Physical Sciences and Mathematics Commons^™

Structure And Dynamics Of Metalloproteins In Live Cells, Jeremy D. Cook, James E. Penner-Hahn, Timothy L. Stemmler

Biochemistry and Molecular Biology Faculty Publications

X-ray absorption spectroscopy (XAS) has emerged as one of the premier tools for investigating the structure and dynamic properties of metals in cells and in metal containing biomolecules. Utilizing the high flux and broad energy range of X-rays supplied by synchrotron light sources, one can selectively excite core electronic transitions in each metal. Spectroscopic signals from these electronic transitions can be used to dissect the chemical architecture of metals in cells, in cellular components and in biomolecules at varying degrees of structural resolution. With the development of ever-brighter X-ray sources, X-ray methods have grown into applications that can be utilized …

Robust Stability And Optimality Conditions For Parametric Infinite And Semi-Infinite Programs, M J. Cánovas, M A. Lopez, Boris S. Mordukhovich, J Parra

Mathematics Research Reports

This paper primarily concerns the study of parametric problems of infinite and semi-infinite programming, where functional constraints are given by systems of infinitely many linear inequalities indexed by an arbitrary set T, where decision variables run over Banach (infinite programming) or finite-dimensional (semi-infinite case) spaces, and where objectives are generally described by nonsmooth and nonconvex cost functions. The parameter space of admissible perturbations in such problems is formed by all bounded functions on T equipped with the standard supremum norm. Unless the index set T is finite, this space is intrinsically infinite-dimensional (nonreflexive and nonseparable) of the l(infinity)-type. By using …

Metric Regularity Of Mappings And Generalized Normals To Set Images, Boris S. Mordukhovich, Nguyen Mau Nam, Bingwu Wang

Mathematics Research Reports

The primary goal of this paper is to study some notions of normals to nonconvex sets in finite-dimensional and infinite-dimensional spaces and their images under single-valued and set-valued mappings. The main motivation for our study comes from variational analysis and optimization, where the problems under consideration play a crucial role in many important aspects of generalized differential calculus and applications. Our major results provide precise equality formulas (sometimes just efficient upper estimates) allowing us to compute generalized normals in various senses to direct and inverse images of nonconvex sets under single-valued and set-valued mappings between Banach spaces. The main tools …

Cooling Of The Crust In The Neutron Star Low-Mass X-Ray Binary Mxb 1659-29, Edward M. Cackett, Rudy Wijnands, Jon M. Miller, Edward F. Brown, Nathalie Degenaar

Physics and Astronomy Faculty Research Publications

In quasi-persistent neutron star transients, long outbursts cause the neutron star crust to be heated out of thermal equilibrium with the rest of the star. During quiescence, the crust then cools back down. Such crustal cooling has been observed in two quasi-persistent sources: KS 1731-260 and MXB 1659-29. Here we present an additional Chandra observation of MXB 1659-29 in quiescence, which extends the baseline of monitoring to 6.6 yr after the end of the outburst. This new observation strongly suggests that the crust has thermally relaxed, with the temperature remaining consistent over 1000 days. Fitting the temperature cooling curve with …

Optimization Of Delay-Differential Inclusions Of Infinite Dimensions, Boris S. Mordukhovich, Dong Wang, Lianwen Wang

Mathematics Research Reports

No abstract provided.

Limiting Subgradients Of Minimal Time Functions In Banach Spaces, Boris S. Mordukhovich, Nguyen Mau Nam

Mathematics Research Reports

The paper mostly concerns the study of generalized differential properties of the so-called minimal time functions associated, in particular, with constant dynamics and arbitrary closed target sets in control theory. Functions of this type play a significant role in many aspects of optimization, control theory: and Hamilton-Jacobi partial differential equations. We pay the main attention to computing and estimating limiting subgradients of the minimal value functions and to deriving the corresponding relations for Frechet type epsilon-subgradients in arbitrary Banach spaces.

