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Preliminary Structural Studies Of The Transcriptional Regulator Cmer From Campylobacter Jejuni, Chih-chia Su, Feng Shi, Ruoyu Gu, Ming Li, Gerry McDermott, Edward Yu, Qijing Zhang 2017 Iowa State University

Preliminary Structural Studies Of The Transcriptional Regulator Cmer From Campylobacter Jejuni, Chih-Chia Su, Feng Shi, Ruoyu Gu, Ming Li, Gerry Mcdermott, Edward Yu, Qijing Zhang

Qijing Zhang

In Campylobacter jejuni, a Gram-negative bacterial pathogen causing gastroenteritis in humans, the CmeR regulatory protein controls transcription of the multidrug transporter gene operon cmeABC. CmeR belongs to the TetR family of transcriptional regulators. The 210-residue CmeR consists of two functional motifs: an N-terminal DNA-binding domain and a C-terminal ligand-binding domain. It is predicted that the DNA-binding domain interacts directly with target promoters, while the C-terminal motif interacts with inducing ligands (such as bile salts). As an initial step towards confirming this structural model, recombinant CmeR protein containing a 6×His tag at the N-terminus was crystallized. Crystals of ligand-free CmeR ...


Tracer Counterpermeation Analysis Of Diffusivity In Finite-Length Nanopores With And Without Single-File Dynamics, David Ackerman, James W. Evans 2017 Iowa State University

Tracer Counterpermeation Analysis Of Diffusivity In Finite-Length Nanopores With And Without Single-File Dynamics, David Ackerman, James W. Evans

James W. Evans

We perform a tracer counterpermeation (TCP) analysis for a stochastic model of diffusive transport through a narrow linear pore where passing of species within the pore is inhibited or even excluded (single-file diffusion). TCP involves differently labeled but otherwise identical particles from two decoupled infinite reservoirs adsorbing into opposite ends of the pore, and desorbing from either end. In addition to transient behavior, we assess steady-state concentration profiles, spatial correlations, particle number fluctuations, and diffusion fluxes through the pore. From the profiles and fluxes, we determine a generalized tracer diffusion coefficient Dtr(x), at various positions x within the pore ...


Optimization Of Cardiac Pacing Stimulation By Current Configuration –A Theoretical, Numerical And Experimental Study., Flavio H. Fenton, Hila Dvir, Neil Hardy 2017 Georgia Institute of Technology

Optimization Of Cardiac Pacing Stimulation By Current Configuration –A Theoretical, Numerical And Experimental Study., Flavio H. Fenton, Hila Dvir, Neil Hardy

Biology and Medicine Through Mathematics Conference

No abstract provided.


Building And Validating A Model For Investigating The Dynamics Of Isolated Water Molecules, Grant Cates 2017 Linfield College

Building And Validating A Model For Investigating The Dynamics Of Isolated Water Molecules, Grant Cates

Senior Theses

Understanding how water molecules behave in isolation is vital to understand many fundamental processes in nature. To that end, scientists have begun studying crystals in which single water molecules become trapped in regularly occurring cavities in the crystal structure. As part of that investigation, numerical models used to investigate the dynamics of isolated water molecules are sought to help bolster our fundamental understanding of how these systems behave. To that end, the efficacy of three computational methods—the Euler Method, the Euler-Aspel Method and the Beeman Method—is compared using a newly defined parameter, called the predictive stability coefficient ρ ...


