Physical Sciences and Mathematics Commons^™

Local Versus Global Search In Channel Graphs, A.H. Hunter, Nicholas Pippenger

All HMC Faculty Publications and Research

Previous studies of search in channel graphs has assumed that the search is global; that is, that the status of any link can be probed by the search algorithm at any time. We consider for the first time local search, for which only links to which an idle path from the source has already been established may be probed. We show that some well known channel graphs may require exponentially more probes, on the average, when search must be local than when it may be global.

Learning To Create Jazz Melodies Using Deep Belief Nets, Greg Bickerman '10, Sam Bosley, Peter Swire, Robert M. Keller

All HMC Faculty Publications and Research

We describe an unsupervised learning technique to facilitate automated creation of jazz melodic improvisation over chord sequences. Specifically we demonstrate training an artificial improvisation algorithm based on unsupervised learning using deep belief nets, a form of probabilistic neural network based on restricted Boltzmann machines. We present a musical encoding scheme and specifics of a learning and creational method. Our approach creates novel jazz licks, albeit not yet in real-time. The present work should be regarded as a feasibility study to determine whether such networks could be used at all. We do not claim superiority of this approach for pragmatically creating …

Direct Measurements Of Island Growth And Step-Edge Barriers In Colloidal Epitaxy, Rajesh Ganapathy, Mark R. Buckley, Sharon J. Gerbode, Itai Cohen

All HMC Faculty Publications and Research

Epitaxial growth, a bottom-up self-assembly process for creating surface nano- and microstructures, has been extensively studied in the context of atoms. This process, however, is also a promising route to self-assembly of nanometer- and micrometer-scale particles into microstructures that have numerous technological applications. To determine whether atomic epitaxial growth laws are applicable to the epitaxy of larger particles with attractive interactions, we investigated the nucleation and growth dynamics of colloidal crystal films with single-particle resolution. We show quantitatively that colloidal epitaxy obeys the same two-dimensional island nucleation and growth laws that govern atomic epitaxy. However, we found that in colloidal …

Recognizing Graph Theoretic Properties With Polynomial Ideals, Jesus A. De Loera, Christopher J. Hillar, Peter N. Malkin, Mohamed Omar

All HMC Faculty Publications and Research

Many hard combinatorial problems can be modeled by a system of polynomial equations. N. Alon coined the term polynomial method to describe the use of nonlinear polynomials when solving combinatorial problems. We continue the exploration of the polynomial method and show how the algorithmic theory of polynomial ideals can be used to detect k-colorability, unique Hamiltonicity, and automorphism rigidity of graphs. Our techniques are diverse and involve Nullstellensatz certificates, linear algebra over finite fields, Gröbner bases, toric algebra, convex programming, and real algebraic geometry.

Distance To U Pegasi By The Dde Algorithm, Todd R. Vaccaro, Dirk Terrell, Robert E. Wilson

Physics and Astronomy Faculty Publications

A distance is found for the W UMa type binary U Pegasi, with a newly modified version of the Wilson-Devinney program (W-D) that makes use of the direct distance estimation (DDE) algorithm. The reported distance of d=123.6pc is an average based on solutions for B and V data and a primary star temperature of 5800K. Standardized light curves (not differential), radial velocities, and a spectroscopic primary star temperature are input to the program. Differential corrections were performed for each light curve band along with the velocities for two primary temperatures that span 100K. Log₁₀d is a model parameter …

Mathematical Biology At An Undergraduate Liberal Arts College, Stephen C. Adolph, Lisette G. De Pillis

All HMC Faculty Publications and Research

Since 2002 we have offered an undergraduate major in Mathematical Biology at Harvey Mudd College. The major was developed and is administered jointly by the mathematics and biology faculty. In this paper we describe the major, courses, and faculty and student research and discuss some of the challenges and opportunities we have experienced.

An Applied Investigation Of Nafion Membranes In Pem Fuel Cells: Durability Issues, Amanda Rose Rodriguez

Theses Digitization Project

The purpose of this study was to perform ex-situ tests and observe the degradation behavior of PEM fuel cells in transportation applications. Improving the efficiency of fuel cells could lead to greatly reduced vehicle energy consumption and similarly reduced vehicle emissions.