Necessary Conditions For Nonsmooth Optimization Problems With Operator Constraints In Metric Spaces, Boris S. Mordukhovich, Libin Mou

Mathematics Research Reports

This paper concerns nonsmooth optimization problems involving operator constraints given by mappings on complete metric spaces with values in nonconvcx subsets of Banach spaces. We derive general first-order necessary optimality conditions for such problems expressed via certain constructions of generalized derivatives for mappings on metric spaces and axiomatically defined subdifferentials for the distance function to nonconvex sets in Banach spaces. Our proofs arc based on variational principles and perturbation/approximation techniques of modern variational analysis. The general necessary conditions obtained are specified in the case of optimization problems with operator constraints dDScribcd by mappings taking values in approximately convex subsets of …

Initial Measurements Of Black Hole Spin In Gx 339-4 From Suzaku Spectroscopy, J. M. Miller, C. S. Reynolds, A. C. Fabian, E. M. Cackett, G. Miniutti, J. Raymond, D. Steeghs, R. Reis, J. Homan

Physics and Astronomy Faculty Research Publications

We report on a deep Suzaku observation of the stellar-mass black hole GX 339-4 in outburst. A clear, strong, relativistically shaped iron emission line from the inner accretion disk is observed. The broadband disk reflection spectrum revealed is one of the most sensitive yet obtained from an accreting black hole. We fit the Suzaku spectra with a physically motivated disk reflection model, blurred by a new relativistic line function in which the black hole spin parameter is a variable. This procedure yielded a black hole spin parameter of a=0.89+/-0.04. Joint modeling of these Suzaku spectra and prior XMM-Newton spectra obtained …

A New Global Model For P Wave Speed Variations In Earth's Mantle, Chang Li, Robert D. Van Der Hilst, E. Robert Engdahl, Scott Burdick

Environmental Science and Geology Faculty Research Publications

We document our tomographic method and present a new global model of three-dimensional (3-D) variations in mantle P wave velocity. The model is parameterized by means of rectangular cells in latitude, longitude, and radius, the size of which adapts to sampling density by short-period (1 Hz) data. The largest single data source is ISC/NEIC data reprocessed by Engdahl and coworkers, from which we use routinely picked, short-period P, Pg, Pn, pP, and pwP data (for earthquakes during the period 1964∼2007). To improve the resolution in the lowermost and uppermost mantle, we use differential times of core phases (PKPAB − PKPDF, …

Investigating The Nature Of Absorption Lines In The Chandra X-Ray Spectra Of The Neutron Star Binary 4u 1820-30, E. M. Cackett, J. M. Miller, J. Raymond, J. Homan, M. Van Der Klis, M. Méndez, D. Steeghs, R. Wijnands

Physics and Astronomy Faculty Research Publications

We use four Chandra gratings spectra of the neutron star low-mass X-ray binary 4U 1820-30 to better understand the nature of certain X-ray absorption lines in X-ray binaries, including the Ne II, Ne III, Ne IX, O VII, and O VIII lines. The equivalent widths of the lines are generally consistent between the observations, as expected if these lines originate in the hot interstellar medium. No evidence was found that the lines were blueshifted, again supporting the interstellar medium origin, although this may be due to poor statistics. There is apparent variability in the O VIII Lyα line equivalent width …

The Influence Of Metal Exposure History And Ultraviolet-B Radiation On Benthic Communities In Colorado Rocky Mountain Streams, Robert E. Zuellig, Donna R. Kashian, Marjorie L. Brooks, Peter M. Kiffney, William H. Clements

Environmental Science and Geology Faculty Research Publications

Interest in understanding the influence of ultraviolet-B (UVB; 280–320 nm) radiation in aquatic ecosystems has increased since the early 1990s. Pollution from historic mining operations coupled with physicochemical characteristics of Rocky Mountain streams that increase exposure of benthic communities to UVB provided an opportunity to examine how UVB interacted with heavy metal contamination to structure stream communities. We integrated a series of UVB addition experiments done in stream microcosms with a large-scale UVB shading experiment to test the hypothesis that effects of UVB were greater on benthic communities from metal-polluted streams than from reference streams. Microcosm experiments involved short-term exposure …

Failure Of Metric Regularity For Major Classes Of Variational Systems, Boris S. Mordukhovich

Mathematics Research Reports

The paper is devoted to the study of metric regularity, which is a remarkable property of set-valued mappings playing an important role in many aspects of nonlinear analysis and its applications. We pay the main attention to metric regularity of the so- called parametric variational systems that contain, in particular, various classes of parameterized/perturbed variational and hemivariational inequalities, complementarity systems, sets of optimal solutions and corresponding Lagrange multipliers in problems of parametric optimization and equilibria, etc. Based on the advanced machinery of generalized differentiation1 we surprisingly reveal that metric regularity fails for certain major classes of parametric variational systems, which …

