalgal Oil To Green Diesel, Kapil Kandel, James W. Anderegg, Nicholas C. Nelson, Umesh Chaudhary, Igor I. Slowing 2017 Iowa State University

Supported Iron Nanoparticles For The Hydrodeoxygenation Of Microalgal Oil To Green Diesel, Kapil Kandel, James W. Anderegg, Nicholas C. Nelson, Umesh Chaudhary, Igor I. Slowing

Igor I. Slowing

Iron nanoparticles supported on mesoporous silica nanoparticles (Fe-MSN) catalyze the hydrotreatment of fatty acids with high selectivity for hydrodeoxygenation over decarbonylation and hydrocracking. The catalysis is likely to involve a reverse Mars–Van Krevelen mechanism, in which the surface of iron is partially oxidized by the carboxylic groups of the substrate during the reaction. The strength of the metal–oxygen bonds that are formed affects the residence time of the reactants facilitating the successive conversion of carboxyl first into carbonyl and then into alcohol intermediates, thus dictating the selectivity of the process. The selectivity is also affected by the pretreatment ...


Substrate Inhibition In The Heterogeneous Catalyzed Aldol Condensation: A Mechanistic Study Of Supported Organocatalysts, Kapil Kandel, Stacey Marie Althaus, Chorthip Peeraphatdit, Takeshi Kobayashi, Brian G. Trewyn, Marek Pruski, Igor I. Slowing 2017 Iowa State University

Substrate Inhibition In The Heterogeneous Catalyzed Aldol Condensation: A Mechanistic Study Of Supported Organocatalysts, Kapil Kandel, Stacey Marie Althaus, Chorthip Peeraphatdit, Takeshi Kobayashi, Brian G. Trewyn, Marek Pruski, Igor I. Slowing

Igor I. Slowing

In this study, we demonstrate how materials science can be combined with the established methods of organic chemistry to find mechanistic bottlenecks and redesign heterogeneous catalysts for improved performance. By using solid-state NMR, infrared spectroscopy, surface and kinetic analysis, we prove the existence of a substrate inhibition in the aldol condensation catalyzed by heterogeneous amines. We show that modifying the structure of the supported amines according to the proposed mechanism dramatically enhances the activity of the heterogeneous catalyst. We also provide evidence that the reaction benefits significantly from the surface chemistry of the silica support, which plays the role of ...


Exocytosis Of Mesoporous Silica Nanoparticles From Mammalian Cells: From Asymmetric Cell-To-Cell Transfer To Protein Harvesting, Igor I. Slowing, Juan L. Vivero-Escoto, Yannan Zhao, Kapil Kandel, Chorthip Peeraphatdit, Brian G. Trewyn, Victor S.Y. Lin 2017 Iowa State University

Exocytosis Of Mesoporous Silica Nanoparticles From Mammalian Cells: From Asymmetric Cell-To-Cell Transfer To Protein Harvesting, Igor I. Slowing, Juan L. Vivero-Escoto, Yannan Zhao, Kapil Kandel, Chorthip Peeraphatdit, Brian G. Trewyn, Victor S.Y. Lin

Igor I. Slowing

The exocytosis of mesoporous silica nanoparticles (MSNs) from mammalian cells is demonstrated for the first time. The differences in the degree of exocytosis of MSNs between healthy and cancer cells are shown to be responsible for the asymmetric transfer of the particles between both cell types. The exo­cytosis of highly adsorbent magnetic MSNs proves to be useful as a means for harvesting biomolecules from living cells.


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