Statistical Analysis Of Wastewater Remediation And Bio-Fuels Production Of Algae, Jay D. Jones

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

The Logan city wastewater treatment system consists of a series of seven large aerated ponds (460 acres) that biologically treats 15 million gallons per day of wastewater from Logan city and six other communities. Tighter regulations of allowed phosphorus levels in the effluent have recently been implemented due to environmental concerns of a downstream reservoir. The Biological Engineering program at Utah State University, the Bio-fuels Center, the Utah Water Research Laboratory (UWRL) and the city of Logan are working together to remediate the wastewater treatment system using microalgae. Algal growth requires the uptake of phosphorus. Thus, phosphorus in the effluent …

Evolving Models: A Density-Based Approach To Modeling Sexual Dimorphism And Adaptive Speciation, Audrey Smith

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

In this paper, we begin by extending existing deterministic and individual-based ecological models for sexual dimorphism and adaptive speciation into density-based mathematical models describing the density or number of individuals with various trait values, or phenotypes. These density-based models describe the dynamics of a population of males and females using both clonal and sexual reproduction. Each generation, the populations are subject to mating, mutation, and ecological dynamics including infraspecific competition and carrying capacity of the environment. By avoiding individual-based models, we are able to avoid simulations and instead achieve repeatable results.

Implementing these models numerically, we are able to show …

Alternative Splicing And Polyadenylation Contribute To The Generation Of Herg1 C-Terminal Isoforms, Qiuming Gong, Matthew R. Stump, A. Russell Dunn, Vivianne Deng, Zhengfeng Zhou

Faculty Publications - Department of Biological & Molecular Science

The human ether-a-go-go-related gene 1 (hERG1) encodes the pore-forming subunit of the rapidly activating delayed rectifier potassium channel. Several hERG1 isoforms with different N- and C-terminal ends have been identified. The hERG1a, hERG1b, and hERG1-3.1 isoforms contain the full-length C terminus, whereas the hERG1_USOisoforms, hERG1a_USO and hERG1b_USO, lack most of the C-terminal domain and contain a unique C-terminal end. The mechanisms underlying the generation of hERG1_USOisoforms are not understood. We show that hERG1 isoforms with different C-terminal ends are generated by alternative splicing and polyadenylation of hERG1 pre-mRNA. We identified an …

Mutational Studies Uncover Non-Native Structure In The Dimeric Kinetic Intermediate Of The H2a–H2b Heterodimer, Matthew R. Stump, Lisa M. Gloss

Faculty Publications - Department of Biological & Molecular Science

The folding pathway of the histone H2A–H2B heterodimer minimally includes an on-pathway, dimeric, burst-phase intermediate, I2. The partially folded H2A and H2B monomers populated at equilibrium were characterized as potential monomeric kinetic intermediates. Folding kinetics were compared for initiation from isolated, folded monomers and the heterodimer unfolded in 4 M urea. The observed rates were virtually identical above 0.4Murea, exhibiting a log-linear relationship on the final denaturant concentration. Below ∼0.4 M urea (concentrations inaccessible from the 4-M urea unfolded state), a rollover in the rates was observed; this suggests that a component of the I2 ensemble contains non-native structure that …

A New Nonlinear Classifier With A Penalized Signed Fuzzy Measure Using Effective Genetic Algorithm, Julia Hua Fang, Maria L. Rizzo, Honggang Wang, Kimberly Espy, Zhenyuan Wang

Mathematics Faculty Publications

This paper proposes a new nonlinear classifier based on a generalized Choquet integral with signed fuzzy measures to enhance the classification accuracy and power by capturing all possible interactions among two or more attributes. This generalized approach was developed to address unsolved Choquet-integral classification issues such as allowing for flexible location of projection lines in n-dimensional space, automatic search for the least misclassification rate based on Choquet distance, and penalty on misclassified points. A special genetic algorithm is designed to implement this classification optimization with fast convergence. Both the numerical experiment and empirical case studies show that this generalized …

General Flips And The Cd-Index, Daniel J. Wells

University of Kentucky Doctoral Dissertations

We generalize bistellar operations (often called flips) on simplicial manifolds to a notion of general flips on PL-spheres. We provide methods for computing the cd-index of these general flips, which is the change in the cd-index of any sphere to which the flip is applied. We provide formulas and relations among flips in certain classes, paying special attention to the classic case of bistellar flips. We also consider questions of "flip-connecticity", that is, we show that any two polytopes in certain classes can be connected via a sequence of flips in an appropriate class.

