Biophysics Commons^™

Homologous And Heterologous Crystallin Protein Interactions As The Molecular Basis Of Inherited Cataract, Priya Ranjan Banerjee

Legacy Theses & Dissertations (2009 - 2024)

Age-related cataract is the most common cause of blindness worldwide. Nearly fifty percent of Americans above the age of 75 are diagnosed with this disease (http://www.nei.nih.gov/eyedata/pbd_tables.asp), and surgical intervention is the sole method of treatment at present (http://www.nei.nih.gov/healthyvision/objective/cataracts.asp). In the developing world, even this treatment is not readily available. These are compelling reasons to search for better treatments to delay, prevent or arrest cataract formation. Recent evidence suggests that age-related cataracts also have a genetic component. Therefore, determining the mechanisms underlying genetic cataracts with a known association to a protein-mutation is one important strategy towards understanding the molecular basis for …

Probing Molecules In Confined Space, Carissa Marie Vetromile

USF Tampa Graduate Theses and Dissertations

Despite the plethora of information regarding cellular crowding and its importance on modulating protein function the effects of confinement on biological molecules are often overlooked when investigating their physiological function. Recently however, the encapsulation of biomolecules in solid state matrices (NafionTM, sol-gels, zirconium phosphate,etc.) has increased in importance as a method for examining protein conformation and dynamics in confined space as well as novel applications in biotechnology. Biotechnological applications include, but are not limited to, bioremediation, biosensors, biocatalysts, etc. In order to better utilize solid state materials as substrates for biological molecules an understanding of the effects of encapsulation on …

Physical Models Of Amyloid Fibril Assembly, Shannon Elizabeth Hill

USF Tampa Graduate Theses and Dissertations

Formation of large fibers and plaques by amyloid proteins is recognized as the molecular hallmark of an increasing number of human disorders, including Parkinson's disease, Alzheimer's disease and even type II diabetes. The broader objective of my research is to unravel the basic mechanisms that initiate and regulate fibril formation by amyloidogenic proteins. This objective is significant because even basic aspects of how fibril formation proceeds from a soluble, monomeric protein to an insoluble amyloid fibril remain much debated. Furthermore, there is increasingly strong evidence suggesting that intermediates of the aggregation process, with properties distinct from those of mature fibrils, …

A Study Of Complex Systems: From Magnetic To Biological, Douglas Carroll Lovelady

USF Tampa Graduate Theses and Dissertations

This work is a study of complex many-body systems with non-trivial interactions. Many such systems can be described with models that are much simpler than the real thing but which can still give good insight into the behavior of realistic systems. We take a look at two such systems. The first part looks at a model that elucidates the variety of magnetic phases observed in rare-earth heterostructures at low temperatures: the six-state clock model. We use an ANNNI-like model Hamiltonian that has a three dimensional parameter space and yields two-dimensional multiphase regions in this space. A low-temperature expansion of the …

Systematic Approach To Electrostatically Induced 2d Crystallization Of Nanoparticles At Liquid Interfaces, Sumit Kewalramani, Suntao Wang, Yuan Lin, Huong Giang Nguyen, Qian Wang, Masafumi Fukuto, Lin Yang

Faculty Publications

We report an experimental demonstration of a strategy for inducing two-dimensional (2D)crystallization of charged nanoparticles on oppositely charged fluid interfaces. This strategy aims to maximize the interfacial adsorption of nanoparticles, and hence their lateral packing density, by utilizing a combination of weakly charged particles and a high surface charge density on the planar interface. In order to test this approach, we investigated the assembly of cowpea mosaic virus (CPMV) on positively charged lipid monolayers at the aqueous solution surface, by means of in situX-ray scattering measurements at the liquid–vapor interface. Theassembly was studied as a function of the solution …

Negative Dielectrophoretic Capture Of Bacterial Spores In Food Matrices, Mehti Koklu, Seungkyung Park, Suresh D. Pillai, Ali Beskok

