Recovering hidden Bloch character: Unfolding Electrons, Phonons, and Slabs

For a quantum state, or classical harmonic normal mode, of a system of spatial periodicity "R", Bloch character is encoded in a wavevector "K". One can ask whether this state has partial Bloch character "k" corresponding to a finer scale of periodicity "r". Answering this is called "unfolding." A theorem is proven that yields a mathematically clear prescription for unfolding, by examining translational properties of the state, requiring no "reference states" or basis functions with the finer periodicity (r,k). A question then arises, how should one assign partial Bloch character to a state of a finite system? A slab, finite in one direction, is used as the example. Perpendicular components k_z of the wavevector are not explicitly defined, but may be hidden in the state (and eigenvector |i>.) A prescription for extracting k_z is offered and tested. An idealized silicon (111) surface is used as the example. Slab-unfolding reveals surface-localized states and resonances which were not evident from dispersion curves alone.Comment: 11 pages, 7 figure

Safe Computing

So-called worms, viruses, and Trojan horses that attack computer systems are defined. The vehicle that allows these attacks to occur, namely, the open computer internetwork, is examined. The problem of providing protection against attack in an internetwork environment is discussed. The need for professional responsibility on the part of the scientific and engineering community in enforcing strong ethical practices and neither tolerating nor condoning such practices is stressed

A Statistical Mechanical Load Balancer for the Web

The maximum entropy principle from statistical mechanics states that a closed system attains an equilibrium distribution that maximizes its entropy. We first show that for graphs with fixed number of edges one can define a stochastic edge dynamic that can serve as an effective thermalization scheme, and hence, the underlying graphs are expected to attain their maximum-entropy states, which turn out to be Erdos-Renyi (ER) random graphs. We next show that (i) a rate-equation based analysis of node degree distribution does indeed confirm the maximum-entropy principle, and (ii) the edge dynamic can be effectively implemented using short random walks on the underlying graphs, leading to a local algorithm for the generation of ER random graphs. The resulting statistical mechanical system can be adapted to provide a distributed and local (i.e., without any centralized monitoring) mechanism for load balancing, which can have a significant impact in increasing the efficiency and utilization of both the Internet (e.g., efficient web mirroring), and large-scale computing infrastructure (e.g., cluster and grid computing).Comment: 11 Pages, 5 Postscript figures; added references, expanded on protocol discussio

The PARSE Programming Paradigm. Part I: Software Development Methodology. Part II: Software Development Support Tools

The programming methodology of PARSE (parallel software environment), a software environment being developed for reconfigurable non-shared memory parallel computers, is described. This environment will consist of an integrated collection of language interfaces, automatic and semi-automatic debugging and analysis tools, and operating system —all of which are made more flexible by the use of a knowledge-based implementation for the tools that make up PARSE. The programming paradigm supports the user freely choosing among three basic approaches /abstractions for programming a parallel machine: logic-based descriptive, sequential-control procedural, and parallel-control procedural programming. All of these result in efficient parallel execution. The current work discusses the methodology underlying PARSE, whereas the companion paper, “The PARSE Programming Paradigm — II: Software Development Support Tools,” details each of the component tools

Experimental Benchmarks and Initial Evaluation of the Performance of the PASM System Prototype

The work reported here represents experiences with the PASM parallel processing system prototype during its first operational year. Most of the experiments were performed by students in the Fall semester of 1987. The first programming, and the first timing measurements, were made during the summer of 1987 by Sam Fineberg. The goal of the collection of experiments presented here was to undertake an Application-driven Architecture Study of the PASM system as a paradigm for parallel architecture evaluation in general. PASM was an excellent vehicle for experimenting with this evaluation technique due to its unique architectural features. Among these are: 1. A reconfigurable, partitionable multistage circuit-switched network. 2. Support for both SIMD and MIMD programs. 3. Ability to execute hybrid SIMD/MIMD programs. 4. An instruction queue which allows overlap of control-flow and data manipulation between micro-control (MC) units and processing elements (PE). It had been hypothesized that superlinear speed-up over the number of PEs could be attained with this feature, and experimental results verified this. 5. Support for barrier synchronization of MIMD tasks. This feature was exploited in some non-standard ways to show the ability to decouple variant length SIMD instructions into multiple MIMD streams for an overall performance benefit. This type of study is expected to continue in the future on PASM and other parallel machines at Purdue. This report should serve as a guide for this future work as well