Measurement Of Single Spin Asymmetries In Semi-Inclusive Deep Inelastic Scattering Reaction N↑(E, Éπ+)X At Jefferson Lab, Kalyan C. Allada

University of Kentucky Doctoral Dissertations

What constitutes the spin of the nucleon? The answer to this question is still not completely understood. Although we know the longitudinal quark spin content very well, the data on the transverse quark spin content of the nucleon is still very sparse. Semi-inclusive Deep Inelastic Scattering (SIDIS) using transversely polarized targets provide crucial information on this aspect. The data that is currently available was taken with proton and deuteron targets.

The E06-010 experiment was performed at Jefferson Lab in Hall-A to measure the single spin asymmetries in the SIDIS reaction n^↑(e,éπ^±/K^±)X using transversely polarized …

Spectroscopy And Structures Of Metal-Cyclic Hydrocarbon Complexes, Jung Sup Lee

University of Kentucky Doctoral Dissertations

Metal-cyclic hydrocarbon complexes were prepared in a laser-vaporization molecular beam source and studied by single-photon zero electron kinetic energy (ZEKE) and IR-UV resonant two-photon ionization (R2PI) spectroscopy. The ionization energies and vibrational frequencies of the metal complexes were measured from the ZEKE spectra. Metal-ligand bonding and low-lying electronic states of the neutral and ionized complexes were analyzed by combining the ZEKE measurements with density functional theory (DFT) calculations. In addition, C-H stretching frequencies were measured from the R2PI spectra.

In this dissertation, metal complexes of 1, 3, 5, 7-cyclo-octatetraene (COT), toluene, p-xylene, mesitylene, hexamethylbenzene, biphenyl, naphthalene, pyrene, perylene, and …

15N Solid-State Nmr Detection Of Flavin Perturbation By H-Bonding In Models And Enzyme Active Sites, Dongtao Cui

University of Kentucky Doctoral Dissertations

Massey and Hemmerich proposed that the different reactivities displayed by different flavoenzymes could be achieved as a result of dominance of different flavin ring resonance structures in different binding sites. Thus, the FMN cofactor would engage in different reactions when it had different electronic structures. To test this proposal and understand how different protein sites could produce different flavin electronic structures, we are developing solid-state NMR as a means of characterizing the electronic state of the flavin ring, via the ¹⁵N chemical shift tensors of the ring N atoms. These provide information on the frontier orbitals. We propose that …

Single View Reconstruction For Human Face And Motion With Priors, Xianwang Wang

University of Kentucky Doctoral Dissertations

Single view reconstruction is fundamentally an under-constrained problem. We aim to develop new approaches to model human face and motion with model priors that restrict the space of possible solutions. First, we develop a novel approach to recover the 3D shape from a single view image under challenging conditions, such as large variations in illumination and pose. The problem is addressed by employing the techniques of non-linear manifold embedding and alignment. Specifically, the local image models for each patch of facial images and the local surface models for each patch of 3D shape are learned using a non-linear dimensionality reduction …

Near-Field Radiative Transfer: Thermal Radiation, Thermophotovoltaic Power Generation And Optical Characterization, Mathieu Francoeur

University of Kentucky Doctoral Dissertations

This dissertation focuses on near-field radiative transfer, which can be defined as the discipline concerned with energy transfer via electromagnetic waves at sub-wavelength distances. Three specific subjects related to this discipline are investigated, namely nearfield thermal radiation, nanoscale-gap thermophotovoltaic (nano-TPV) power generation and optical characterization. An algorithm for the solution of near-field thermal radiation problems in one-dimensional layered media is developed, and several tests are performed showing the accuracy, consistency and versatility of the procedure. The possibility of tuning near-field radiative heat transfer via thin films supporting surface phononpolaritons (SPhPs) in the infrared is afterwards investigated via the computation of …

Algorithms For Upper Bounds Of Low Dimensional Group Homology, Joshua D. Roberts

University of Kentucky Doctoral Dissertations

A motivational problem for group homology is a conjecture of Quillen that states, as reformulated by Anton, that the second homology of the general linear group over R = Z[1/p; ζ_p], for p an odd prime, is isomorphic to the second homology of the group of units of R, where the homology calculations are over the field of order p. By considering the group extension spectral sequence applied to the short exact sequence 1 → SL₂ → GL₂ → GL₁ → 1 we show that the calculation of the homology …