A Study In Cross-Beam Polarization Fluorescence Photoactivation Localization Microscopy On Dendra2-Hemagluttinin In Fixed Nih3t3 Cells, Matthew M. Valles 2017 University of Maine

A Study In Cross-Beam Polarization Fluorescence Photoactivation Localization Microscopy On Dendra2-Hemagluttinin In Fixed Nih3t3 Cells, Matthew M. Valles

Electronic Theses and Dissertations

Fluorescence microscopy is popular for its noninvasive properties and its use in imaging multiple species, simultaneously. Furthermore, superresolution fluorescence microscopy (SRFLM) utilizes photoswitchable proteins to improve the lateral resolution of conventional fluorescence microscopy by an order of magnitude. There is little work conducted on the study of excitation laser polarizations and their effect on the number of localizations as well as the brightness of molecules. This thesis attempts to study the effect of excitation wavelength polarization on the number of localizations and the brightness of molecules by comparing two orientations of circularly-polarized, excitation lasers. The first type of orientation involves ...


Physical Principles Governing Colloidal Particle Deposition At Low Reynold’S Number: Applications To Microbial Biofilms, Sophia Wiedmann 2017 Macalester College

Physical Principles Governing Colloidal Particle Deposition At Low Reynold’S Number: Applications To Microbial Biofilms, Sophia Wiedmann

Macalester Journal of Physics and Astronomy

Biofilms formed from the adhesion of microbes to a surface hold great relevance to public health and wastewater management. However, the physical principles underlying the attachment stage of biofilm formation, when individual microbes first come into contact with a substrate, are not well understood. Here I report on a model of colloidal particle attachment to a surface that incorporates the effects of diffusion, advection, gravity, and the hydrodynamic lift and drag forces experienced by polystyrene beads at low Reynold’s number. The simulation predicts attachment rates of 1.04x10^(-8)m/s, 0.73x10^(-8)m/s, and 1.29x10 ...


Evolution, Ecology, And Disparities: Constructing Stature, Immune Functioning, And Reproduction, In Brazilian Quilombo, And United States, Women, Anna C. Rivara 2017 University of South Florida

Evolution, Ecology, And Disparities: Constructing Stature, Immune Functioning, And Reproduction, In Brazilian Quilombo, And United States, Women, Anna C. Rivara

Graduate Theses and Dissertations

The purpose of this dissertation is to test how growth, reproduction, and immune functioning interact in two populations of adult women residing in vastly different socio-economic and ecological environments, the Kalunga quilombo in Brazil, and the United States of America. The presence of life history trade-offs was tested to determine how the different envirnonments, and socio-ecological contexts of the populations were creating differential risks for health and reproductive outcomes, and life history trade-offs.

I hypothesized that the Kalunga people, living in very difficult and harsh conditions, would experience greater amounts of, and more severe, life history trade-offs than the U ...


Determination Of The Zinc Concentration In Human Fingernails By Laser-Induced Breakdown Spectroscopy, Steven J. Rehse, Vlora A. Riberdy, Christopher J. Frederickson 2017 University of Windsor

Determination Of The Zinc Concentration In Human Fingernails By Laser-Induced Breakdown Spectroscopy, Steven J. Rehse, Vlora A. Riberdy, Christopher J. Frederickson

Physics Publications

The absolute concentration of zinc in human fingernail clippings tested ex vivo was determined by 1064 nm laser-induced breakdown spectroscopy and confirmed by speciated isotope dilution mass spectrometry. A nail testing protocol that sampled across the nail (perpendicular to the direction of growth) was developed and validated by scanning electron microscopy energy dispersive x-ray spectroscopy. Using this protocol, a partial least squares regression model predicted the zinc concentration in five subjects’ fingernails to within 7 ppm on average. The variation of the zinc concentration with depth into the nail as determined by laser-induced breakdown spectroscopy was studied and found to ...


