BioNessie - a grid enabled biochemical networks simulation environment

The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations

Ecoéthologie des vecteurs et transmission du paludisme dans la région rizicole de basse altitude de Mandritsara, Madagascar

International audienceTo evaluate the determining factors of the malaria transmission in the northwest region of Madagascar, transversal studies were carried out through one year, from March 1997 to April 1998, in two villages located near Mandritsara, at less than 300 meters above sea level. The rice-growingregion forms an intermediate zone between the central highlands with epidemic and instable malaria and the coastal zone with endemic and stable malaria. Mosquitoes were collected when landing on humans during the night and by pyrethrum spray catches as regards endophilic mosquitoes. Three vectors were identified : Anopheles arabiensis, An.gambiae and An. funestus. An. arabiensis and An. gambiae were exophagic and zoophilic.An.funestus was endo-exophagic and anthropophilic but this species shows also a zoophilic trophic deviation. In both villages, An. funestus is the main vector of human malaria. Malaria transmission was estimated to be around 50 and 70 infective bites/person/year in each village.Pour évaluer les facteurs qui déterminent la transmission du paludisme dans la région nord-est de Madagascar, des enquêtes entomologiques ont été menées d’avril 1997 à mars 1998 dans deux villages situés dans la région de Mandritsara, à moins de 300 mètres d’altitude. Cette région est une zone rizicole importante et fait partie de la zone intermédiaire entre les Hautes terres à paludisme instable, épidémique et la région côtière à paludisme stable endémique.Les moustiques ont été récoltés par des captures sur hommes volontaires et par des collectes matinales des moustiques endophiles. Les vecteurs ont été Anopheles arabiensis, An. gambiae et An. funestus. An. funestus a été le vecteur majeur du paludisme; il n'a pas présenté d'aptitude particulière pour l'endophagie ou l'exophagie; il a essentiellement présenté une anthropophilie mais avec une tendance zoophile marquée. Le taux entomologique d’inoculation a été d’environ 50 piqûres infectantes par homme et par an dans le premier village et 70 dans le deuxième

Estimates of amounts of soil removal for clean-up of transuranics at NAEG offsite safety-shot sites

Rough estimates are given for the amount of soil removal necessary to decontaminate five representative safety-shot areas. In order to decontaminate to levels of less than 160 pCi /sup 239/Pu per gram of surface soil, it is estimated that over one-half million tons of soil would have to be removed from the five areas. This is a preliminary estimate based on summary data and concentration contour maps readily available in NAEG publications. More accurate estimates could be obtained by applying Kriging techniques to available soil data if the need arises. The inclusion of /sup 241/Am and /sup 238/Pu activities do not significantly increase the soil tonnage estimates obtained for /sup 239/ /sup 240/Pu because of their relatively small contributions to total transuranic activity. The magnitude of the errors inherent in our use of summary data to obtain rough estimates also suggests that a revision of the tonnage estimates for /sup 239/ /sup 240/Pu to include /sup 241/Am and /sup 238/Pu is not warranted

Quasi-Local Density Functional Theory and its Application within Extended Thomas-Fermi Approximation

A generalization of the Density Functional Theory is proposed. The theory developed leads to single-particle equations of motion with a quasi-local mean-field operator, which contains a quasi-particle position-dependent effective mass and a spin-orbit potential. The energy density functional is constructed using the Extended Thomas-Fermi approximation. Within the framework of this approach the ground-state properties of the doubly magic nuclei are considered. The calculations have been performed using the finite-range Gogny D1S force. The results are compared with the exact Hartree-Fock calculations

Methane Flux in Cropland and Adjacent Riparian Buff ers with Different Vegetation Covers

While water quality functions of conservation buffers established adjacent to cropped fields have been widely documented, the relative contribution of these re-established perennial plant systems to greenhouse gases has not been completely documented. In the case of methane (CH(4)), these systems have the potential to serve as sinks of CH(4) or may provide favorable conditions for CH(4) production. This study quantifies CH(4) flux from soils of riparian buffer systems comprised of three vegetation types and compares these fluxes with those of adjacent crop fields. We measured soil properties and diel and seasonal variations of CH(4) flux in 7 to 17 yr-old re-established riparian forest buffers, warm-season and cool-season grass filters, and an adjacent crop field located in the Bear Creek watershed in central Iowa. Forest buffer and grass filter soils had significantly lower bulk density (P \u3c 0.01); and higher pH (P \u3c 0.01), total carbon (TC) (P \u3c 0.01), and total nitrogen (TN) (P \u3c 0.01) than crop field soils. There was no significant relationship between CH(4) flux and soil moisture or soil temperature among sites within the range of conditions observed. Cumulative CH(4) flux was -0.80 kg CH(4)-C ha(-1) yr(-1) in the cropped field, -0.46 kg CH(4)-C ha(-1) yr(-1) within the forest buffers, and 0.04 kg CH(4)-C ha(-1) yr(-1) within grass filters, but difference among vegetation covers was not significant. Results suggest that CH(4) flux was not changed after establishment of perennial vegetation on cropped soils, despite significant changes in soil properties

Long-term trends in tropical cyclone tracks around Korea and Japan in late summer and early fall

This study investigates long-term trends in tropical cyclones (TCs) over the extratropical western North Pacific (WNP) over a period of 35 years (1982-2016). The area analyzed extended across 30-45 degrees N and 120-150 degrees E, including the regions of Korea and Japan that were seriously affected by TCs. The northward migration of TCs over the WNP to the mid-latitudes showed a sharp increase in early fall. In addition, the duration of TCs over the WNP that migrated northwards showed an increase, specifically in early to mid-September. Therefore, more recently, TC tracks have been observed to significantly extend into the mid-latitudes. The recent northward extension of TC tracks over the WNP in early fall was observed to be associated with changes in environmental conditions that were favorable for TC activities, including an increase in sea surface temperature (SST), decrease in vertical wind shear, expansion of subtropical highs, strong easterly steering winds, and an increase in relative vorticity. In contrast, northward migrations of TCs to Korea and Japan showed a decline in late August, because of the presence of unfavorable environmental conditions for TC activities. These changes in environmental conditions, such as SST and vertical wind shear, can be partially associated with the Pacific decadal oscillation

Density-functional embedding using a plane-wave basis

The constrained electron density method of embedding a Kohn-Sham system in a substrate system (first described by P. Cortona, Phys. Rev. B {\bf 44}, 8454 (1991) and T.A. Wesolowski and A. Warshel, J. Phys. Chem {\bf 97}, 8050 (1993)) is applied with a plane-wave basis and both local and non-local pseudopotentials. This method divides the electron density of the system into substrate and embedded electron densities, the sum of which is the electron density of the system of interest. Coupling between the substrate and embedded systems is achieved via approximate kinetic energy functionals. Bulk aluminium is examined as a test case for which there is a strong interaction between the substrate and embedded systems. A number of approximations to the kinetic-energy functional, both semi-local and non-local, are investigated. It is found that Kohn-Sham results can be well reproduced using a non-local kinetic energy functional, with the total energy accurate to better than 0.1 eV per atom and good agreement between the electron densities.Comment: 11 pages, 4 figure