Applied Mathematics Commons^™

Fast Protein Structure Alignment, Yosi Shibberu, Allen Holder, Kyla Lutz

Mathematical Sciences Technical Reports (MSTR)

We address the problem of aligning the 3D structures of two proteins. Our pairwise comparisons are based on a new optimization model that is succinctly expressed in terms of linear transformations and highlights the problem’s intrinsic geometry. The optimization problem is approximately solved with a new polynomial time algorithm. The worst case analysis of the algorithm shows that the solution is bounded by a constant depending only on the data of the problem.

Enhanced Metric Regularity And Lipschitzian Properties Of Variational Systems, Francisco J. Aragón Artacho, Boris S. Mordukhovich

Mathematics Research Reports

This paper mainly concerns the study of a large class of variational systems governed by parametric generalized equations, which encompass variational and hemivariational inequalities, complementarity problems, first-order necessary optimality conditions, and other optimization-related models important for optimization theory and applications. An efficient approach to these issues has been developed in our preceding work [1] establishing qualitative and quantitative relationships between conventional metric regularity jsubregularity and Lipschitzian/calmness properties in the framework of parametric generalized equations in arbitrary Banach spaces. This paper provides, on one hand, significant extensions of the major results in [1] to new partial metric regularity and hemiregularity properties. …

Improved Automated Monitoring And New Analysis Algorithm For Circadean Phototaxis Rhythms In Chlamydomonas, Christa Gaskill, Jennifer Forbes-Stovall, Bruce Kessler, Mike Young, Claire A. Rinehart, Sigrid Jacobshagen

Mathematics Faculty Publications

Automated monitoring of circadian rhythms is an efficient way of gaining insight into oscillation parameters like period and phase for the underlying pacemaker of the circadian clock. Measurement of the circadian rhythm of phototaxis (swimming towards light) exhibited by the green alga Chlamydomonas reinhardtii has been automated by directing a narrow and dim light beam through a culture at regular intervals and determining the decrease in light transmittance due to the accumulation of cells in the beam. In this study, the monitoring process was optimized by constructing a new computercontrolled measuring machine that limits the test beam to wavelengths reported …

Integer Functions On The Cycle Space And Edges Of A Graph, Dan Slilaty

Mathematics and Statistics Faculty Publications

A directed graph has a natural Z-module homomorphism from the underlying graph’s cycle space to Z where the image of an oriented cycle is the number of forward edges minus the number of backward edges. Such a homomorphism preserves the parity of the length of a cycle and the image of a cycle is bounded by the length of that cycle. Pretzel and Youngs (SIAM J. Discrete Math. 3(4):544–553, 1990) showed that any Z-module homomorphism of a graph’s cycle space to Z that satisfies these two properties for all cycles must be such a map induced from an edge direction …

Higher Homotopy Operations And Cohomology, David Blanc, Mark W. Johnson, James M. Turner

University Faculty Publications and Creative Works

We explain how higher homotopy operations, defined topologically, may be identified under mild assumptions with (the last of) the Dwyer-Kan-Smith cohomological obstructions to rectifying homotopy-commutative diagrams. © 2010 ISOPP.

A Majorization Algorithm For Constrained Correlation Matrix Approximation, Daniel J. Simon, Jeff Abell

Electrical and Computer Engineering Faculty Publications

We desire to find a correlation matrix of a given rank that is as close as possible to an input matrix R, subject to the constraint that specified elements in must be zero. Our optimality criterion is the weighted Frobenius norm of the approximation error, and we use a constrained majorization algorithm to solve the problem. Although many correlation matrix approximation approaches have been proposed, this specific problem, with the rank specification and the constraints, has not been studied until now. We discuss solution feasibility, convergence, and computational effort. We also present several examples.

