Showing papers by "Purdue University published in 2005"

Quantum Transport: Atom to Transistor

Abstract: This book presents the conceptual framework underlying the atomistic theory of matter, emphasizing those aspects that relate to current flow. This includes some of the most advanced concepts of non-equilibrium quantum statistical mechanics. No prior acquaintance with quantum mechanics is assumed. Chapter 1 provides a description of quantum transport in elementary terms accessible to a beginner. The book then works its way from hydrogen to nanostructures, with extensive coverage of current flow. The final chapter summarizes the equations for quantum transport with illustrative examples showing how conductors evolve from the atomic to the ohmic regime as they get larger. Many numerical examples are used to provide concrete illustrations and the corresponding Matlab codes can be downloaded from the web. Videostreamed lectures, keyed to specific sections of the book, are also available through the web. This book is primarily aimed at senior and graduate students.

Teacher Pedagogical Beliefs: The Final Frontier in Our Quest for Technology Integration?.

Abstract: Although the conditions for successful technology integration finally appear to be in place, including ready access to technology, increased training for teachers, and a favorable policy environment, high-level technology use is still surprisingly low. This suggests that additional barriers, specifically related to teachers’ pedagogical beliefs, may be at work. Previous researchers have noted the influence of teachers’ beliefs on classroom instruction specifically in math, reading, and science, yet little research has been done to establish a similar link to teachers’ classroom uses of technology. In this article, I argue for the importance of such research and present a conceptual overview of teacher pedagogical beliefs as a vital first step. After defining and describing the nature of teacher beliefs, including how they are likely to impact teachers’ classroom practice, I describe important implications for teacher professional development and offer suggestions for future research.

The Variety and Quality of a Nation's Exports

Abstract: Large economies export more in absolute terms than do small economies. We use data on shipments by 126 exporting countries to 59 importing countries in 5,000 product categories to answer the question: How? Do big economies export larger quantities of each good (the intensive margin), a wider set of goods (the extensive margin), or higher-quality goods? We find that the extensive margin accounts for around 60 percent of the greater exports of larger economies. Within categories, richer countries export higher quantities at modestly higher prices. We compare these findings to some workhorse trade models. Models with Armington national product differentiation have no extensive margin, and incorrectly predict lower prices for the exports of larger economies. Models with Krugman firm-level product differentiation do feature a prominent extensive margin, but overpredict the rate at which variety responds to exporter size. Models with quality differentiation, meanwhile, can match the price facts. Finally, models with fixed costs of exporting to a given market might explain the tendency of larger economies to export a given product to more countries.

High-Order Collocation Methods for Differential Equations with Random Inputs

Abstract: Recently there has been a growing interest in designing efficient methods for the solution of ordinary/partial differential equations with random inputs. To this end, stochastic Galerkin methods appear to be superior to other nonsampling methods and, in many cases, to several sampling methods. However, when the governing equations take complicated forms, numerical implementations of stochastic Galerkin methods can become nontrivial and care is needed to design robust and efficient solvers for the resulting equations. On the other hand, the traditional sampling methods, e.g., Monte Carlo methods, are straightforward to implement, but they do not offer convergence as fast as stochastic Galerkin methods. In this paper, a high-order stochastic collocation approach is proposed. Similar to stochastic Galerkin methods, the collocation methods take advantage of an assumption of smoothness of the solution in random space to achieve fast convergence. However, the numerical implementation of stochastic collocation is trivial, as it requires only repetitive runs of an existing deterministic solver, similar to Monte Carlo methods. The computational cost of the collocation methods depends on the choice of the collocation points, and we present several feasible constructions. One particular choice, based on sparse grids, depends weakly on the dimensionality of the random space and is more suitable for highly accurate computations of practical applications with large dimensional random inputs. Numerical examples are presented to demonstrate the accuracy and efficiency of the stochastic collocation methods.