Enhancement Of The Superconducting Gap By Nesting In Cakfe4as4: A New High Temperature Superconductor, Daixiang Mou, Tai Kong, William R. Meier, Felix Lochner, Lin-Lin Wang, Qisheng Lin, Yun Wu, S. L. Bud’ko, Ilya Eremin, Duane D. Johnson, Paul C. Canfield, Adam Kaminski 2017 Iowa State University

Enhancement Of The Superconducting Gap By Nesting In Cakfe4as4: A New High Temperature Superconductor, Daixiang Mou, Tai Kong, William R. Meier, Felix Lochner, Lin-Lin Wang, Qisheng Lin, Yun Wu, S. L. Bud’Ko, Ilya Eremin, Duane D. Johnson, Paul C. Canfield, Adam Kaminski

Duane D. Johnson

We use high resolution angle resolved photoemission spectroscopy and density functional theory with measured crystal structure parameters to study the electronic properties of CaKFe4As4. In contrast to the related CaFe2As2 compounds, CaKFe4As4 has a high Tc of 35 K at stochiometric composition. This presents a unique opportunity to study the properties of high temperature superconductivity in the iron arsenides in the absence of doping or substitution. The Fermi surface consists of several hole and electron pockets that have a range of diameters. We find that the values of the superconducting gap are nearly isotropic (within the explored portions of the ...


Removal Of Chlorine From Chlorine-Nitrogen Mixture In A Film Of Liquid Water, Sarwan S. Sandhu 2017 University of Dayton

Removal Of Chlorine From Chlorine-Nitrogen Mixture In A Film Of Liquid Water, Sarwan S. Sandhu

Sarwan S. Sandhu

In industry there are many examples of absorption of a gas with or without chemical reaction in the liquid phase. In physical absorption, a particular gaseous component is removed from a gas mixture due to its larger solubility in the liquid phase solvent. The removal of butane and pentane from a refinery gas mixture by a heavy oil in the liquid phase is an example of physical absorption. In absorption with chemical reaction, the gaseous component to be removed transfers across the gas-liquid interface due to a difference in the bulk chemical potentials or concentrations in the two phases. The ...


Improving Sers-Based Readout Strategy For Biomarker Detecting Immunoassays, Joseph Smolsky 2017 U.N.O. Physics Department

Improving Sers-Based Readout Strategy For Biomarker Detecting Immunoassays, Joseph Smolsky

Student Research and Creative Activity Fair

Detection and monitoring of disease biomarkers increases probability of successful disease treatment. Surface enhanced Raman scattering (SERS) has several advantages over conventional readout strategies utilized in detecting immunoassays. SERS provides a method for chemical characterization based on molecular vibrational spectra. Raman signals are typically weak and need to be enhanced. This can be done using plasmons in nanoparticles of noble metals, we use gold (Au). Molecules with known spectra, Raman reporter molecules (RRM), can be adsorbed to Au nanoparticles. This enhances the Raman signal of the RRM when illuminated by a laser of optimal wavelength. Adding antibodies to nanoparticles modified ...


Structural Model Of The Rev Regulatory Protein From Equine Infectious Anemia Virus, Yungok Ihm, Wendy O. Sparks, Jae-Hyung Lee, Haibo Cao, Susan Carpenter, Cai-Zhuang Wang, Kai-Ming Ho, Drena Dobbs 2017 Iowa State University

Structural Model Of The Rev Regulatory Protein From Equine Infectious Anemia Virus, Yungok Ihm, Wendy O. Sparks, Jae-Hyung Lee, Haibo Cao, Susan Carpenter, Cai-Zhuang Wang, Kai-Ming Ho, Drena Dobbs

Drena Dobbs

Rev is an essential regulatory protein in the equine infectious anemia virus (EIAV) and other lentiviruses, including HIV-1. It binds incompletely spliced viral mRNAs and shuttles them from the nucleus to the cytoplasm, a critical prerequisite for the production of viral structural proteins and genomic RNA. Despite its important role in production of infectious virus, the development of antiviral therapies directed against Rev has been hampered by the lack of an experimentally-determined structure of the full length protein. We have used a combined computational and biochemical approach to generate and evaluate a structural model of the Rev protein. The modeled ...


