Physical Sciences and Mathematics Commons^™

The Role Of Funding Programs In Promotion Of Best Management Practices For Effective Stream Restoration, Tracy R. Wendt

Graduate Student Theses, Dissertations, & Professional Papers

Large amounts of money are spent on stream restoration projects across the United States every year. Restoration researchers and professionals commonly recommend a suite of Best Management Practices (BMPs), including project goals, objectives, monitoring, consideration of future conditions, adaptive management, and public reporting of results, which are widely recognized as contributing to effective projects. Studies over the last two decades demonstrated that these BMPs were not consistently incorporated into restoration projects, which highlighted the need to improve practices and for funding programs to incorporate BMPs into funding requirements. I reviewed 28 programs that fund stream restoration in the Rocky Mountain …

Robust Estimates For Hp-Adaptive Approximations Of Non-Self-Adjoint Eigenvalue Problems, Stefano Giani, Luka Grubišić, Agnieszka Międlar, Jeffrey S. Ovall

Mathematics and Statistics Faculty Publications and Presentations

We present new residual estimates based on Kato’s square root theorem for spectral approximations of non-self-adjoint differential operators of convection–diffusion–reaction type. These estimates are incorporated as part of an hp-adaptive finite element algorithm for practical spectral computations, where it is shown that the resulting a posteriori error estimates are reliable. Provided experiments demonstrate the efficiency and reliability of our approach.

Mathematical Model For Bone Mineralization, Svetlana V. Komarova, Lee Safranek, Jay Gopalakrishnan, Miao-Jung Yvonne Ou, Marc D. Mckee, Monzur Murshed, Frank Rauch, Erica Zuhr

Mathematics and Statistics Faculty Publications and Presentations

Defective bone mineralization has serious clinical manifestations, including deformities and fractures, but the regulation of this extracellular process is not fully understood. We have developed a mathematical model consisting of ordinary differential equations that describe collagen maturation, production and degradation of inhibitors, and mineral nucleation and growth. We examined the roles of individual processes in generating normal and abnormal mineralization patterns characterized using two outcome measures: mineralization lag time and degree of mineralization. Model parameters describing the formation of hydroxyapatite mineral on the nucleating centers most potently affected the degree of mineralization, while the parameters describing inhibitor homeostasis most effectively …

New Results In Ell_1 Penalized Regression, Edward A. Roualdes

Theses and Dissertations--Statistics

Here we consider penalized regression methods, and extend on the results surrounding the l1 norm penalty. We address a more recent development that generalizes previous methods by penalizing a linear transformation of the coefficients of interest instead of penalizing just the coefficients themselves. We introduce an approximate algorithm to fit this generalization and a fully Bayesian hierarchical model that is a direct analogue of the frequentist version. A number of benefits are derived from the Bayesian persepective; most notably choice of the tuning parameter and natural means to estimate the variation of estimates – a notoriously difficult task for the …

Stability Of A Circular System With Multiple Asymmetric Laplacians, Ivo Herman, Dan Martinec, J. J. P. Veerman, Michael Sebek

Mathematics and Statistics Faculty Publications and Presentations

We consider an asymptotic stability of a circular system where the coupling Laplacians are different for each state used for synchronization. It is shown that there must be a symmetric coupling in the output state to guarantee the stability for agents with two integrators in the open loop. Systems with agents having three or more integrators cannot be stabilized by any coupling. In addition, recent works in analysis of a scaling in vehicular platoons relate the asymptotic stability of a circular system to a string stability. Therefore, as confirmed by simulations in the paper, our results have an application also …

Periodic State Revivals In Commensurate Waveguide Arrays, Jovan Petrovic, J. J. P. Veerman

Mathematics and Statistics Faculty Publications and Presentations

Emerging optical and quantum computers require hardware capable of coherent transport of and operations on quantum states. Here, we investigate finite optical waveguide arrays with linear coupling as means of efficient and compact coherent state transfer. Coherent transfer with periodic state revivals is enabled by engineering coupling coefficients between neighbouring waveguides to yield commensurate eigenvalue spectrum. Particular cases of finite arrays have been actively studied to achieve the perfect state transfer by mirroring the input into the output state.

