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Brigham Young University

2000

Articles 1 - 20 of 20

Full-Text Articles in Physical Sciences and Mathematics

Parallel Phylogenetic Inference, Mark J. Clement, David Mclaughlin, Quinn O. Snell, Michael Whiting Nov 2000

Parallel Phylogenetic Inference, Mark J. Clement, David Mclaughlin, Quinn O. Snell, Michael Whiting

Faculty Publications

Recent advances in DNA sequencing technology have created large data sets upon which phylogenetic inference can be performed. However, current research is limited by the prohibitive time necessary to perform tree search on even a reasonably sized data set. Some parallel algorithms have been developed but the biological research community does not use them because they don’t trust the results from newly developed parallel software. This paper presents a new phylogenetic algorithm that allows existing, trusted phylogenetic software packages to be executed in parallel using the DOGMA parallel processing system. The results presented here indicate that data sets that currently …

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Toward Automated Abstraction For Protocols On Branching Networks, Michael D. Jones, Ganesh Gopalakrishnan Nov 2000

Toward Automated Abstraction For Protocols On Branching Networks, Michael D. Jones, Ganesh Gopalakrishnan

Faculty Publications

We have used various manual abstraction techniques to formally verify a transaction ordering property for an IO protocol over bus/bridge networks. In the context of network protocol verification, an abstraction is needed to reduce the unbounded number of network configurations to a small number of representative networks that can be checked using algorithmic methods. The manually derived abstraction was both brittle and difficult to validate. In this report, we discuss the need for abstraction techniques in the formal verification of protocols over networks and present our recent efforts to create an automatic abstraction technique for network protocols using predicate abstraction …

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Nonsteroidal Anti-Inflammatory Drugs, Acetaminophen, Cyclooxygenase 2, And Fever, Daniel L. Simmons, David Wagner, Kenneth Westover Oct 2000

Nonsteroidal Anti-Inflammatory Drugs, Acetaminophen, Cyclooxygenase 2, And Fever, Daniel L. Simmons, David Wagner, Kenneth Westover

Faculty Publications

Nonsteroidal anti-inflammatory drugs (NSAIDs) are frequently used antipyretic agents that most probably exert their antifever effect by inhibiting cyclooxygenase (COX)–2. Thus, COX-2–selective drugs or null mutation of the COX-2 gene reduce or prevent fever. Acetaminophen is antipyretic and analgesic, as are NSAIDs, but it lacks the anti-inflammatory and anticoagulatory properties of these drugs. This has led to the speculation that a COX variant exists that is inhibitable by acetaminophen. An acetaminophen-inhibitable enzyme is inducible in the mouse J774.2 monocyte cell line. Induction of acetaminophen-inhibitable prostaglandin E2 synthesis parallels induction of COX-2. Thus, inhibition of pharmacologically distinct COX-2 enzyme activity by …

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Optically Simulating A Quantum Associative Memory, Dan A. Ventura, John C. Howell, John A. Yeazell Sep 2000

Optically Simulating A Quantum Associative Memory, Dan A. Ventura, John C. Howell, John A. Yeazell

Faculty Publications

This paper discusses the realization of a quantum associative memory using linear integrated optics. An associative memory produces a full pattern of bits when presented with only a partial pattern. Quantum computers have the potential to store large numbers of patterns and hence have the ability to far surpass any classical neural network realization of an associative memory. In this work two 3-qubit associative memories will be discussed using linear integrated optics. In addition, corrupted, invented and degenerate memories are discussed.