Predicting Binding Sites Of Hydrolase-Inhibitor Complexes By Combining Several Methods, Taner Z. Sen, Andrzej Kloczkowski, Robert L. Jernigan, Changhui Yan, Vasant Honovar, Kai-Ming Ho, Cai-Zhuang Wang, Yungok Ihm, Haibo Cao, Xun Gu, Drena Dobbs 2017 Iowa State University

Predicting Binding Sites Of Hydrolase-Inhibitor Complexes By Combining Several Methods, Taner Z. Sen, Andrzej Kloczkowski, Robert L. Jernigan, Changhui Yan, Vasant Honovar, Kai-Ming Ho, Cai-Zhuang Wang, Yungok Ihm, Haibo Cao, Xun Gu, Drena Dobbs

Drena Dobbs

Background Protein-protein interactions play a critical role in protein function. Completion of many genomes is being followed rapidly by major efforts to identify interacting protein pairs experimentally in order to decipher the networks of interacting, coordinated-in-action proteins. Identification of protein-protein interaction sites and detection of specific amino acids that contribute to the specificity and the strength of protein interactions is an important problem with broad applications ranging from rational drug design to the analysis of metabolic and signal transduction networks. Results In order to increase the power of predictive methods for protein-protein interaction sites, we have developed a consensus methodology ...


Stochastic Simulation Of Reaction-Diffusion Systems: A Fluctuating-Hydrodynamics Approach, Alejandro Garcia, Changho Kim, Andy Nonaka, John B. Bell, Aleksandar Donev 2017 San Jose State University

Stochastic Simulation Of Reaction-Diffusion Systems: A Fluctuating-Hydrodynamics Approach, Alejandro Garcia, Changho Kim, Andy Nonaka, John B. Bell, Aleksandar Donev

Alejandro Garcia

We develop numerical methods for reaction-diffusion systems based on the equations of fluctuating hydrodynamics (FHD). While the FHD formulation is formally described by stochastic partial differential equations (SPDEs), it becomes similar to the reaction-diffusion master equation (RDME) description when those SPDEs are spatially discretized and reactions are modeled as a source term having Poisson fluctuations. However, unlike the RDME, the FHD description naturally extends from the regime where fluctuations are strong, i.e., each hydrodynamic cell has few (reactive) molecules, to regimes with moderate or weak fluctuations, and ultimately to the deterministic limit. By treating diffusion implicitly, we avoid the ...


Simulation Model Of An Automatic Commercial Ice Machine, Haithem Murgham, David Myszka, Vijay Bahel, Rajan Rajendran, Kurt Knapke, Suresh Shivashankar, Kyaw Wynn 2017 University of Dayton

Simulation Model Of An Automatic Commercial Ice Machine, Haithem Murgham, David Myszka, Vijay Bahel, Rajan Rajendran, Kurt Knapke, Suresh Shivashankar, Kyaw Wynn

David Myszka

Automatic commercial ice-making machines that produce a batch of cube ice at regular intervals are known as “cubers." Such machines are commonly used in food service, food preservation, hotel, and health service industries. The machines are typically rated for the weight of ice produced over a 24-hour period at ambient air temperatures of 90°F and water inlet temperature of 70°F.

These cubers typically utilize an air-cooled, vapor-compression cycle to freeze circulating water flowing over an evaporator grid. Once a sufficient amount ice is formed, a valve switches to enable a harvest mode, where the compressor’s discharge gas ...


Student Resources For: From Photon To Neuron, Light, Imaging, Vision, Philip C. Nelson 2017 University of Pennsylvania

Student Resources For: From Photon To Neuron, Light, Imaging, Vision, Philip C. Nelson

Department of Physics Papers

This zip archive contains datasets and additional media associated to the book "From Photon to Neuron (Princeton University Press, 2017).


