Measurement of Indeterminacy in Packings of Perfectly Rigid Disks

Static packings of perfectly rigid particles are investigated theoretically and numerically. The problem of finding the contact forces in such packings is formulated mathematically. Letting the values of the contact forces define a vector in a high-dimensional space enable us to show that the set of all possible contact forces is convex, facilitating its numerical exploration. It is also found that the boundary of the set is connected with the presence of sliding contacts, suggesting that a stable packing should not have more than 2M-3N sliding contacts in two dimensions, where M is the number of contacts and N is the number of particles. These results were used to analyze packings generated in different ways by either molecular dynamics or contact dynamics simulations. The dimension of the set of possible forces and the number of sliding contacts agrees with the theoretical expectations. The indeterminacy of each component of the contact forces are found, as well as the an estimate for the diameter of the set of possible contact forces. We also show that contacts with high indeterminacy are located on force chains. The question of whether the simulation methods can represent a packing's memory of its formation is addressed.Comment: 12 pages, 13 figures, submitted to Phys Rev

Dynamic Provenance for SPARQL Update

While the Semantic Web currently can exhibit provenance information by using the W3C PROV standards, there is a "missing link" in connecting PROV to storing and querying for dynamic changes to RDF graphs using SPARQL. Solving this problem would be required for such clear use-cases as the creation of version control systems for RDF. While some provenance models and annotation techniques for storing and querying provenance data originally developed with databases or workflows in mind transfer readily to RDF and SPARQL, these techniques do not readily adapt to describing changes in dynamic RDF datasets over time. In this paper we explore how to adapt the dynamic copy-paste provenance model of Buneman et al. [2] to RDF datasets that change over time in response to SPARQL updates, how to represent the resulting provenance records themselves as RDF in a manner compatible with W3C PROV, and how the provenance information can be defined by reinterpreting SPARQL updates. The primary contribution of this paper is a semantic framework that enables the semantics of SPARQL Update to be used as the basis for a 'cut-and-paste' provenance model in a principled manner.Comment: Pre-publication version of ISWC 2014 pape

Environments for term rewriting engines for free!

Term rewriting can only be applied if practical implementations of term rewriting engines exist. New rewriting engines are designed and implemented either to experiment with new (theoretical) results or to be able to tackle new application areas. In this paper we present the Meta-Environment: an environment for rapidly implementing the syntax and semantics of term rewriting based formalisms. We provide not only the basic building blocks, but complete interactive programming environments that only need to be instantiated by the details of a new formalism

Elastic behavior in Contact Dynamics of rigid particles

The systematic errors due to the practical implementation of the Contact Dynamics method for simulation of dense granular media are examined. It is shown that, using the usual iterative solver to simulate a chain of rigid particles, effective elasticity and sound propagation with a finite velocity occur. The characteristics of these phenomena are investigated analytically and numerically in order to assess the limits of applicability of this simulation method and to compare it with soft particle molecular dynamics.Comment: submitted to PRE, 7 pages, 6 figure

Viral markers of hepatitis B, C and D and HB vaccination status of a health care team in a rural district of Cameroon

UNLABELLED: Ninety-three health care workers (HCW) in the Tokombere sahelian district volunteered to participate in a trial to investigate viral markers of hepatitis B, C, and D and HB vaccination status. METHODS: . Sera were tested using the Vikia HBsAg kit followed by CMIA for detection of HBsAg, anti-HBs, anti-HBc, and anti-HCV. HBsAg-positive HCW were tested for HBV-DNA, anti-HDV, and, if positive for anti-HDV, HDV-RNA.RESULTS: Analysis of anti-HBc positivity indicated that 91% of HCW had been infected by HBV, regardless of vaccination history. Vikia HBsAg results were confirmed by chemiluminescent microparticle immunoassay (CMIA) in all HCW and were positive in 17 HCW with virus load >2000 IU/mL in 6 and HDV co-infection in 6. Anti-HCV was found in 6 HCW. Among the 55 HCW that had not been vaccinated, only 3 needed vaccination because of anti-HBc negativity. Among HCW considered for HBV treatment, one patient presenting HBV/HDV co-infection was excluded after diagnosis of hepatocarcinoma. CONCLUSION: Systematic HB vaccination of new HCW appears unnecessary in this rural region of Africa. Anti-HBc screening is cost-effective for identifying HCW requiring vaccination. Vikia HBsAg is effective for point-of-care screening. We underline the need for universal early (preferably neonatal) HB vaccination and for availability of anti-HBV drug in limited-resource countries