Gene Discovery and Functional Genomics in the Pig

Advances in gene mapping and genomics in farm animals have been considerable over the past decade. Medium resolution linkage and physical maps have been reported, and specific chromosomal regions and genes associated with traits of biological and economic interest have been identified. We have reached an exciting stage in gene identification, mapping and quantitative trait locus discovery in pigs, as new molecular information is accumulating rapidly. Significant progress has been made by identifying candidate gene associations and low-resolution regions containing quantitative trail loci (QTL). However, we are still disadvantaged by the lack of tools available to efficiently use much of this new information. For example, current pig maps are neither of high enough resolution nor sufficiently informative at the comparative level for positional candidate gene cloning within QTL regions. As well, studying biological mechanisms underlying economically important traits such as reproduction is limited by the lack of molecular resources. This is especially important, as reproduction is very difficult to genetically improve by classical breeding methods due to the relatively low heritability and high expense in data collection. Thus, an improved understanding of porcine reproductive biology is of crucial economic importance, yet reproductive processes are poorly characterized at the molecular level. Recently, new methodologies have been brought to bear on a better understanding of pig molecular biology for accelerating genetic improvement in pigs. Several groups are developing molecular information in the pig, and the total Genbank sequence entries for porcine expressed genes have recently topped 100,000. Our Midwest EST Consortium has produced cDNA libraries containing the majority of genes expressed in major female reproductive tissues, and we have deposited nearly 15,000 gene sequences into public databases. These sequences represent over 8,900 different genes, based on sequence comparison among these data. Furthermore, we have developed computer software to automatically extract sequence similarity of these pig genes with their human counterparts, as well as the mapping information of these human homologues. Within our data set, we have identified nearly 1,500 pig genes with strong similarity to mapped human genes, and we are in the process of mapping 700 of these genes to improve the human-pig comparative map. This work and the complementary work of others can now be used to more rapidly understand and identify the genes controlling reproduction, so that genetic improvement of reproduction phenotypes can accelerate

Impact of Bordetella pertussis exposures on a Massachusetts tertiary care medical system

OBJECTIVE: To assess the impact of outbreaks of Bordetella pertussis infection on a tertiary care medical system. DESIGN: Retrospective study. SETTING: Academic tertiary care medical center and affiliated ambulatory care settings. SUBJECTS: All patients and healthcare workers (HCWs) who were in close contact with patients with laboratory-confirmed cases of B. pertussis infection from October 1, 2003, through September 30, 2004. INTERVENTION: Direct and indirect medical center costs were determined, including low and high estimates of time expended in the evaluation and management of exposed patients and HCWs during outbreak investigations of laboratory-confirmed cases of B. pertussis infection. RESULTS: During this period, 20 primary and 3 secondary laboratory-confirmed cases of B. pertussis infection occurred, with 2 primary pertussis cases and 1 secondary case occurring in HCWs. Outbreak investigations prompted screening of 353 medical center employees. Probable or definitive exposure was identified for 296 HCWs, and 287 subsequently received treatment or prophylaxis for B. pertussis infection. Direct medical center costs for treatment and prophylaxis were $13,416 and costs for personnel time were$19,500-$31,190. Indirect medical center costs for time lost from work were$51,300-$52,300. The total cost of these investigations was estimated to be$85,066-$98,456. CONCLUSIONS: Frequent B. pertussis exposures had a major impact on our facility. Given the impact of exposures on healthcare institutions, routine vaccination for HCWs may be beneficial

Development of New Placental and Fetal Expressed Sequence Tags (EST) for Gene Discovery in Pig Reproduction

One major problem that has high economic impact on pig reproduction is the unexplained loss of potential porcine conceptuses during the first month of gestation. To better understand when and how these losses occur, it is imperative to investigate the underlying genetic regulatory mechanisms. We have recently initiated a large-scale cDNA sequencing project to provide molecular information regarding the genes expressed in female reproductive tissues. cDNA libraries are planned for ovary, hypothalamus, pituitary, placenta, uterus, and several stages of embryonic development. Sequence information will also be highly useful in developing sequence-tagged sites for physical mapping and developing comparative links between the human, mouse, and pig genome maps. We have previously reported the creation of two cDNA libraries, porcine fetal (day 20), and conceptus (day 17). Sequencing of these libraries produced 220 Expressed Sequence Tags (ESTs), with 180 sequences analyzed by clustering algorithms, and 139 clusters identified within these sequences. We now report the creation of two more libraries from porcine fetal (day 45) and placental tissues. The day 45 fetal library has 971,150 independent clones (average insert: 1.4 kb), whereas the placental library has 1,320,000 independent clones. Initial sequencing of the fetal library has produced 119 ESTs (81 clusters), whereas we have obtained 1411 ESTs (1056 clusters) from the placental library. After clustering all sequences thus far obtained, we have identified 1,233 unique clusters. Sequences obtained in this project will be deposited into Genbank dbEST, and all comparative homolog

Progress on the Experimental Search for Charge Symmetry Breaking (CSB) in n-p Scattering

This work was supported by the National Science Foundation Grant NSF PHY 81-14339 and by Indiana Universit

Bioinformatic Analysis of Gene Sets Regulated by Ligand-Activated and Dominant-Negative Peroxisome Proliferator-Activated Receptor in Mouse Aorta

Drugs that activate PPARγ improve glucose sensitivity and lower blood pressure, whereas dominant negative mutations in PPARγ cause severe insulin resistance and hypertension. We hypothesize that these PPARγ mutants regulate target genes opposite to that of ligand-mediated activation and tested this hypothesis on a genome-wide scale