Upper Bounds On The Splitting Of The Eigenvalues, Phuoc L. Ho

University of Kentucky Doctoral Dissertations

We establish the upper bounds for the difference between the first two eigenvalues of the relative and absolute eigenvalue problems. Relative and absolute boundary conditions are generalization of Dirichlet and Neumann boundary conditions on functions to differential forms respectively. The domains are taken to be a family of symmetric regions in Rⁿ consisting of two cavities joined by a straight thin tube. Our operators are Hodge Laplacian operators acting on k-forms given by the formula Δ^(k) = dδ+δd, where d and δ are the exterior derivatives and the codifferentials respectively. A result …

In Vivo Oxidative Stress In Alzheimer Disease Brain And A Mouse Model Thereof: Effects Of Lipid Asymmetry And The Single Methionine Residue Of Amyloid-Β Peptide, Miranda Lu Bader Lange

University of Kentucky Doctoral Dissertations

Studies presented in this dissertation were conducted to gain more insight into the role of phospholipid asymmetry and amyloid-β (Aβ)-induced oxidative stress in brain of subjects with amnestic mild cognitive impairment (aMCI) and Alzheimer disease (AD). AD is a largely sporadic, age-associated neurodegenerative disorder clinically characterized by the vast, progressive loss of memory and cognition commonly in populations over the age of ~65 years, with the exception of those with familial AD, which develop AD symptoms as early as ~30 years-old. Neuropathologically, both AD and FAD can be characterized by synapse and neuronal cell loss in conjunction with accumulation of …

The No. 5 Block In Eastern Kentucky: A Critical Re-Examination Of The Petrology With Special Attention To The Origin Of Inertinite Macerals In The Splint Lithotypes, Allison Ranae Richardson

University of Kentucky Master's Theses

Microbes, including fungi and bacteria, and insects are responsible for the consumption and subsequent degradation of plant materials into humus. These microbes directly and indirectly affect the physical and chemical characteristics of coal macerals. Efforts to understand and determine the origins of inertinite macerals are largely misrepresented in the literature, conforming to a single origin of fire. This study focuses on the variability of physical and inferred chemical differences observed petrographically between the different inertinite macerals and discusses the multiple pathways plant material may take to form and or degrade these macerals.

Petrographic results show that fungal activity plays a …

Latest Quaternary Paleoclimate Reconstruction Utilizing Stable Isotopic And Trace Element Proxies In A Stalagmite From Culverson Creek Cave, West Virginia, Ashley Nicole Gilbert

University of Kentucky Master's Theses

A reconstruction of regional climate variability in southern West Virginia that spans the last glacial/interglacial transition is presented. Paleoclimate interpretations obtained from the 50-cm long stalagmite provide key insights regarding the timing, magnitude, and forcing mechanisms responsible for past climate variability. Stable isotopic (δ¹⁸O and δ¹³C) and trace element (Ba, Sr, Mg) signatures from samples contiguously milled along the growth-axis of a ²³⁰Th-dated stalagmite which grew between approximately 20 and 5 thousand years before present (kyr BP) provide critical constraints for above-cave mean annual temperature, seasonality of moisture mean annual precipitation, and potential vegetation shifts. …

On Baryon Number Non-Conservation In Two-Dimensional O(2n+1) Qcd, Tamar Friedmann

Mathematics Sciences: Faculty Publications

We construct a classical dynamical system whose phase space is a certain infinite dimensional Grassmannian manifold, and propose that it is equivalent to the large N limit of two-dimensional QCD with an O(2N + 1) gauge group. In this theory, we find that baryon number is a topological quantity that is conserved only modulo 2. We also relate this theory to the master field approach to matrix models.

Development Of Reductive Metal Systems For The Degradation Of Energetic Compounds (Tatp, Tnt, And Rdx), Rebecca L. Albo

Electronic Theses and Dissertations

Triacetone triperoxide (TATP), a cyclic peroxide explosive, is frequently used by terrorists and amateur chemists due to the ease of synthesis and the availability of reagents. TATP is extremely sensitive to shock, heat, and friction thus a safe and rapid method for treating TATP is needed. The major objective of this dissertation was to develop in situ methodologies that could safely degrade TATP in various field situations. Initial studies focused on using zero-valent metals and mechanically alloyed metals to decompose TATP samples in both aqueous and organic solutions. The metal systems tested included zero-valent iron, magnesium, and magnesium bimetal, Mg/Pd. …

Foraging Effort Of Juvenile Steller Sea Lions Eumetopias Jubatus With Respect To Heterogeneity Of Sea Surface Temperature, Michelle E. Lander, Thomas R. Loughlin, Miles G. Logsdon, Glenn R. Vanblaricom, Brian Fadely