We explore a much wider scope of coherent propagation and revivals of both the state amplitude and phase. We analytically solve …

Mathematical Modeling For Platform-Based Product Configuration Considering Total Life-Cycle Sustainability, Tian Lan

Theses and Dissertations--Mechanical Engineering

Many companies are using platform-based product designs to fulfill the requirements of customers while maintaining low cost. However, research that integrates sustainability into platform-based product design is still limited. Considering sustainability during platform-based design process is a challenge because the total life-cycle from pre-manufacturing, manufacturing and use to post-use stages as well as economic, environmental and societal performance in these stages must be considered. In this research, an approach for quantifying sustainability is introduced and a mathematical model is developed for identifying a more sustainable platform. Data from life-cycle assessment is used to quantify environmental factors; criteria from the Product …

Inhalable Nanocomposites And Anticancer Agents For Cancer Therapy, Nathanael A. Stocke

Theses and Dissertations--Chemical and Materials Engineering

Cancer is designated as the leading cause of mortality worldwide and lung cancer is responsible for nearly 30% of all cancer related deaths. Over the last few decades mortality rates have only marginally increased and rates of recurrence remain high. These factors, among others, suggest the need for more innovative treatment modalities in lung cancer therapy. Targeted pulmonary delivery is well established for treating pulmonary diseases such as asthma and provides a promising platform for lung cancer therapy. Increasing local deposition of anticancer agents (ACAs) and reducing systemic exposure of these toxic moieties could lead to better therapeutic outcomes and …

Topological Complexity In Protein Structures, Erica Flapan, Gabriella Heller '14

Pomona Faculty Publications and Research

For DNA molecules, topological complexity occurs exclusively as the result of knotting or linking of the polynucleotide backbone. By contrast, while a few knots and links have been found within the polypeptide backbones of some protein structures, non-planarity can also result from the connectivity between a polypeptide chain and inter- and intra-chain linking via cofactors and disulfide bonds. In this article, we survey the known types of knots, links, and non-planar graphs in protein structures with and without including such bonds and cofactors. Then we present new examples of protein structures containing Möbius ladders and other non-planar graphs as a …

An Exhibition Of Exponential Sums: Visualizing Supercharacters, Paula Burkhardt '16, Gabriel Currier '16, Stephan Ramon Garcia, Mathieu De Langis '15, Bob Lutz '13, Hong Suh '16

Pomona Faculty Publications and Research

We discuss a simple mathematical mechanism that produces a variety of striking images of great complexity and subtlety. We briefly explain this approach and present a selection of attractive images obtained using this technique.

Model Spaces: A Survey, Stephan Ramon Garcia, William T. Ross

Pomona Faculty Publications and Research

This is a brief and gentle introduction, aimed at graduate students, to the subject of model subspaces of the Hardy space.

Empirical Likelihood Confidence Band, Shihong Zhu

Theses and Dissertations--Statistics

The confidence band represents an important measure of uncertainty associated with a functional estimator and empirical likelihood method has been proved to be a viable approach to constructing confidence bands in many cases. Using the empirical likelihood ratio principle, this dissertation developed simultaneous confidence bands for many functions of fundamental importance in survival analysis, including the survival function, the difference and ratio of survival functions, the hazards ratio function, and other parameters involving residual lifetimes. Covariate adjustment was incorporated under the proportional hazards assumption. The proposed method can be very useful when, for example, an individualized survival function is desired …

Reactive Nitrogen Species Emission Trends In Three Light-/Medium-Duty United States Fleets, Gary A. Bishop, Donald H. Stedman

Fuel Efficiency Automobile Test Publications

Repeated, fuel specific, emission measurements in Denver (2005/2013), Los Angeles (2008/2013) and Tulsa (2005/2013) provide long-term trends in on-road reactive nitrogen emissions from three light/medium duty U.S. fleets. Reductions in oxides of nitrogen (NO_x) emissions ranged from 21% in Denver (5.6 ± 1.3 to 4.4 ± 0.2 gNO_x/kg of fuel) to 43% in Tulsa (4.4 ± 0.3 to 2.5 ± 0.1 gNOx/kg of fuel) since 2005 while decreases in fleet ammonia (NH₃) emissions ranged from no change in Denver (0.45 ± 0.09 to 0.44 ± 0.02 gNH₃/kg of fuel) since 2005 to …

On Zeros Of Certain Dirichlet Polynomials, Kajtaz H. Bllaca

Turkish Journal of Mathematics

In this article we establish the zero-free region of certain Dirichlet polynomials $L_{F, X}$ arising in approximate functional equation for functions in the Selberg class and we prove an asymptotic formula for the number of zeros of $L_{F, X}$.

Evidence Of Attenuation Of Vhe Blazar Spectra By Extragalactic Background Light, Cameron Allen

Physics

The spectrum of two blazar objects, 1ES 1959+650 and 1ES 2344+514, are analyzed for evidence of interactions with the Extragalactic Background Light (EBL), using combined data from the Very Energetic Radiation Imaging Telescope Array System and the Fermi Gamma-ray Space Telescope, By analyzing the distinct curvature across the combined spectrum, we infer that the very-high energy (VHE) gamma-rays must be attenuated by interactions with the EBL. We also find that the measured 1ES 1959+650 spectrum is sensitive to the intrinsic blazar model, with a preference for a power-law with an exponential cutoff (EPWL). The measured curvature is a combination of …