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Biological Implications Of A Discrete Mathematical Model For Collagen Deposition And Alignment In Dermal Wound Repair, J. C. Dallon, J. A. Sherratt, P. K. Maini, M. W. Ferguson Aug 2000

Biological Implications Of A Discrete Mathematical Model For Collagen Deposition And Alignment In Dermal Wound Repair, J. C. Dallon, J. A. Sherratt, P. K. Maini, M. W. Ferguson

Faculty Publications

We develop a novel mathematical model for collagen deposition and alignment during dermal wound healing. We focus on the interactions between fibroblasts, modelled as discrete entities, and a continuous extracellular matrix composed of collagen and a fibrin based blood clot. There are four basic interactions assumed in the model: fibroblasts orient the collagen matrix, fibroblasts produce and degrade collagen and fibrin and the matrix directs the fibroblasts and determines the speed of the cells. Several factors which influence the alignment of collagen are examined and related to current anti-scarring therapies using transforming growth factor " The most influential of these …

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Rescaling The Energy Function In Hopfield Networks, Tony R. Martinez, Xinchuan Zeng Jul 2000

Rescaling The Energy Function In Hopfield Networks, Tony R. Martinez, Xinchuan Zeng

Faculty Publications

In this paper we propose an approach that rescales the distance matrix of the energy function in the Hopfield network for solving optimization problems. We rescale the distance matrix by normalizing each row in the matrix and then adjusting the parameter for the distance term. This scheme has the capability of reducing the effects of clustering in data distributions, which is one of main reasons for the formation of invalid solutions. We evaluate this approach through a large number (20,000) simulations based on 200 randomly generated city distributions of the 10-city traveling salesman problem. The result shows that, compared to …

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The Inefficiency Of Batch Training For Large Training Sets, Tony R. Martinez, D. Randall Wilson Jul 2000

The Inefficiency Of Batch Training For Large Training Sets, Tony R. Martinez, D. Randall Wilson

Faculty Publications

Multilayer perceptrons are often trained using error backpropagation (BP). BP training can be done in either a batch or continuous manner. Claims have frequently been made that batch training is faster and/or more "correct" than continuous training because it uses a better approximation of the true gradient for its weight updates. These claims are often supported by empirical evidence on very small data sets. These claims are untrue, however, for large training sets. This paper explains why batch training is much slower than continuous training for large training sets. Various levels of semi-batch training used on a 20,000-instance speech recognition …

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Plasma Oscillations And Expansion Of An Ultracold Neutral Plasma, Scott D. Bergeson, S. Kulin, T. C. Killian, S. L. Rolston Jul 2000

Plasma Oscillations And Expansion Of An Ultracold Neutral Plasma, Scott D. Bergeson, S. Kulin, T. C. Killian, S. L. Rolston

Faculty Publications

We report the observation of plasma oscillations in an ultracold neutral plasma. With this collective mode we probe the electron density distribution and study the expansion of the plasma as a function of time. For classical plasma conditions, i.e., weak Coulomb coupling, the expansion is dominated by the pressure of the electron gas and is described by a hydrodynamic model. Discrepancies between the model and observations at low temperature and high density may be due to strong coupling of the electrons.

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Electronic Structure Of Bas And Boride Iii-V Alloys, Gus L. W. Hart, Alex Zunger Jun 2000

Electronic Structure Of Bas And Boride Iii-V Alloys, Gus L. W. Hart, Alex Zunger

Faculty Publications

Boron arsenide, the typically ignored member of the Group-III–V arsenide series BAs-AlAs-GaAs-InAs is found to resemble silicon electronically: its Γ conduction-band minimum is p-like (Γ15), not s-like (Γ1c), it has an X1c-like indirect band gap, and its bond charge is distributed almost equally on the two atoms in the unit cell, exhibiting nearly perfect covalency. The reasons for these are tracked down to the anomalously low atomic p orbital energy in the boron and to the unusually strong s–s repulsion in BAs relative to most other Group-III–V compounds. We find unexpected valence-band offsets of BAs with respect to GaAs and …

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Intelligent Selection Tools, William A. Barrett, Eric N. Mortensen, L. Jack Reese Jun 2000

Intelligent Selection Tools, William A. Barrett, Eric N. Mortensen, L. Jack Reese

Faculty Publications

Intelligent Scissors and Intelligent Paint are complementary interactive image segmentation tools that allow a user to quickly and accurately select objects of interest. This demonstration provides a means for participants to experience the dynamic nature of these tools.