Mechanical & Aerospace Engineering Faculty Publications

A microfluidic device with planar square electrodes is developed for capturing particles from high conductivity media using negative dielectrophoresis (n-DEP). Specifically, Bacillus subtilis and Clostridium sporogenes spores, and polystyrene particles are tested in NaCl solution (0.05 and 0.225 S/m), apple juice (0.225 S/m), and milk (0.525 S/m). Depending on the conductivity of the medium, the Joule heating produces electrothermal flow (ETF), which continuously circulates and transports the particles to the DEP capture sites. Combination of the ETF and n-DEP results in different particle capture efficiencies as a function of the conductivity. Utilizing 20 μm height DEP chambers, “almost complete” and …

Experimental Investigation Of A Non-Thermal Atmospheric Pressure Plasma Jet, Asma Begum

Electrical & Computer Engineering Theses & Dissertations

The main objective of this dissertation is to understand the formation of the plasma jet from the plasma pencil, and the propagation of the plasma jet in the ambient atmosphere where the effect of the external electric field is almost zero. Before investigating the formation and propagation phenomenon of the plasma jet, common physical properties of plasma jets are determined by using the imaging technique and optical emission spectroscopy. The first goal of this dissertation is to establish the laminar helium gas flow channel through a plasma pencil.

The formation position, formation time, and the criterion of the plasma jet …

Coupling Into Waveguide Evanescent Modes With Applications In Electron Paramagnetic Resonance, Jason Walter Sidabras

Master's Theses (2009 -)

The use of analytical and numerical techniques in solving the coupling of evanescent modes in a microwave waveguide through slots can be optimized to create a uniform magnetic field excitation on axis within a waveguide. This work has direct applications in Electron Paramagnetic Resonance (EPR) where a 100~kHz time-varying magnetic field is incident on a sample contained in a microwave cavity. Typical cavity designs do not take into consideration the uniformity of the 100~kHz field modulation and assume it to be uniform enough over the sample region from quasi-static principles. This work shows otherwise and uses Ansoft (Pittsburgh, PA) High …

Conformational Change And Topological Stability Of Proteins, Jeffrey Andrew Tibbitt

Chemistry & Biochemistry Theses & Dissertations

The conformation and topology of a protein changes when stabilizing forces are absent, but the mechanisms by which these changes occur remains elusive. This dissertation aims to broaden the understandings. On the conformational level, the M20 loop conformers of E. coli dihydrofolate reductase are interrogated to identify factors responsible for their stability as well as to determine how one conformer might change into another. Molecular dynamics is used to simulate the open, closed and occluded conformers (observed in X-ray crystal structures) under a series of different single ligand conditions. Analysis shows that all open conformers move to a similar new …

Dielectrophoretic Choking Phenomenon In A Converging-Diverging Microchannel, Ye Ai, Shizhi Qian, Sheng Liu, Sang W. Joo

Mechanical & Aerospace Engineering Faculty Publications

Experiments show that particles smaller than the throat size of converging-diverging microchannels can sometimes be trapped near the throat. This critical phenomenon is associated with the negative dc dielectrophoresis arising from nonuniform electric fields in the microchannels. A finite-element model, accounting for the particle-fluid-electric field interactions, is employed to investigate the conditions for this dielectrophoretic (DEP) choking in a converging-diverging microchannel for the first time. It is shown quantitatively that the DEP choking occurs for high nonuniformity of electric fields, high ratio of particle size to throat size, and high ratio of particle's zeta potential to that of microchannel. © …

Protein Folding, Aggregation And Unfolding In Monte Carlo Simulations, Sandipan Mohanty, Anders Irbäck, Simon Mitternacht, Giorgio Favrin, U. H.E. Hansmann

Michigan Tech Publications, Part 1

An implicit water all-atom model is used to study folding, aggregation and mechanical unfolding of small proteins. Physically reasonable results obtained for a variety of applications indicate healthy global properties of the interaction potential.

