Biological and Chemical Physics Commons^™

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

USF Tampa 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.S. …

Characterization Of Neutron And Proton Exposure On The Radiation Resistant Bacterium, Deinococcus Radiodurans, Ronald C. Lenker

Theses and Dissertations

Deinococcus radiodurans is a robust bacterium that is known for its extraordinary resistance to ionizing radiation. In general, many of the investigations of this bacterium's resistance have revolved around low linear energy transfer radiation, such as gamma and electron radiation. This study explored Deinococcus radiodurans's ability to survive high linear energy transfer radiation, specifically proton and neutron radiation. Deinococcus radiodurans was dehydrated to reduce the effects of low linear energy transfer radiation. The bacteria were exposed to both neutron and proton radiation of varying amounts and rehydrated. The resulting colonies were counted and compared to colonies of non-irradiated control samples …

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

UNO 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 …

Higher-Order Power Harmonics Of Pulsed Electrical Stimulation Modulates Corticospinal Contribution Of Peripheral Nerve Stimulation, Chiun-Fan Chen, Marom Bikson, Li-Wei Chou, Chunlei Shan, Niranjan Khadka, Wen-Shiang Chen, Felipe Fregni

Engineering Science Faculty Publications

It is well established that electrical-stimulation frequency is crucial to determining the scale of induced neuromodulation, particularly when attempting to modulate corticospinal excitability. However, the modulatory effects of stimulation frequency are not only determined by its absolute value but also by other parameters such as power at harmonics. The stimulus pulse shape further influences parameters such as excitation threshold and fiber selectivity. The explicit role of the power in these harmonics in determining the outcome of stimulation has not previously been analyzed. In this study, we adopted an animal model of peripheral electrical stimulation that includes an amplitude-adapted pulse train …

The Impact Of Base Stacking On The Conformations And Electrostatics Of Single-Stranded Dna, Alex Plumridge, Steve P. Meisburger, Kurt Andresen, Lois Pollack

Physics and Astronomy Faculty Publications

Single-stranded DNA (ssDNA) is notable for its interactions with ssDNA binding proteins (SSBs) during fundamentally important biological processes including DNA repair and replication. Previous work has begun to characterize the conformational and electrostatic properties of ssDNA in association with SSBs. However, the conformational distributions of free ssDNA have been difficult to determine. To capture the vast array of ssDNA conformations in solution, we pair small angle X-ray scattering with novel ensemble fitting methods, obtaining key parameters such as the size, shape and stacking character of strands with different sequences. Complementary ion counting measurements using inductively coupled plasma atomic emission spectroscopy …

Second Harmonic Generation – A Novel Approach In Retinal Imaging, Denis Y. Sharoukhov

Dissertations, Theses, and Capstone Projects

Here we present the utilization of Second Harmonic Generation (SHG) for label-free imaging of microtubules (MTs) in the retinal nerve fiber layer (RNFL). MTs are an important part of axonal cytoskeleton, providing structural support and serving as a railroad in intracellular transport. We demonstrate the application of SHG microscopy to the following studies: 1) Can changes in MT conformation be detected when treated with a stabilizing drug (Taxol); 2) if disruption in MT precedes loss of axons in a mouse model of glaucoma (DBA/2J); and 3) if elevated levels of intraocular pressure affect MT integrity. Our results validate SHG imaging …

The Statistical Mechanics Of Solar Wind Hydroxylation At The Moon, Within Lunar Magnetic Anomalies, And At Phobos, W. M. Farrell, D. M. Hurley, Vincent J. Esposito, J. L. Mclain, M. I. Zimmerman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We present a new formalism to describe the outgassing of hydrogen initially implanted by the solar wind protons into exposed soils on airless bodies. The formalism applies a statistical mechanics approach similar to that applied recently to molecular adsorption onto activated surfaces. The key element enabling this formalism is the recognition that the interatomic potential between the implanted H and regolith-residing oxides is not of singular value but possess a distribution of trapped energy values at a given temperature, F(U,T). All subsequent derivations of the outward diffusion and H retention rely on the specific properties of this distribution. We …

Characterization Of The Atcc Α-Tc1-6 Pancreatic Alpha Cell Line To Study Glucagon Secretion, Larissa M. Ikenouye