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Bounding Interval Rational Bézier Curves With Interval Polynomial Bézier Curves, Thomas W. Sederberg, Falai Chen, Wenping Lou Apr 2000

Bounding Interval Rational Bézier Curves With Interval Polynomial Bézier Curves, Thomas W. Sederberg, Falai Chen, Wenping Lou

Faculty Publications

In this paper, we put forward and study the problem of bounding an interval rational Bézier curve with an interval polynomial Bézier curve. We propose three different methods—Hybrid Method, Perturbation Method and Linear Programming Method to solve this problem. Examples are illustrated to compare the three different methods. The empirical results show that the Perturbation Method and the Linear Programming Method produce much tighter bounds than the Hybrid Method, though they are computationally several times more expensive.

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Average Energy Flow Of Optical Pulses In Dispersive Media, Scott Glasgow, Michael Ware, Justin Peatross Mar 2000

Average Energy Flow Of Optical Pulses In Dispersive Media, Scott Glasgow, Michael Ware, Justin Peatross

Faculty Publications

The arrival time of a light pulse at a point in space is defined using a time expectation integral over the Poynting vector. The delay between pulse arrival times at two distinct points is shown to consist of two parts: a spectral superposition of group delays (inverse of group velocity) and a delay due to spectral reshaping via absorption or amplification. The result provides a context wherein group velocity is always meaningful even for broad band pulses and when the group velocity is superluminal or negative. The result imposes luminality on sharply defined pulses.

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Designing Human-Centered Automation: Tradeoffs In Collision Avoidance System Design, Michael A. Goodrich, Erwin R. Boer Mar 2000

Designing Human-Centered Automation: Tradeoffs In Collision Avoidance System Design, Michael A. Goodrich, Erwin R. Boer

Faculty Publications

Technological advances have made plausible the design of automated systems that share responsibility with a human operator. The decision to use automation to assist or replace a human operator in safety-critical tasks must account for not only the technological capabilities of the sensor and control subsystems, but also the autonomy, capabilities, and preferences of the human operator. By their nature, such human-centered automation problems have multiple attributes: an attribute reflecting human goals and capabilities, and an attribute reflecting automation goals and capabilities. Although good theories exist that describe portions of human behavior generation, in the absence of a general theory …

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Learning Quantum Operators, Dan A. Ventura Mar 2000

Learning Quantum Operators, Dan A. Ventura

Faculty Publications

Consider the system Fx = w where F is unknown. We examine the possibility of learning the operator F inductively, drawing analogies with ideas from classical computational learning.

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Alternate Path Routing For Multicast, Daniel Zappala Mar 2000

Alternate Path Routing For Multicast, Daniel Zappala

Faculty Publications

Alternate path routing has been well-explored in telecommunication networks as a means of decreasing the call blocking rate and increasing network utility. However, aside from some work applying these concepts to unicast flows, alternate path routing has received little attention in the Internet community. We describe and evaluate an architecture for alternate path routing for multicast flows. For path installation, we design a receiver-oriented alternate path protocol and prove that it reconfigures multicast trees without introducing loops. For path computation, we propose a scalable local search heuristic that allows receivers to find alternate paths using only partial network information. We …

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Electronic Structure Of Cu1-Xnixrh2s4 And Curh2se4: Band-Structure Calculations, X-Ray Photoemission, And Fluorescence Measurements, Gus L. W. Hart, W. E. Pickett, E. Z. Kurmaev, M. Neumann, D. Hartmann, A. Moewes, D. L. Ederer, R. Endoh, K. Taniguchi, S. Nagata Feb 2000