United States Department of Commerce: Staff Publications

Among many other factors, the decline of the western distinct population segment of Steller sea lions Eumetopias jubatus in Alaska (USA) has been attributed to changes in the distribution or abundance of prey due to the cumulative effects of fisheries and large-scale climate change. However, the depletion of localized prey resources due to small-scale environmental variability and perturbations may be impeding recovery, resulting in the need to understand how the environment currently affects this species on smaller spatial and temporal scales. The objective of this study, there-fore, was to assess how Steller sea lions respond to changes in localized environmental …

International Geomagnetic Reference Field: The Eleventh Generation, C. C. Finlay, S. Maus, C. D. Beggan, T. N. Bondar, A. Chambodut, T. A. Chernova, A. Chulliat, V. P. Golovkov, B. Hamilton, M. Hamoudi, R. Holme, G. Hulot, W. Kuang, B. Langlais, V. Lesur, F. J. Lowes, H. Lühr, S. Macmillan, M. Mandea, S. Mclean, C. Manoj, M. Menvielle, I. Michaelis, N. Olsen, J. Rauberg, M. Rother, T. J. Sabaka, A. Tangborn, L. Tøffner-Clausen, E. Thébault, A. W. P. Thomson, I. Wardinski, Z. Wei, T. I. Zvereva

United States Department of Commerce: Staff Publications

The eleventh generation of the International Geomagnetic Reference Field (IGRF)was adopted in December 2009 by the International Association of Geomagnetism and AeronomyWorking Group V-MOD. It updates the previous IGRF generation with a definitive main field model for epoch 2005.0, a main field model for epoch 2010.0, and a linear predictive secular variation model for 2010.0–2015.0. In this note the equations defining the IGRF model are provided along with the spherical harmonic coefficients for the eleventh generation. Maps of the magnetic declination, inclination and total intensity for epoch 2010.0 and their predicted rates of change for 2010.0–2015.0 are presented. The recent …

Hydrological Connectivity For Riverine Fish: Measurement Challenges And Research Opportunities, A. H. Fullerton, K. M. Burnett, E. A. Steel, R. L. Flitcroft, G. R. Pess, B. E. Feist, C. E. Torgersen, D. J. Miller, B. L. Sanderson

United States Department of Commerce: Staff Publications

1. In this review,we first summarize how hydrologic connectivity has been studied for riverine fish capable of moving long distances, and then identify research opportunities that have clear conservation significance. Migratory species, such as anadromous salmonids, are good model organisms for understanding ecological connectivity in rivers because the spatial scale over which movements occur among freshwater habitats is large enough to be easily observed with available techniques; they are often economically or culturally valuable with habitats that can be easily fragmented by human activities; and they integrate landscape conditions from multiple surrounding catchment(s) with in-river conditions. Studies have focussed on …

Dynamics Of Strongly Nonlinear Kinks And Solitons In A Two-Layer Fluid, K. Gorshkov, L. A. Ostrovsky, I. Soustova

United States Department of Commerce: Staff Publications

Perturbation theory is developed for interaction of strongly nonlinear solitary waves close to the limiting, tabletop solitons (∏-solitons). The method is based on representing each soliton as a compound of two kinks so that the interaction of N solitons is treated as the interaction of 2N kinks. As an example the Miyata–Choi–Camassa equations for a two-layer fluid is considered. Equations for kink coordinates are obtained and analyzed. Some nontrivial features of two-soliton interaction characteristic of the strongly nonlinear case are established.

Meridional Patterns In The Deep Scattering Layers And Top Predator Distribution In The Central Equatorial Pacific, Elliott L. Hazen, David W. Johnston

United States Department of Commerce: Staff Publications

The deep scattering layers (DSL) in the central equatorial Pacific form an important prey resource in a relatively oligotrophic habitat. In March of 2006, we used a calibrated 38-kHz SIMRAD EK60 scientific sonar to assess the spatial distribution of the deep scattering layer relative to broad-scale oceanographic features and fine-scale physical and biological measurements. We conducted a single continuous transect from approximately 10°S to 20°N at 170°W while measuring acoustic backscatter, current velocity and direction, temperature, salinity, oxygen, and fluorescence with depth, coincident with marine mammal occurrence. These data were combined with remotely sensed sea surface height, chlorophyll, and sea …