Phosphate Acquisition

Abstract: Phosphate (Pi) is considered to be one of the least available plant nutrients in the soil. High-affinity Pi transporters are generally accepted as entry points for Pi in the roots. The physiological, genetic, molecular and biochemical analysis of phosphate starvation response mechanisms highlight the ability of plants to adapt and thrive under phosphate limiting conditions. These responses help them enhance the availability of Pi, increase its uptake and improve the use-efficiency of Pi within a plant. Enhanced ability to acquire Pi appears to be regulated at the level of transcription of high-affinity phosphate transporters. These transporters are encoded by a family of small number of genes having characteristic tissue and organ associated expression patterns. Many of them are strongly induced during phosphate deficiency thus providing plants with enhanced ability to acquire and transfer phosphate. In addition, plants also activate biochemical mechanisms that could lead to increased acquisition of phosphate from both inorganic and organic phosphorus sources in the soil. Furthermore, altered root morphology and mycorrhizal symbiosis further enhance the ability of plants to acquire Pi. Interestingly most of these responses appear to be coordinated by changes in cellular phosphate levels. It is becoming apparent that phosphate acquisition and utilization are associated with activation or inactivation of a host of genes in plants. In this article we describe molecular, biochemical and physiological factors associated with phosphate acquisition by plants.

Negative index of refraction in optical metamaterials.

Abstract: A double-periodic array of pairs of parallel gold nanorods is shown to have a negative refractive index in the optical range. Such behavior results from the plasmon resonance in the pairs of nanorods for both the electric and the magnetic components of light. The refractive index is retrieved from direct phase and amplitude measurements for transmission and reflection, which are all in excellent agreement with simulations. Both experiments and simulations demonstrate that a negative refractive index n???0.3 is achieved at the optical communication wavelength of 1.5??m using the array of nanorods. The retrieved refractive index critically depends on the phase of the transmitted wave, which emphasizes the importance of phase measurements in finding n?.

The genome sequence of the rice blast fungus Magnaporthe grisea

Abstract: Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.

The Orbitrap: a new mass spectrometer

Abstract: Research areas such as proteomics and metabolomics are driving the demand for mass spectrometers that have high performance but modest power requirements, size, and cost. This paper describes such an instrument, the Orbitrap, based on a new type of mass analyzer invented by Makarov. The Orbitrap operates by radially trapping ions about a central spindle electrode. An outer barrel-like electrode is coaxial with the inner spindlelike electrode and mass/charge values are measured from the frequency of harmonic ion oscillations, along the axis of the electric field, undergone by the orbitally trapped ions. This axial frequency is independent of the energy and spatial spread of the ions. Ion frequencies are measured non-destructively by acquisition of time-domain image current transients, with subsequent fast Fourier transforms (FFTs) being used to obtain the mass spectra. In addition to describing the Orbitrap mass analyzer, this paper also describes a complete Orbitrap-based mass spectrometer, equipped with an electrospray ionization source (ESI). Ions are transferred from the ESI source through three stages of differential pumping using RF guide quadrupoles. The third quadrupole, pressurized to less than 10(-3) Torr with collision gas, acts as an ion accumulator; ion/neutral collisions slow the ions and cause them to pool in an axial potential well at the end of the quadrupole. Ion bunches are injected from this pool into the Orbitrap analyzer for mass analysis. The ion injection process is described in a simplified way, including a description of electrodynamic squeezing, field compensation for the effects of the ion injection slit, and criteria for orbital stability. Features of the Orbitrap at its present stage of development include high mass resolution (up to 150,000), large space charge capacity, high mass accuracy (2-5 ppm), a mass/charge range of at least 6000, and dynamic range greater than 10(3). Applications based on electrospray ionization are described, including characterization of transition-metal complexes, oligosaccharides, peptides, and proteins. Use is also made of the high-resolution capabilities of the Orbitrap to confirm the presence of metaclusters of serine octamers in ESI mass spectra and to perform H/D exchange experiments on these ions in the storage quadrupole.

A meta-analysis of the relationship between organizational citizenship behavior and counterproductive work behavior.

Abstract: Job performance is increasingly being seen to encompass constructs such as organizational citizenship behavior (OCB) and counterproductive work behavior (CWB). To clarify the OCB-CWB relationship, a meta-analysis was conducted. Results indicate a modest negative relationship (p = -0.32). The relationship strength did not increase appreciably when the target of the behavior (the organization vs. other employees) was the same. Moreover, OCB and CWB exhibited somewhat distinct patterns of relationships with antecedents. The OCB-CWB relationship was moderated by the source of the ratings, the presence of antithetical items, and the type of response options. An employee-centric perspective is proposed whereby both OCB and CWB are perceived as adaptive behavior. Implications for organizations are discussed.