Pressure-Driven Transport Of Particles Through A Converging-Diverging Microchannel, Ye Ai, Sang W. Joo, Xiangchun Xuan, Shizhi Qian

Mechanical & Aerospace Engineering Faculty Publications

Pressure-driven transport of particles through a symmetric converging-diverging microchannel is studied by solving a coupled nonlinear system, which is composed of the Navier-Stokes and continuity equations using the arbitrary Lagrangian-Eulerian finite-element technique. The predicted particle translation is in good agreement with existing experimental observations. The effects of pressure gradient, particle size, channel geometry, and a particle's initial location on the particle transport are investigated. The pressure gradient has no effect on the ratio of the translational velocity of particles through a converging-diverging channel to that in the upstream straight channel. Particles are generally accelerated in the converging region and then …

The Evolution Of Thermal Reaction Norms For Growth Rate: Is Hotter Better?, Dee Ann Asbury

All-Inclusive List of Electronic Theses and Dissertations

Several researchers have proposed that warm-adapted organisms should outperform cold-adapted organisms because of the greater rates ofreactions at higher temperatures. This hypothesis-commonly referred to as 'hotter is better'-predicts that maximal performance should increase as the thermal optimum increases. I used published thermal reaction norms for 23 species of fish to test the hypothesis that hotter is better for individual growth rate. These studies reported a wide range of thermal optima among species. Using a phylogenetic hypothesis derived from multiple published sources, I calculated independent contrasts of thermal optima and maximal growth rates. The maximal growth rate appears unrelated to the …

Cold Atmospheric Pressure Air Plasma Jet For Medical Applications, Juergen Friedrich Kolb, A.-A H. Mohamed, R. O. Price, R. J. Swanson, A. Bowman, R. L. Chiavarini, Michael W. Stacey

Bioelectrics Publications

By flowing atmospheric pressure air through a direct current powered microhollow cathode discharge, we were able to generate a 2 cm long plasma jet. With increasing flow rate, the flow becomes turbulent and temperatures of the jet are reduced to values close to room temperature. Utilizing the jet, yeast grown on agar can be eradicated with a treatment of only a few seconds. Conversely, animal studies show no skin damage even with exposures ten times longer than needed for pathogen extermination. This cold plasma jet provides an effective mode of treatment for yeast infections of the skin.

The Biophysical Analysis Of The Human Telomeric Repeat (Ttaggg)4 And Characterization Of Porphyrin Binding In Potassium Solutions, Cosimo Antonacci

Seton Hall University Dissertations and Theses (ETDs)

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Development Of A High Spatial Selectivity Tri-Polar Concentric Ring Electrode For Laplacian Electroencephalography (Leeg) System, Kanthaiah Koka

Doctoral Dissertations

Brain activity generates electrical potentials that are spatio-temporal in nature. Electroencephalography (EEG) is the least costly and most widely used non-invasive technique for diagnosing many brain problems. It has high temporal resolution but lacks high spatial resolution.

The surface Laplacian will enhance the spatial resolution of EEG as it performs the second spatial derivative of the surface potentials. In an attempt to increase the spatial selectivity, researchers introduced a bipolar electrode configuration using a five point finite difference method (FPM) and others applied a quasi-bipolar (tri-polar with two elements shorted) concentric electrode configuration. To further increase the spatial resolution, the …

A High -Order Finite Difference Method For Solving Bioheat Transfer Equations In Three-Dimensional Triple -Layered Skin Structure, Haofeng Yu

Doctoral Dissertations

Investigations on instantaneous skin burns are useful for an accurate assessment of burn-evaluation and for establishing thermal protections for various purposes. Meanwhile, hyperthermia with radiation is important in the treatment of cancer, and it is essential for developers and users of hyperthermia systems to predict, and interpret correctly the biomass thermal and vascular response to heating. In this dissertation, we employ the well-known Pennes' bioheat transfer equation to predict the degree of skin burn and the temperature distribution in hyperthermia cancer treatment.