The Camassa-Holm Hierarchy And Soliton Perturbations, Georgi Grahovski, Rossen Ivanov

Conference papers

The theory of soliton perturbations is considered. The focus is on the usefulness of the so-called Generalised Fourier Transform (GFT). This is a method that involves expansions over the complete basis of “squared solutions” of the spectral problem, associated to the soliton equation. The Inverse Scattering Transform for the corresponding hierarchy of soliton equations can be viewed as a GFT where the expansions of the solutions have generalised Fourier coefficients given by the scattering data. The GFT provides a natural setting for the analysis of small perturbations to an integrable equation: starting from a purely soliton solution one can ’modify’ …

Interaction Of Excited States In Two-Species Bose-Einstein Condensates: A Case Study, Todd Kapitula, Kody J. H. Law, Panayotis G. Kevrekidis

University Faculty Publications and Creative Works

In this paper we consider the existence and spectral stability of excited states in two-species Bose-Einstein condensates in the case of a pancake magnetic trap. Each new excited state found in this paper is to leading order a linear combination of two one-species dipoles, each of which is a spectrally stable excited state for one-species condensates. The analysis is done via a Lyapunov-Schmidt reduction and is valid in the limit of weak nonlinear interactions. Some conclusions, however, can be made at this limit which remain true even when the interactions are large.

Singular Points Of Real Sextic Curves I, David A. Weinberg, Nicholas J. Willis

Faculty Publications - Department of Mathematics

A complete classification of the individual types of singular points is given for irreducible real sextic curves. This classification is derived by using the computer algebra system Maple. There are 191 types of singular points for real irreducible sextic curves. We clarify that the classification is based on computing just enough of the Puiseux expansion to separate the branches. A significant portion of the proof consists of a sequence of large symbolic computations that can be done nicely using Maple.

Parallelization Of The Wolff Single-Cluster Algorithm, Jevgenijs Kaupužs, Jānis Rimšāns, Roderick V.N. Melnik

Mathematics Faculty Publications

A parallel [open multiprocessing (OpenMP)] implementation of the Wolff single-cluster algorithm has been developed and tested for the three-dimensional (3D) Ising model. The developed procedure is generalizable to other lattice spin models and its effectiveness depends on the specific application at hand. The applicability of the developed methodology is discussed in the context of the applications, where a sophisticated shuffling scheme is used to generate pseudorandom numbers of high quality, and an iterative method is applied to find the critical temperature of the 3D Ising model with a great accuracy. For the lattice with linear size L=1024, we have …

Optimal Control And Feedback Design Of State-Constrained Parabolic Systems In Uncertainty Conditions, Boris S. Mordukhovich

Mathematics Research Reports

The paper concerns minimax control problems for linear multidimensional parabolic systems with distributed uncertain perturbations and control functions acting in the Dirichlet boundary conditions. The underlying parabolic control system is functioning under hard/pointwise constraints on control and state variables. The main goal is to design a feedback control regulator that ensures the required state performance and robust stability under any feasible perturbations and minimize an energy-type functional under the worst perturbations from the given area. We develop a constructive approach to the minimax control design of constrained parabolic systems that is based on certain characteristic features of the parabolic dynamics …

Two Soliton Interactions Of Bd.I Multicomponent Nls Equations And Their Gauge Equivalent, Vladimir Gerdjikov, Georgi Grahovski

Conference papers

Using the dressing Zakharov-Shabat method we re-derive the effects of the two-soliton interactions for the MNLS equations related to the BD.I-type symmetric spaces. Next we generalize this analysis for the Heisenberg ferromagnet type equations, gauge equivalent to MNLS.

Periodic Solutions Of Neutral Delay Integral Equations Of Advanced Type, Muhammad Islam, Nasrin Sultana, James Booth

Mathematics Faculty Publications

We study the existence of continuous periodic solutions of a neutral delay integral equation of advanced type. In the analysis we employ three fixed point theorems: Banach, Krasnosel'skii, and Krasnosel'skii-Schaefer. Krasnosel'skii-Schaefer fixed point theorem requires an a priori bound on all solutions. We employ a Liapunov type method to obtain such bound.