The axonal transport of mitochondria

Abstract: Organelle transport is vital for the development and maintenance of axons, in which the distances between sites of organelle biogenesis, function, and recycling or degradation can be vast. Movement of mitochondria in axons can serve as a general model for how all organelles move: mitochondria are easy to identify, they move along both microtubule and actin tracks, they pause and change direction, and their transport is modulated in response to physiological signals. However, they can be distinguished from other axonal organelles by the complexity of their movement and their unique functions in aerobic metabolism, calcium homeostasis and cell death. Mitochondria are thus of special interest in relating defects in axonal transport to neuropathies and degenerative diseases of the nervous system. Studies of mitochondrial transport in axons are beginning to illuminate fundamental aspects of the distribution mechanism. They use motors of one or more kinesin families, along with cytoplasmic dynein, to translocate along microtubules, and bidirectional movement may be coordinated through interaction between dynein and kinesin-1. Translocation along actin filaments is probably driven by myosin V, but the protein(s) that mediate docking with actin filaments remain unknown. Signaling through the PI 3-kinase pathway has been implicated in regulation of mitochondrial movement and docking in the axon, and additional mitochondrial linker and regulatory proteins, such as Milton and Miro, have recently been described.

A polyhedral branch-and-cut approach to global optimization

Abstract: A variety of nonlinear, including semidefinite, relaxations have been developed in recent years for nonconvex optimization problems. Their potential can be realized only if they can be solved with sufficient speed and reliability. Unfortunately, state-of-the-art nonlinear programming codes are significantly slower and numerically unstable compared to linear programming software.In this paper, we facilitate the reliable use of nonlinear convex relaxations in global optimization via a polyhedral branch-and-cut approach. Our algorithm exploits convexity, either identified automatically or supplied through a suitable modeling language construct, in order to generate polyhedral cutting planes and relaxations for multivariate nonconvex problems. We prove that, if the convexity of a univariate or multivariate function is apparent by decomposing it into convex subexpressions, our relaxation constructor automatically exploits this convexity in a manner that is much superior to developing polyhedral outer approximators for the original function. The convexity of functional expressions that are composed to form nonconvex expressions is also automatically exploited.Root-node relaxations are computed for 87 problems from globallib and minlplib, and detailed computational results are presented for globally solving 26 of these problems with BARON 7.2, which implements the proposed techniques. The use of cutting planes for these problems reduces root-node relaxation gaps by up to 100% and expedites the solution process, often by several orders of magnitude.

A structural perspective of the flavivirus life cycle

Abstract: Dengue, Japanese encephalitis, West Nile and yellow fever belong to the Flavivirus genus, which is a member of the Flaviviridae family. They are human pathogens that cause large epidemics and tens of thousands of deaths annually in many parts of the world. The structural organization of these viruses and their associated structural proteins has provided insight into the molecular transitions that occur during the viral life cycle, such as assembly, budding, maturation and fusion. This review focuses mainly on structural studies of dengue virus.

Log-concave probability and its applications

Abstract: In many applications, assumptions about the log-concavity of a probability distribution allow just enough special structure to yield a workable theory. This paper catalogs a series of theorems relating log-concavity and/or log-convexity of probability density functions, distribution functions, reliability functions, and their integrals. We list a large number of commonly-used probability distributions and report the log-concavity or log-convexity of their density functions and their integrals. We also discuss a variety of applications of log-concavity that have appeared in the literature.

In vitro and in vivo two-photon luminescence imaging of single gold nanorods

Abstract: Gold nanorods excited at 830 nm on a far-field laser-scanning microscope produced strong two-photon luminescence (TPL) intensities, with a cos4 dependence on the incident polarization. The TPL excitation spectrum can be superimposed onto the longitudinal plasmon band, indicating a plasmon-enhanced two-photon absorption cross section. The TPL signal from a single nanorod is 58 times that of the two-photon fluorescence signal from a single rhodamine molecule. The application of gold nanorods as TPL imaging agents is demonstrated by in vivo imaging of single nanorods flowing in mouse ear blood vessels.

Limited feedback unitary precoding for spatial multiplexing systems

Abstract: Multiple-input multiple-output (MIMO) wireless systems use antenna arrays at both the transmitter and receiver to provide communication links with substantial diversity and capacity. Spatial multiplexing is a common space-time modulation technique for MIMO communication systems where independent information streams are sent over different transmit antennas. Unfortunately, spatial multiplexing is sensitive to ill-conditioning of the channel matrix. Precoding can improve the resilience of spatial multiplexing at the expense of full channel knowledge at the transmitter-which is often not realistic. This correspondence proposes a quantized precoding system where the optimal precoder is chosen from a finite codebook known to both receiver and transmitter. The index of the optimal precoder is conveyed from the receiver to the transmitter over a low-delay feedback link. Criteria are presented for selecting the optimal precoding matrix based on the error rate and mutual information for different receiver designs. Codebook design criteria are proposed for each selection criterion by minimizing a bound on the average distortion assuming a Rayleigh-fading matrix channel. The design criteria are shown to be equivalent to packing subspaces in the Grassmann manifold using the projection two-norm and Fubini-Study distances. Simulation results show that the proposed system outperforms antenna subset selection and performs close to optimal unitary precoding with a minimal amount of feedback.