A fourth-order compact finite difference scheme is developed to solve Pennes' bioheat transfer equation in a three-dimensional single …

Modeling Of The Inverse Heat -Conduction Problem With Application To Laser Chemical Vapor Deposition And Bioheat Transfer, Peng Zhen

Doctoral Dissertations

This dissertation consists of two parts. Part one deals with three-dimensional laser induced chemical vapor deposition (3D-LCVD), whereas part two deals with a Pennes model of a 3D skin structure. LCVD is an important technique in manufacturing complex micro-structures with high aspect ratio. In part one, a numerical model was developed for simulating kinetically-limited growth of an axisymmetric cylindrical rod by pre-specifying the surface temperature distribution required for growing the rod and then by obtaining optimized laser power that gives rise to the pre-specified temperature distribution. The temperature distribution at the surface of the rod was assumed to be at …

Phase Modulation At 125 Khz In A Michelson Interferometer Using An Inexpensive Piezoelectric Stack Driven At Resonance, Barbara M. Hoeling, Andrew D. Fernandez, Richard C. Haskell, Daniel C. Petersen

All HMC Faculty Publications and Research

Fast phase modulation has been achieved in a Michelson interferometer by attaching a lightweight reference mirror to a piezoelectric stack and driving the stack at a resonance frequency of about 125 kHz. The electrical behavior of the piezo stack and the mechanical properties of the piezo-mirror arrangement are described. A displacement amplitude at resonance of about 350 nm was achieved using a standard function generator. Phase drift in the interferometer and piezo wobble were readily circumvented. This approach to phase modulation is less expensive by a factor of roughly 50 than one based on an electro-optic effect.

Rotational Symmetries Of Nuclear States: Spin Determinations In Advanced Laboratory, Wilfred J. Braithwaite

Journal of the Arkansas Academy of Science

An advanced laboratory experiment is described which shows the connection between the rotational symmetries of nuclear states and the assignments of spins to discrete nuclear states. Standard angular correlation methods were used to study the two sequential gamma ray transitions in each ⁶⁰Ni nucleus, populated by unobserved beta decays from a weak radioactive ⁶⁰Co source. The chosen electronics and detectors were inexpensive and easy to operate. This experiment was extended to introduce students to real-world data acquisition, using finite-geometry detectors, which resulted in enormously larger coincident data rates.

The Synthesis And Evaluation Of 5-Phenyloxazolidines As Potential Cardiovascular Drugs, Tammy C. Wang

Chemistry & Biochemistry Theses & Dissertations

Drugs such as adrenoceptor antagonists and certain centrally acting agents are known to lower blood pressure and thus serve as clinically useful antihypertensive agents. Norepinephrine 4, a natural ∝-adrenoceptor agonist, is the major agent associated with increased blood pressure in the periphery. Based on a careful structure-activity comparison, a series of substituted oxazolidines, 20, 21, 22 and 23, have been designed as possible antihypertensive candidates. Specifically, 22 and 23 have been synthesized to serve as potential norepinephrine antagonists.

Preliminary evaluation of these compounds indicated that they were not antihypertensive in nature. The more active compound, 23, …

Mössbauer Spectroscopic Studies Of Hemoglobin And Its Isolated Subunits, G. R. Hoy, D. C. Cook, R. L. Berger, F. K. Friedman

Physics Faculty Publications

Samples of 90% enriched ⁵⁷Fe hemoglobin and its isolated subunits have been prepared. Mössbauer spectroscopic measurements have been made on three such samples. Sample one contained contributions of oxyhemoglobin, deoxyhemoglobin, and carbonmonoxyhemoglobin. This sample was studied from a temperature of 90 K down to 230 mK. Measurements were also made at 4.2 K using a small applied magnetic field of 1.0 T. In general, the measured quadrupole splittings and isomer shifts for each component agreed with previous measurements on single component samples in the literature, and thus demonstrated that chemically enriched hemoglobin has not been altered. The second and …

Model For Estimating Soil Water Flow, Water Content, Evapotranspiration And Root Extraction, Musa N. Nimah

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

A mathematical model was developed to predict water content profiles, evapotranspiration, water flow from or to the water table, root extraction and root water potential at the surface as functions of time under unsteady state conditions.

The model was tested in the field at The Hullinger Farm near Vernal, Utah, in 1970 and 1971. Comparison of water content-depth profiles show excellent agreement at the end of a 9- day run in 1970 on oats seeded to alfalfa. In 1971 with alfalfa as the crop, the data show best agreement, between predicted and computed water content-depth profiles, 48 hours after any …