Basic Social Math: A Linguistic Upgrade For Decision Analysis And Social Dynamics Research., Jared Hanson

MA TESOL Collection

There are foundational errors in the mathematical frameworks currently used in Economic and Decision Theories. Recent systemic failures in the interdependent business and educational sectors also show that many practices based on these theories are unsustainable in the changing dynamics of the global economy. A new approach is needed in social science research and systems engineering. This paper examines how the new understandings of complex systems, the role of emotion in cognition, and the core dynamics of decision making can help us correct these errors and to create a general framework for systemic innovation. It argues for the development of …

Oscillatory And Monotonic Modes Of Long-Wave Marangoni Convection In A Thin Film, Sergey Shklyaev, Mikhail Khenner, Alexei Alabuzhev

Mathematics Faculty Publications

We study long-wave Marangoni convection in a layer heated from below. Using the scaling k=O Bi, where k is the wave number and Bi is the Biot number, we derive a set of amplitude equations. Analysis of this set shows presence of monotonic and oscillatory modes of instability. Oscillatory mode has not been previously found for such direction of heating. Studies of weakly nonlinear dynamics demonstrate that stable steady and oscillatory patterns can be found near the stability threshold.

Strong Orbit Equivalence And Residuality, Brett M. Werner

Electronic Theses and Dissertations

In this dissertation, we consider notions of equivalence between minimal Cantor systems, in particular strong orbit equivalence. By constructing the systems, we show that there exist two nonisomorphic substitution systems that are both Kakutani equivalent and strongly orbit equivalent. We go on to define a metric on a strong orbit equivalence class of minimal Cantor systems and prove several properties about the metric space. If the strong orbit equivalence class contains a finite rank system, we show that the set of finite rank systems is residual in the metric space. The last result shown is that set of systems with …

On The Accuracy Of Explicit Finite-Volume Schemes For Fluctuating Hydrodynamics, Aleksandar Donev, Eric Vanden-Eijnden, Alejandro Garcia, John B. Bell

Faculty Publications

This paper describes the development and analysis of finite-volume methods for the Landau–Lifshitz Navier–Stokes (LLNS) equations and related stochastic partial differential equations in fluid dynamics. The LLNS equations incorporate thermal fluctuations into macroscopic hydrodynamics by the addition of white noise fluxes whose magnitudes are set by a fluctuation-dissipation relation. Originally derived for equilibrium fluctuations, the LLNS equations have also been shown to be accurate for nonequilibrium systems. Previous studies of numerical methods for the LLNS equations focused primarily on measuring variances and correlations computed at equilibrium and for selected nonequilibrium flows. In this paper, we introduce a more systematic approach …

Oscillatory And Monotonic Modes Of Long-Wave Marangoni Convection In A Thin Film, Sergey Shklyaev, Mikhail Khenner, Alexei Alabuzhev

Mathematics Faculty Publications

We study long-wave Marangoni convection in a layer heated from below. Using the scaling k=O Bi, where k is the wave number and Bi is the Biot number, we derive a set of amplitude equations. Analysis of this set shows presence of monotonic and oscillatory modes of instability. Oscillatory mode has not been previously found for such direction of heating. Studies of weakly nonlinear dynamics demonstrate that stable steady and oscillatory patterns can be found near the stability threshold.

A Vision For Acms, James Bradley

ACMS Journal 2010-2011

This paper presents a vision for the mission of the ACMS. It considers some plausible connections between mathematics and theology as well as some big questions that Christian mathematicians might fruitfully explore. It examines the current cultural norms of the mathematics guild, why these are problematic for Christians, and some possible ways the ACMS might respond.

Spectral Methods For The Hamiltonian Systems, Nairat Kanyamee

Wayne State University Dissertations

We conduct a systematic comparison of spectral methods with some

symplectic methods in solving Hamiltonian dynamical systems. Our

main emphasis is on the non-linear problems. Numerical evidence has

demonstrated that the proposed spectral collocation method preserves

both energy and symplectic structure up to the machine error in each

time (large) step, and therefore has a better long time behavior.