Characterizing Double And Triple Laser Beam Interference Patterns In The Context Of Trapping Atoms For Quantum Computing, Ian E. Powell

Physics

We propose two optical neutral atom traps for quantum computing involving the intersection of two or three laser beams. We simulate both the intensity and the potential energy of the interference pattern. From these simulations we create animations of how the potential energy and intensity change with varying angles of separation between the laser beams in the system. We parameterize lines through our interference pattern and fit simple harmonic oscillator potential energies to the potential energy wells calculated to characterize our interference pattern’s atom trapping capabilities. Finally, we investigate a possible quantum entanglement routine by observing how the geometry of …

A New Heuristic Method To Solve Unit Commitment By Using A Time-Variant Acceleration Coefficients Particle Swarm Optimization Algorithm, Arsalan Najafi, Mohsen Farshad, Hamid Falaghi

Turkish Journal of Electrical Engineering and Computer Sciences

Unit commitment is one of the most important problems in power system operation. Because of the large amount of parameters and constraints, it contains a high level of complexity. In this paper a new method based on a time-variant acceleration coefficients particle swarm optimization algorithm has been proposed to solve the unit commitment problem. Integer coding (for satisfying minimum up/down constraints) and binary coding (for satisfying spinning reserve constraint) have been utilized in the proposed method. Simulations in the different cases have been done with different sizes. Numerical results have shown the superiority and better convergence of the proposed method …

Internally Hydrogen-Bonded Prodan Derivatives, Douglas William Cheek

Dissertations, Theses, and Masters Projects

No abstract provided.

Development Of A Three Step Cascade Synthesis Of 2,4-Dihydro-1h-Benzo[F]Isochromenes, Shane E. Lewis

Dissertations, Theses, and Masters Projects

No abstract provided.

Signature Of Recent Sediment Accumulating In Prince William Sound, Alaska: A Record Of Storms, Earthquakes, And Seasonal Inputs, Nicole R. Marshall

Dissertations, Theses, and Masters Projects

This study focuses on the development o f provenance signatures for sediments accumulating in Prince William Sound, with an emphasis on interpreting mechanisms of sediment deposition using historical earthquake, wave, river discharge, and glacial outburst flood records. A highresolution sedimentary sequence in Prince William Sound, Alaska contains sediments sourced from local watersheds as a result of seasonal and event-driven sedimentation. This study contributes to the development of paleo-proxies for sediment provenance, earthquakes, shelf sediment resuspension, and Copper River discharge. Geochemical studies of sediment cores and end-member samples using X-ray fluorescence and inductively coupled plasma mass spectrometry allows for the development …

Assessing The Impact Of Climate Change On Proposed Restoration Of The Lynnhaven River Ecosystem, Emily E. Skeehan

Dissertations, Theses, and Masters Projects

Environmental degradation of the Chesapeake Bay (CB) and its sub-estuaries has been linked to population growth in the surrounding coastal zone, rapid development in the watershed and resultant nutrient loading into the Bay. Consequently, the federal government and its partners have developed restoration plans to mitigate the effects of eutrophication and improve essential ecosystem functions, though few restoration plans have considered the interactive effects of climate change. Climate change and other anthropogenic drivers are causing changes in ecosystem structure and function, thereby impacting the beneficial services ecosystems provide. While some studies have attempted to quantitatively predict the benefits of ecosystem …

Adaptive Graph Construction For Isomap Manifold Learning, Loc Tran, Zezhong Zheng, Guoquing Zhou, Jiang Li, Karen O. Egiazarian (Ed.), Sos S. Agaian (Ed.), Atanas P. Gotchev (Ed.)

Electrical & Computer Engineering Faculty Publications

Isomap is a classical manifold learning approach that preserves geodesic distance of nonlinear data sets. One of the main drawbacks of this method is that it is susceptible to leaking, where a shortcut appears between normally separated portions of a manifold. We propose an adaptive graph construction approach that is based upon the sparsity property of the ℓ₁ norm. The ℓ₁ enhanced graph construction method replaces k-nearest neighbors in the classical approach. The proposed algorithm is first tested on the data sets from the UCI data base repository which showed that the proposed approach performs better than …

The Forbidden Number Of A Knot, Alissa S. Crans, Blake Mellor, Sandy Ganzell

Mathematics, Statistics and Data Science Faculty Works

Every classical or virtual knot is equivalent to the unknot via a sequence of extended Reidemeister moves and the so-called forbidden moves. The minimum number of forbidden moves necessary to unknot a given knot is an invariant we call the forbid- den number. We relate the forbidden number to several known invariants, and calculate bounds for some classes of virtual knots.