Enhancement Of The Superconducting Gap By Nesting In Cakfe4as4: A New High Temperature Superconductor, Daixiang Mou, Tai Kong, William R. Meier, Felix Lochner, Lin-Lin Wang, Qisheng Lin, Yun Wu, S. L. Bud’ko, Ilya Eremin, Duane D. Johnson, Paul C. Canfield, Adam Kaminski 2017 Iowa State University

Enhancement Of The Superconducting Gap By Nesting In Cakfe4as4: A New High Temperature Superconductor, Daixiang Mou, Tai Kong, William R. Meier, Felix Lochner, Lin-Lin Wang, Qisheng Lin, Yun Wu, S. L. Bud’Ko, Ilya Eremin, Duane D. Johnson, Paul C. Canfield, Adam Kaminski

Qisheng Lin

We use high resolution angle resolved photoemission spectroscopy and density functional theory with measured crystal structure parameters to study the electronic properties of CaKFe4As4. In contrast to the related CaFe2As2 compounds, CaKFe4As4 has a high Tc of 35 K at stochiometric composition. This presents a unique opportunity to study the properties of high temperature superconductivity in the iron arsenides in the absence of doping or substitution. The Fermi surface consists of several hole and electron pockets that have a range of diameters. We find that the values of the superconducting gap are nearly isotropic (within the explored portions of the ...


Tracer Counterpermeation Analysis Of Diffusivity In Finite-Length Nanopores With And Without Single-File Dynamics, David Ackerman, James W. Evans 2017 Iowa State University

Tracer Counterpermeation Analysis Of Diffusivity In Finite-Length Nanopores With And Without Single-File Dynamics, David Ackerman, James W. Evans

Physics and Astronomy Publications

We perform a tracer counterpermeation (TCP) analysis for a stochastic model of diffusive transport through a narrow linear pore where passing of species within the pore is inhibited or even excluded (single-file diffusion). TCP involves differently labeled but otherwise identical particles from two decoupled infinite reservoirs adsorbing into opposite ends of the pore, and desorbing from either end. In addition to transient behavior, we assess steady-state concentration profiles, spatial correlations, particle number fluctuations, and diffusion fluxes through the pore. From the profiles and fluxes, we determine a generalized tracer diffusion coefficient Dtr(x), at various positions x within the pore ...


Temperature-Dependent Growth Shapes Of Ni Nanoclusters On Nial(110), Yong Han, Baris Unal, Dapeng Jing, Patricia A. Thiel, James W. Evans 2017 Iowa State University, Bejing Computational Science Research Center

Temperature-Dependent Growth Shapes Of Ni Nanoclusters On Nial(110), Yong Han, Baris Unal, Dapeng Jing, Patricia A. Thiel, James W. Evans

Patricia A. Thiel

Scanning tunneling microscopy studies reveal that two-dimensional nanoscale Ni islands formed by deposition of Ni on NiAl(110) between 200–400 K exhibit far-from-equilibrium growth shapes which change systematically with temperature. Island structure reflects the two types of adsorption sites available for Ni adatoms, and island shapes are controlled by the details of adatom diffusion along island edges accounting for numerous local configurations. The temperature dependence of the island shapes is captured and elucidated by kinetic Monte Carlo simulation of a realistic atomistic-level multisite lattice-gas model incorporating precise diffusion barriers. These barriers are obtained by utilizing density functional theory to ...


Mri-Based Susceptibility Mapping For In-Vivo Iron And Blood Oximetry Measurements, Hannah Erdevig 2017 University of Colorado, Boulder

Mri-Based Susceptibility Mapping For In-Vivo Iron And Blood Oximetry Measurements, Hannah Erdevig

Undergraduate Honors Theses

MRI is increasingly used in mapping tissue susceptibility to identify cerebral microbleeds associated with traumatic brain injury and pathological iron deposits associated with neurodegenerative diseases such as Parkinson's and Alzheimer's disease [1,2]. Accurate measurement is important for determining oxygen and iron content in blood vessels and tissue in the brain, which are in turn used for noninvasive clinical diagnosis and treatment assessments. Magnetic field distortions with a resolution of a few parts per billion can be measured using MRI phase maps. The field distortion map can then be inverted to obtain a quantitative susceptibility map. The primary ...


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