Relativistic Iron Emission Lines In Neutron Star Low-Mass X-Ray Binaries As Probes Of Neutron Star Radii, Edward M. Cackett, Jon M. Miller, Sudip Bhattacharyya, Jonathan E. Grindlay, Jeroen Homan, Michiel Van Der Klis, M. Coleman Miller, Tod E. Strohmayer, Rudy Wijnands

Physics and Astronomy Faculty Research Publications

Using Suzaku observations of three neutron star low-mass X-ray binaries (Ser X-1, 4U 1820-30, and GX 349+2) we have found broad, asymmetric, relativistic Fe K emission lines in all three objects. These Fe K lines can be well fit by a model for lines from a relativistic accretion disk (``diskline''), allowing a measurement of the inner radius of the accretion disk and hence an upper limit on the neutron star radius. These upper limits correspond to 14.5-16.5 km for a 1.4 M_solar neutron star. The inner disk radii that we measure with Fe K lines are in good agreement …

Cross Sections For 11–14-Ev E-H2 Resonant Collisions: Vibrational Excitation, R Celiberto, R. K. Janev, J. M. Wadehra, A Laricchiuta

Physics and Astronomy Faculty Research Publications

Resonant vibrational excitation (RVE) cross sections have been calculated for the electron-H₂ molecule collisions in the energy range 11–14 eV involving the ²Σ⁺_g excited electronic state of the molecular hydrogen ion H₂⁻. This state, whose threshold is located around 14 eV, gives rise to the so-called series a of the observed peaks in electron-impact differential cross-section measurements. The calculations have been performed within the local complex potential approximation by using the available theoretical potential energy and width for the ²Σ⁺_g resonant state. The cross sections for all v_{i …}

Optimal Control Of Delay-Differential Inclusions With Multivalued Initial Conditions In Infinite Dimensions, Boris S. Mordukhovich, Dong Wang, Lianwen Wang

Mathematics Research Reports

This paper is devoted to the study of a general class of optimal control problems described by delay-differential inclusions with infinite-dimensional state spaces, endpoints constraints, and multivalued initial conditions. To the best of our knowledge, problems of this type have not been considered in the literature, except some particular cases when either the state space is finite-dimensional or there is no delay in the dynamics. We develop the method of discrete approximations to derive necessary optimality conditions in the extended Euler-Lagrange form by using advanced tools of variational analysis and generalized differentiation in infinite dimensions. This method consists of the …

Stochastic Differential Equations With Jumps, Jose L. Menaldi

Mathematics Faculty Research Publications

Part I Stochastic Processes with Jumps Chapters: Probability Spaces, Semigroup Theory - Part II Stochastic Differential Equations with Jumps Chapters: Stochastic Calculus, Stochastic Differential Equations - Part III Reflected SDE with Jumps Chapters: Stochastic Differential Equations II, Stochastic Differential Equations III.

Comment: This is last version from 2014-01-07. *This Initial version 15/May/2008 was corrected and augmented to produce the others 5 volumes.

Droid: The Drosophila Interactions Database, A Comprehensive Resource For Annotated Gene And Protein Interactions, Jingkai Yu, Svetlana Pacifico, Guozhen Liu, Russell L. Finley Jr

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Charting the interactions among genes and among their protein products is essential for understanding biological systems. A flood of interaction data is emerging from high throughput technologies, computational approaches, and literature mining methods. Quick and efficient access to this data has become a critical issue for biologists. Several excellent multi-organism databases for gene and protein interactions are available, yet most of these have understandable difficulty maintaining comprehensive information for any one organism. No single database, for example, includes all available interactions, integrated gene expression data, and comprehensive and searchable gene information for the important model organism, Drosophila melanogaster. …

Mcm-Test: A Fuzzy-Set-Theory-Based Approach To Differential Analysis Of Gene Pathways, Lily R. Liang, Vinay Mandal, Yi Lu, Deepak Kumar

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Gene pathway can be defined as a group of genes that interact with each other to perform some biological processes. Along with the efforts to identify the individual genes that play vital roles in a particular disease, there is a growing interest in identifying the roles of gene pathways in such diseases.

Results

This paper proposes an innovative fuzzy-set-theory-based approach, Multi-dimensional Cluster Misclassification test (MCM-test), to measure the significance of gene pathways in a particular disease. Experiments have been conducted on both synthetic data and real world data. Results on published diabetes gene expression dataset and a list …