Implementing false discovery rate control: increasing your power

Abstract: Popular procedures to control the chance of making type I errors when multiple statistical tests are performed come at a high cost: a reduction in power. As the number of tests increases, power for an individual test may become unacceptably low. This is a consequence of minimizing the chance of making even a single type I error, which is the aim of, for instance, the Bonferroni and sequential Bonferroni procedures. An alternative approach, control of the false discovery rate (FDR), has recently been advocated for ecological studies. This approach aims at controlling the proportion of significant results that are in fact type I errors. Keeping the proportion of type I errors low among all significant results is a sensible, powerful, and easy-to-interpret way of addressing the multiple testing issue. To encourage practical use of the approach, in this note we illustrate how the proposed procedure works, we compare it to more traditional methods that control the familywise error rate, and we discuss some recent useful developments in FDR control.

Application of Multicriteria Decision Analysis in Environmental Decision Making

Abstract: Decision making in environmental projects can be complex and seemingly intractable, principally because of the inherent trade-offs between sociopolitical, environmental, ecological, and economic factors. The selection of appropriate remedial and abatement strategies for contaminated sites, land use planning, and regulatory processes often involves multiple additional criteria such as the distribution of costs and benefits, environmental impacts for different populations, safety, ecological risk, or human values. Some of these criteria cannot be easily condensed into a monetary value, partly because environmental concerns often involve ethical and moral principles that may not be related to any economic use or value. Furthermore, even if it were possible to aggregate multiple criteria rankings into a common unit, this approach would not always be desirable because the ability to track conflicting stakeholder preferences may be lost in the process. Consequently, selecting from among many different alternatives often involves making trade-offs that fail to satisfy 1 or more stakeholder groups. Nevertheless, considerable research in the area of multicriteria decision analysis (MCDA) has made available practical methods for applying scientific decision theoretical approaches to complex multicriteria problems. This paper presents a review of the available literature and provides recommendations for applying MCDA techniques in environmental projects. A generalized framework for decision analysis is proposed to highlight the fundamental ingredients for more structured and tractable environmental decision making.

An Episodic Process Model of Affective Influences on Performance

Abstract: In this article, the authors present a model linking immediate affective experiences to within-person performance. First, the authors define a time structure for performance (the performance episode) that is commensurate with the dynamic nature of affect. Next, the authors examine the core cognitive and regulatory processes that determine performance for 1 person during any particular episode. Third, the authors describe how various emotions and moods influence the intermediary performance processes, thereby affecting performance. In the final section of the article, the authors discuss limitations, future research directions, and practical implications for their episodic process model of affect and performance.

Ambient mass spectrometry using desorption electrospray ionization (DESI): instrumentation, mechanisms and applications in forensics, chemistry, and biology

Abstract: Analytical characteristics of DESI are summarized. Examples of applications to small and large molecules, to in situ analysis, and to high-throughput analyses are presented. Evidence is provided for both a heterogeneous charge-transfer mechanism and a droplet pick-up mechanism of ionization. The speed, lack of the need for sample preparation, selectivity, and sensitivity of DESI are all demonstrated and discussed. Instrumentation is also discussed. Forensic applications as well as emerging areas of application including tissue imaging are given emphasis.