Electronic Structure Of Cu1-Xnixrh2s4 And Curh2se4: Band-Structure Calculations, X-Ray Photoemission, And Fluorescence Measurements, Gus L. W. Hart, W. E. Pickett, E. Z. Kurmaev, M. Neumann, D. Hartmann, A. Moewes, D. L. Ederer, R. Endoh, K. Taniguchi, S. Nagata

Faculty Publications

The electronic structure of spinel-type Cu1-xNixRh2S4 (x=0.0, 0.1, 0.3, 0.5, 1.0) and CuRh2Se4 compounds has been studied by means of x-ray photoelectron (SPS) and fluorescent spectroscopy. Cu L3, Ni L3, S L2,3, and Se M2,3 x-ray emission spectra (XES) were measured near thresholds at Beamline 8.0 of the Lawrence Berkeley Laboratory's Advanced Light Source. XES measurements of the constituent atoms of these compounds, reduced to the same binding energy scale, are found to be in excellent agreement with XPS valence bands. The calculated XES spectra which include dipole matrix elements show that the partial density of states reproduce experimental spectra …

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Numerical Aspects Of Discrete And Continuum Hybrid Models In Cell Biology, J. C. Dallon Feb 2000

Numerical Aspects Of Discrete And Continuum Hybrid Models In Cell Biology, J. C. Dallon

Faculty Publications

In this paper we introduce a method of modeling which mixes continuum and discrete variables, and explain two models in cell biology that use this method. The first application deals with wound healing, more specifically the collagen alignment in scar tissue formation and the second models early aggregation in the cellular slime mold Dictyostelium discoideum. We solve these models using numerical techniques similar to the particle-in-cell method which requires that the discrete and continuum variables are interpolated one to the other. The implementational and numerical details are discussed in an informal and practical manner with particular attention given to the …

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An Extension Of Zermelo's Model For Ranking By Paired Comparisons, Christopher P. Grant, Gregory R. Conner Jan 2000

An Extension Of Zermelo's Model For Ranking By Paired Comparisons, Christopher P. Grant, Gregory R. Conner

Faculty Publications

In 1929, Zermelo proposed a probabilistic model for ranking by paired comparisons and showed that this model produces a unique ranking of the objects under consideration when the outcome matrix is irreducible. When the matrix is reducible, the model may yield only a partial ordering of the objects. In this paper, we analyse a natural extension of Zermelo's model resulting from a singular perturbation. We show that this extension produces a ranking for arbitrary (nonnegative) outcome matrices and retains several of the desirable properties of the original model. In addition, we discuss computational techniques and provide examples of their use.

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A Mathematical Model For Spatially Varying Extracellular Matrix, J. C. Dallon, J. A. Sherratt Jan 2000

A Mathematical Model For Spatially Varying Extracellular Matrix, J. C. Dallon, J. A. Sherratt

Faculty Publications

Orientation of extracellular matrix fibers in the skin is a key ingredient of tissue appearance and function, and differences in fiber alignment are one of the main distinctions between scar tissue and normal skin. In this paper, the authors develop a mathematical model for alignment of collagen fibers and the fibroblast cells that remodel them; the model extends previous work in which spatial variation was excluded. Numerical simulations of the model are presented, which show spatial variations in alignment over long transients, but with spatially uniform behavior in the long term. This is investigated further via asymptotic analysis, using the …

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Estimating Tessellation Parameter Intervals For Rational Curves And Surfaces, Thomas W. Sederberg, Jianmin Zheng Jan 2000

Estimating Tessellation Parameter Intervals For Rational Curves And Surfaces, Thomas W. Sederberg, Jianmin Zheng

Faculty Publications

This paper presents a method for determining a priori a constant parameter interval with which a rational curve or surface can be tessellated such that the deviation of the curve or surface from its piecewise linear approximation is within a specified tolerance. The parameter interval is estimated based on information about the second order derivatives in the homogeneous coordinates, instead of using affine coordinates directly. This new step size can be found with roughly the same amount of computation as the step size presented in [Cheng 1992], though it can be proven to always be larger than Cheng's step size. …

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