How Spherical Is A Cube (Gravitationally)?, Jeff Sanny, David M. Smith

Physics Faculty Works

An important concept that is presented in the discussion of Newton's law of universal gravitation is that the gravitational effect external to a spherically symmetric mass distribution is the same as if all of the mass of the distribution were concentrated at the center.1,2 By integrating over ring elements of a spherical shell, we show that the gravitational force on a point mass outside the shell is the same as that of a particle with the same mass as the shell at its center. This derivation works for objects with spherical symmetry while depending on the fact that the gravitational …

Inhibition Of Toxic Iapp Amyloid By Extracts Of Common Fruits, David A. Moffet, Pei-Yu Kao, Evangeline Green, Catalina Pereirab, Shauna Ekimura, Dennis Juarez, Travis Whyte, Taylor Arhar, Bianca Malaspina, Luiza A. Nogaj

Chemistry and Biochemistry Faculty Works

The aggregation of the 37-amino acid polypeptide islet amyloid polypeptide (IAPP, amylin), as either insoluble amyloid or as small oligomers, appears to play a direct role in the death of pancreatic β-islet cells in type 2 diabetes. It is believed that inhibiting the aggregation of IAPP may slow down, if not prevent entirely, the progression of this disease. Extracts of thirteen different common fruits were analyzed for their ability to prevent the aggregation of amyloidogenic IAPP. Thioflavin T binding, immuno-detection and circular dichroism assays were performed to test the in vitro inhibitory potential of each extract. Atomic force microscopy was …

Modifications On Translation Initiation, Sarah F. Mitchell

Chemistry and Biochemistry Faculty Works

Two studies by Meyer et al. and Wang et al. demonstrate a role for m6A modification of mRNA in stimulating translation initiation. These findings add to the growing number of diverse mechanisms for translation initiation in eukaryotes.

Dynamic Motions Of The Hiv-1 Frameshift Site Rna, Kathryn Mouzakis

Chemistry and Biochemistry Faculty Works

The HIV-1 frameshift site (FS) plays a critical role in viral replication. During translation, the HIV-1 FS transitions from a 3-helix to a 2-helix junction RNA secondary structure. The 2-helix junction structure contains a GGA bulge, and purine-rich bulges are common motifs in RNA secondary structure. Here, we investigate the dynamics of the HIV-1 FS 2-helix junction RNA. Interhelical motions were studied under different ionic conditions using NMR order tensor analysis of residual dipolar couplings. In 150 mM potassium, the RNA adopts a 43°(±4°) interhelical bend angle (β) and displays large amplitude, anisotropic interhelical motions characterized by a 0.52(±0.04) internal …

Inhibition Of Toxic Iapp Amyloid By Extracts Of Common Fruits, David Moffet

Chemistry and Biochemistry Faculty Works

The aggregation of the 37-amino acid polypeptide islet amyloid polypeptide (IAPP, amylin), as either insoluble amyloid or as small oligomers, appears to play a direct role in the death of pancreatic β-islet cells in type 2 diabetes. It is believed that inhibiting the aggregation of IAPP may slow down, if not prevent entirely, the progression of this disease. Extracts of 13 different common fruits were analyzed for their ability to prevent the aggregation of amyloidogenic IAPP. Thioflavin T binding, immuno-detection and circular dichroism assays were performed to test the in vitro inhibitory potential of each extract. Atomic force microscopy was …

Global Shape Mimicry Of Trna Within A Viral Internal Ribosome Entry Site Mediates Translational Reading Frame Selection, Kathryn Mouzakis

Chemistry and Biochemistry Faculty Works

The dicistrovirus intergenic region internal ribosome entry site (IRES) adopts a triple-pseudoknotted RNA structure and occupies the core ribosomal E, P, and A sites to directly recruit the ribosome and initiate translation at a non-AUG codon. A subset of dicistrovirus IRESs directs translation in the 0 and +1 frames to produce the viral structural proteins and a +1 overlapping open reading frame called ORFx, respectively. Here we show that specific mutations of two unpaired adenosines located at the core of the threehelical junction of the honey bee dicistrovirus Israeli acute paralysis virus (IAPV) IRES PKI domain can uncouple 0 and …

Shear Wave Splitting Analysis Beneath Tien Shan: Geodynamic Implications Of Complex Anisotropy, Solomon Gerra Cherie

Doctoral Dissertations

"In spite of numerous studies, the mechanisms for the crustal shortening, mountain formation and associated tectonism leading to complex or simply seismic anisotropy formation beneath the Tien Shan Orogenic Belt is still debated. The most popular hypotheses suggested for the existence of seismic anisotropy are small-scale mantle convection, regional scale resistive basal shear and APM induced asthenospheric flow. Here, we used shear-wave splitting (SWS) measurements with good azimuthal coverage to provide additional constraints on the various models proposed by previous studies. One of the most effective approaches utilized to constrain convective mantle flow patterns is the splitting of P-to-S converted …