Polarimetric observations of 15 active galactic nuclei at high frequencies: jet kinematics from bimonthly monitoring with the very long baseline array

Abstract: We present total and polarized intensity images of 15 active galactic nuclei obtained with the Very Long Baseline Array at 7 mm wavelength at 17 epochs from 1998 March to 2001 April. At some epochs the images are accompanied by nearly simultaneous polarization measurements at 3 mm, 1.35/0.85 mm, and optical wavelengths. Here we analyze the 7 mm images to define the properties of the jets of two radio galaxies, five BL Lac objects, and eight quasars on angular scales 0.1 mas. We determine the apparent velocities of 106 features in the jets. For many of the features we derive Doppler factors using a new method based on a comparison of the timescale of decline in flux density with the light-travel time across the emitting region. This allows us to estimate the Lorentz factors (Γ), intrinsic brightness temperatures, and viewing angles of 73 superluminal knots, as well as the opening angle of the jet for each source. The Lorentz factors of the jet flows in the different blazars range from Γ ~ 5 to 40 with the majority of the quasar components having Γ ~ 16–18, while the values in the BL Lac objects are more uniformly distributed. The brightest knots in the quasars have the highest apparent speeds, while the more slowly moving components are pronounced in the BL Lac objects. The quasars in our sample have similar opening angles and marginally smaller viewing angles than the BL Lacs. The two radio galaxies have lower Lorentz factors and wider viewing angles than the blazars. Opening angle and Lorentz factor are inversely proportional, as predicted by gasdynamical models. The brightness temperature drops more abruptly with distance from the core in the BL Lac objects than in the quasars and radio galaxies, perhaps owing to stronger magnetic fields in the former resulting in more severe synchrotron losses of the highest energy electrons. In nine sources we detect statistically meaningful deviations from ballistic motion, with the majority of components accelerating with distance from the core. In six sources we identify jet features with characteristics of trailing shocks that form behind the primary strong perturbations in jet simulations. The apparent speeds of these components increase with distance from the core, suggestive of acceleration of the underlying jet.

Technical aspects of immunohistochemistry.

Abstract: Immunohistochemistry is an integral technique in many veterinary laboratories for diagnostic and research purposes. In the last decade, the ability to detect antigens (Ags) in tissue sections has improved dramatically, mainly by countering the deleterious effects of formaldehyde with antigen retrieval (AR) and increasing sensitivity of the detection systems. In this review, I address these topics and provide an overview of technical aspects of immunohistochemistry, including those related to antibodies (Abs) and Ags, fixation, AR, detection methods, background, and troubleshooting. Microarray technology and the use of rabbit monoclonal Abs in immunohistochemistry are also discussed.

Quantum Theory of the Electron Liquid

Abstract: Modern electronic devices and novel materials often derive their extraordinary properties from the intriguing, complex behavior of large numbers of electrons forming what is known as an electron liquid. This book provides an in-depth introduction to the physics of the interacting electron liquid in a broad variety of systems, including metals, semiconductors, artificial nano-structures, atoms and molecules. One, two and three dimensional systems are treated separately and in parallel. Different phases of the electron liquid, from the Landau Fermi liquid to the Wigner crystal, from the Luttinger liquid to the quantum Hall liquid are extensively discussed. Both static and time-dependent density functional theory are presented in detail. Although the emphasis is on the development of the basic physical ideas and on a critical discussion of the most useful approximations, the formal derivation of the results is highly detailed and based on the simplest, most direct methods.

Residual-life distributions from component degradation signals: A Bayesian approach

Abstract: Real-time condition monitoring is becoming an important tool in maintenance decision-making. Condition monitoring is the process of collecting real-time sensor information from a functioning device in order to reason about the health of the device. To make effective use of condition information, it is useful to characterize a device degradation signal, a quantity computed from condition information that captures the current state of the device and provides information on how that condition is likely to evolve in the future. If properly modeled, the degradation signal can be used to compute a residual-life distribution for the device being monitored, which can then be used in decision models. In this work, we develop Bayesian updating methods that use real-time condition monitoring information to update the stochastic parameters of exponential degradation models. We use these degradation models to develop a closed-form residual-life distribution for the monitored device. Finally, we apply these degradation...

Earthquake triggering by static, dynamic, and postseismic stress transfer

Abstract: ▪ Abstract Earthquake triggering is the process by which stress changes associated with an earthquake can induce or retard seismic activity in the surrounding region or trigger other earthquakes at great distances. Calculations of static Coulomb stress changes associated with earthquake slip have proven to be a powerful tool in explaining many seismic observations, including aftershock distributions, earthquake sequences, and the quiescence of broad, normally active regions following large earthquakes. Delayed earthquake triggering, which can range from seconds to decades, can be explained by a variety of time-dependent stress transfer mechanisms, such as viscous relaxation, poroelastic rebound, or afterslip, or by reductions in fault friction, such as predicted by rate and state constitutive relations. Rapid remote triggering of earthquakes at great distances (from several fault lengths to 1000s of km) is best explained by the passage of transient (dynamic) seismic waves, which either immediately induce ...