Selective protein unfolding: a universal mechanism of action for the development of irreversible inhibitors

High-throughput differential scanning fluorimetry of GFP-tagged proteins (HT-DSF-GTP) was applied for the identification of novel enzyme inhibitors acting by a mechanism termed: selective protein unfolding (SPU). Four different protein targets were interrogated with the same library to identify target-selective hits. Several hits selectively destabilized bacterial biotin protein ligase. Structure–activity relationship data confirmed a structure-dependent mechanism of protein unfolding. Simvastatin and altenusin were confirmed to irreversibly inactivate biotin protein ligase. The principle of SPU combined with HT-DSF-GTP affords an invaluable and innovative workflow for the identification of new inhibitors with potential applications as antimicrobials and other biocides

Delineation of the ancestral tus-dependent replication fork trap

In Escherichia coli, DNA replication termination is orchestrated by two clusters of Ter sites forming a DNA replication fork trap when bound by Tus proteins. The formation of a ‘locked’ Tus– Ter complex is essential for halting incoming DNA replication forks. However, the absence of replication fork arrest at some Ter sites raised questions about their significance. In this study, we examined the genome-wide distribution of Tus and found that only the six innermost Ter sites (TerA–E and G) were significantly bound by Tus. We also found that a single ectopic insertion of TerB in its non-permissive orientation could not be achieved, advocating against a need for ‘back-up’ Ter sites. Finally, examination of the genomes of a variety of Enterobacterales revealed a new replication fork trap architecture mostly found outside the Enterobacteriaceae family. Taken together, our data enabled the delineation of a narrow ancestral Tus-dependent DNA replication fork trap consisting of only two Ter sites

Orchidectomy Models of Osteoporosis

Long considered a disease of post-menopausal women, osteoporosis is increasingly being recognized among the growing population of elderly men. Androgen deficiency may be associated with an increase of bone resorption in elderly men and so, with remodeling imbalance and fracture risk. It is firmly established that androgen withdrawal induced by orchidectomy (ORX) results in decreased bone mass in animal models especially in rodents. The mature rat is the model of choice. Skeletal effects of ORX in rats have been studied at the tissular and cellular level. It induces a decrease of BMD and BV/TV with microarchitecture alterations due to an increased bone remodeling. The present chapter focuses on the ORX surgery in rats and mice

Sub-microsecond correlations in photoluminescence from InAs quantum dots

Photon correlation measurements reveal memory effects in the optical emission of single InAs quantum dots with timescales from 10 to 800 ns. With above-band optical excitation, a long-timescale negative correlation (antibunching) is observed, while with quasi-resonant excitation, a positive correlation (blinking) is observed. A simple model based on long-lived charged states is presented that approximately explains the observed behavior, providing insight into the excitation process. Such memory effects can limit the internal efficiency of light emitters based on single quantum dots, and could also be problematic for proposed quantum-computation schemes.Comment: 8 pages, 8 figure

The Degasperis-Procesi equation as a non-metric Euler equation

In this paper we present a geometric interpretation of the periodic Degasperis-Procesi equation as the geodesic flow of a right invariant symmetric linear connection on the diffeomorphism group of the circle. We also show that for any evolution in the family of $b$-equations there is neither gain nor loss of the spatial regularity of solutions. This in turn allows us to view the Degasperis-Procesi and the Camassa-Holm equation as an ODE on the Fr\'echet space of all smooth functions on the circle.Comment: 17 page