Electronic Theses and Dissertations

The endocrine pancreas is responsible for maintaining glycemic equilibrium in the body. Given the importance of this blood-glucose homeostasis and the implication an unbalance has on Diabetes mellitus, the study of the glucose-sensing alpha and beta cells in the pancreas is a popular field for scientific researchers. In this study, we use immunofluorescence, qPCR analysis, intracellular calcium experiments, and biochemical glucagon secretion assays to determine if the commercially available tumor cell line clone, α-TC1-6 obtained from American Type Culture Collection, is an appropriate model system for glucagon secretion in pancreatic alpha cells. We confirm the production of the hormone peptide …

Design And Activation Of Frequency Tunable 200ghz Gyrotron, Natalie Golota, Faith Scott, Edward Saliba, Brice Albert, Alexander Barnes

Undergraduate Research Symposium Posters

Dynamic Nuclear Polarization (DNP) when combined with Nuclear Magnetic Resonance (NMR) yields high sensitivity spectra while decreasing sample acquisition time. DNP transfers polarization from electron to nuclear spins, giving a strong enhancement of NMR signal. DNP is rapidly developing area of research due in part to application of cyclotron resonance masers (gyrotron) as high power microwave sources. Gyrotrons provide a high-power, high-frequency microwave source that can be used in close proximity to high field NMR magnets. Gyrotrons are operated under strong vacuum and within a cryogenic superconducting magnetic. Gyrotron microwave power is generated by a magnetron injection gun (MIG) composed …

Micro-Spectroscopy Of Bio-Assemblies At The Single Cell Level, Jeslin Kera

Honors Undergraduate Theses

In this thesis, we investigate biological molecules on a micron scale in the ultraviolet spectral region through the non-destructive confocal absorption microscopy. The setup involves a combination of confocal microscope with a UV light excitation beam to measure the optical absorption spectra with spatial resolution of 1.4 μm in the lateral and 3.6 μm in the axial direction. Confocal absorption microscopy has the benefits of requiring no labels and only low light intensity for excitation while providing a strong signal from the contrast generated by the attenuation of propagating light due to absorption. This enables spatially resolved measurements of single …

Including Wrist Flexion In The Human Arm Model Changes Everything!, William B. Laing Iii, Austin Johnson, Albert D. Gonzalez, Chris S. Hansen

Faculty Works

Does your introductory physics laboratory experiment that analyzes the human arm as a lever assume an inflexible wrist? If so, the analysis of the biceps force required to perform a biceps curl will lead to results that contradict experience: one does not expect the required biceps force to decrease as the mass is raised. We will show that allowing for wrist flexion leads to agreement with empirical data: that the required force does increase as the mass is raised if the wrist angle is allowed to be optimal.

Rules And Mechanisms For Efficient Two-Stage Learning In Neural Circuits, Tiberiu Teşileanu, Bence Ölveczky, Vijay Balasubramanian

Publications and Research

Trial-and-error learning requires evaluating variable actions and reinforcing successful variants. In songbirds, vocal exploration is induced by LMAN, the output of a basal ganglia-related circuit that also contributes a corrective bias to the vocal output. This bias is gradually consolidated in RA, a motor cortex analogue downstream of LMAN. We develop a new model of such two-stage learning. Using stochastic gradient descent, we derive how the activity in ‘tutor’ circuits (e.g., LMAN) should match plasticity mechanisms in ‘student’ circuits (e.g., RA) to achieve efficient learning. We further describe a reinforcement learning framework through which the tutor can build its teaching …

Study Of Nano-Bio Interfaces In Nano-Bio Conjugates: Nanoparticles Of Zinc Oxide (Zno) And Biomolecules Of Glucose, Cytosine, And Thymine, Bithi Paul

Graduate Theses/Dissertations

Nano conjugates, composites of inorganic nanomaterials and bio molecules such as DNA, RNA and proteins, establish a sequence of wide varieties of nano-bio boundaries. The formation of these boundaries strongly depends on bio physicochemical reaction of biomolecules coated on the surface of nanomaterials. I am investigating various nano-bio conjugates consisting of zinc oxide (ZnO) nanoparticles with simple biomolecules including glucose and the nitrogenous bases of DNA such as cytosine and thymine. All nano-bio conjugates were fabricated using a standard bio-chemical synthesis process. Structural, physical, bio-chemical interface properties of nano-bio composites were probed using X-ray diffraction (XRD), Raman spectroscopy, and photoluminescence …

Nanopore Thermodynamics Via Infrared Laser Heating, Christopher Angevine

Theses and Dissertations

Single molecule nanopore spectroscopy is a label-free method for characterizing a wide variety of water-soluble molecules. Recently there have been efforts to expand nanopore sensing to new areas of study. Forensic investigators require an easy to deploy method to identify an unknown number of contributors in a solution. Currently there is no easily available method to distinguish between a single or multiple contributor solution of DNA before being processed by more advanced analytical techniques which has led to wasted time and resources increasing the backlog of samples waiting to be processed. In this work we present a new nanopore technique …

Application Of The Fisher Dimer Model To Dna Condensation, John C. Baker Iii

Theses and Dissertations

This paper considers the statistical mechanics occupation of the edge of a single helix of DNA by simple polymers. Using Fisher's exact closed form solution for dimers on a two-dimensional lattice, a one-dimensional lattice is created mathematically that is occupied by dimers, monomers, and holes. The free energy, entropy, average occupation, and total charge on the lattice are found through the usual statistical methods. The results demonstrate the charge inversion required for a DNA helix to undergo DNA condensation.

Quantitative Analysis And Process Of High Speed Live Cell Interferometry Measurements, Daniel Guest

Theses and Dissertations

The application of auto focus, using an optical beam deflection technique, to existing live cell interferometry measurements was developed and examined. The benefit to relevant experiments, currently being performed, is shown as well as its performance across various magnifications. Enough information is given so that the system can be reproduced to fit any end users needs.

Crystallography And Magnetism Of Magnetocalorically Important Ni-Mn-X Based Heusler Alloys, Amila S. B. Madiligama

Dissertations

Ni-Mn-X Heusler alloys, demonstrating strong coupling between crystalline structure and magnetic state, were studied. They undergo field-induced, first-order transformations from a low symmetry martensite to a high-symmetry austenitic phase around room temperature. The substantial difference between the entropies of the two phases results in a large adiabatic temperature change, called “Giant Magnetocaloric Effect (GMCE)”. Consequently, these alloys are promising refrigerants for near-room temperature cooling systems. This magnetic cooling is an energy-efficient and eco-friendly technology.

Crystalline structures and magnetic states of these alloys, which determine their magnetocaloric performances, highly depend on their composition. To examine new paths to optimize their magnetocaloric …

Splitting Nodes And Linking Channels: A Method For Assembling Biocircuits From Stochastic Elementary Units, Cameron Ferwerda, Ovidiu Lipan

Physics Faculty Publications

Akin to electric circuits, we construct biocircuits that are manipulated by cutting and assembling channels through which stochastic information flows. This diagrammatic manipulation allows us to create a method which constructs networks by joining building blocks selected so that (a) they cover only basic processes; (b) it is scalable to large networks; (c) the mean and variance-covariance from the Pauli master equation form a closed system; and (d) given the initial probability distribution, no special boundary conditions are necessary to solve the master equation. The method aims to help with both designing new synthetic signaling pathways and quantifying naturally existing …

Vibrationally Resolved Lifetimes Of The 21Σ+U State Of Na2, Seth Ashman, Roy Anunciado, Lutz Hüwel

Engineering & Physics Faculty Publications

Lifetimes of partially resolved ro-vibrational levels of the Na2 21Σu + double well state have been measured for the first time. Ground state sodium dimer molecules in a molecular beam are resonantly excited by the doubled output of a 10 ns pulsed dye laser in the range 333–357 nm. After being allowed to decay for a predetermined time interval, the surviving excited molecules are ionized by 532 nm photons from a delayed Nd:YAG laser and detected in a linear time-of flight mass spectrometer. By appropriate tuning of the excitation laser and systematic variation of the probe laser delay, lifetimes are …

Heart Attack Physics, John Zwart

Faculty Work Comprehensive List

I recently had a first-hand opportunity to learn some interesting biomedical applications of physics which provide application examples for introductory classes. While there were many such applications, from X-rays to ultrasonic imaging, I’ll focus on fluid flow through clogged coronary arteries and the use of radioactive materials in a nuclear stress test.