An integral equation method for a boundary value problem arising in unsteady water wave problems

In this paper we consider the 2D Dirichlet boundary value problem for Laplace’s equation in a non-locally perturbed half-plane, with data in the space of bounded and continuous functions. We show uniqueness of solution, using standard Phragmen-Lindelof arguments. The main result is to propose a boundary integral equation formulation, to prove equivalence with the boundary value problem, and to show that the integral equation is well posed by applying a recent partial generalisation of the Fredholm alternative in Arens et al [J. Int. Equ. Appl. 15 (2003) pp. 1-35]. This then leads to an existence proof for the boundary value problem. Keywords. Boundary integral equation method, Water waves, Laplace’

estMOI: estimating multiplicity of infection using parasite deep sequencing data.

Individuals living in endemic areas generally harbour multiple parasite strains. Multiplicity of infection (MOI) can be an indicator of immune status and transmission intensity. It has a potentially confounding effect on a number of population genetic analyses, which often assume isolates are clonal. Polymerase chain reaction-based approaches to estimate MOI can lack sensitivity. For example, in the human malaria parasite Plasmodium falciparum, genotyping of the merozoite surface protein (MSP1/2) genes is a standard method for assessing MOI, despite the apparent problem of underestimation. The availability of deep coverage data from massively parallizable sequencing technologies means that MOI can be detected genome wide by considering the abundance of heterozygous genotypes. Here, we present a method to estimate MOI, which considers unique combinations of polymorphisms from sequence reads. The method is implemented within the estMOI software. When applied to clinical P.falciparum isolates from three continents, we find that multiple infections are common, especially in regions with high transmission

Connection between effective-range expansion and nuclear vertex constant or asymptotic normalization coefficient

Explicit relations between the effective-range expansion and the nuclear vertex constant or asymptotic normalization coefficient (ANC) for the virtual decay $B\to A+a$ are derived for an arbitrary orbital momentum together with the corresponding location condition for the ($A+a$) bound-state energy. They are valid both for the charged case and for the neutral case. Combining these relations with the standard effective-range function up to order six makes it possible to reduce to two the number of free effective-range parameters if an ANC value is known from experiment. Values for the scattering length, effective range, and form parameter are determined in this way for the $^{16}$O+$p$, $\alpha+t$ and $\alpha+^3$He collisions in partial waves where a bound state exists by using available ANCs deduced from experiments. The resulting effective-range expansions for these collisions are valid up to energies larger 5 MeV.Comment: 17 pages, 6 figure

The general relativistic infinite plane

Uniform fields are one of the simplest and most pedagogically useful examples in introductory courses on electrostatics or Newtonian gravity. In general relativity there have been several proposals as to what constitutes a uniform field. In this article we examine two metrics that can be considered the general relativistic version of the infinite plane with finite mass per unit area. The first metric is the 4D version of the 5D "brane" world models which are the starting point for many current research papers. The second case is the cosmological domain wall metric. We examine to what extent these different metrics match or deviate from our Newtonian intuition about the gravitational field of an infinite plane. These solutions provide the beginning student in general relativity both computational practice and conceptual insight into Einstein's field equations. In addition they do this by introducing the student to material that is at the forefront of current research.Comment: Accepted for publication in the American Journal of Physic

Biological Records Centre Annual Report 2005-2006

The period covered by this report is the first year of a new six-year partnership between CEH and JNCC. For this period, there is increased emphasis on targeted survey, on analysis and interpretation and on communications and outreach. These activities were always part of BRC’s work, but they have been given greater prominence as a result of rapid developments in information technology. Data are increasingly reaching BRC in electronic form, so that the effort of data entry and collation is reduced. The data, collected by many volunteers and then collated and analysed at BRC, document the changing status and distribution of plants and animals in Britain. Distribution maps are published in atlases and are available via the internet through the NBN Gateway. The effects of change or loss of habitats, the influence of climate change and the consequences of changing water quality are all examples of the environmental factors that affect our biodiversity and which BRC aims to document and understand. The results are vital for developing environmental policies, to support conservation, and for fundamental ecological research. BRC is funded jointly by JNCC and NERC through a partnership based on a Memorandum of Agreement (MoA). The partnership started in 1973 when the Nature Conservancy was divided to form the successor bodies Nature Conservancy Council (NCC) and Institute of Terrestrial Ecology (ITE). NCC was in turn divided further to form JNCC and three Country Agencies, while ITE was merged with other NERC units to form CEH. Through all these changes, the partnership has been maintained. A six-year memorandum of agreement ended on 31 January 2005 (Hill et al. 2005). The present report covers the first full year, 2005-6, of the new agreement for 2005-2010. Rapid progress in information technology continues to be highly beneficial for BRC, whose data are increasingly used by the UK country conservation agencies, environmental consultants, NGOs, research workers, policy makers and volunteers. It is gratifying to know that, through our ability to display data on the National Biodiversity Network (NBN) Gateway, some of our data suppliers now have immediate access to their own data in a convenient form. The year 2005-6 has been one of steady progress, with new datasets added to BRC, substantial additions to existing data, and improved communication with the NBN Gateway. The most high profile activity of the year has been the Harlequin Ladybird Survey, which has enabled us to observe the early stages of colonization by a mobile insect in greater detail than has been possible in any previous case

Stress in Swine

Stress appears to be increasing in swine and its toll ranges from death of animals to undesirable meat characteristics. The authors review the problem and list some preventive measures you can take

Spectroscopic Constraints on the Surface Magnetic Field of the Accreting Neutron Star EXO 0748-676

Gravitationally redshifted absorption lines of Fe XXVI, Fe XXV, and O VIII were inferred recently in the X-ray spectrum of the bursting neutron star EXO 0748-676. We place an upper limit on the stellar magnetic field based on the iron lines. The oxygen absorption feature shows a multiple component profile that is consistent with Zeeman splitting in a magnetic field of ~(1-2)x10^9 gauss, and for which the corresponding Zeeman components of the iron lines are expected to be blended together. In other systems, a field strength >5x10^{10} gauss could induce a blueshift of the line centroids that would counteract gravitational redshift and complicate the derivation of constraints on the equation of state of the neutron star.Comment: 5 pages, submitted to Phys. Rev. Let

The energy partitioning of non-thermal particles in a plasma: or the Coulomb logarithm revisited

The charged particle stopping power in a highly ionized and weakly to moderately coupled plasma has been calculated to leading and next-to-leading order by Brown, Preston, and Singleton (BPS). After reviewing the main ideas behind this calculation, we use a Fokker-Planck equation derived by BPS to compute the electron-ion energy partitioning of a charged particle traversing a plasma. The motivation for this application is ignition for inertial confinement fusion -- more energy delivered to the ions means a better chance of ignition, and conversely. It is therefore important to calculate the fractional energy loss to electrons and ions as accurately as possible, as this could have implications for the Laser Megajoule (LMJ) facility in France and the National Ignition Facility (NIF) in the United States. The traditional method by which one calculates the electron-ion energy splitting of a charged particle traversing a plasma involves integrating the stopping power dE/dx. However, as the charged particle slows down and becomes thermalized into the background plasma, this method of calculating the electron-ion energy splitting breaks down. As a result, the method suffers a systematic error of order T/E0, where T is the plasma temperature and E0 is the initial energy of the charged particle. In the case of DT fusion, for example, this can lead to uncertainties as high as 10% or so. The formalism presented here is designed to account for the thermalization process, and in contrast, it provides results that are near-exact.Comment: 10 pages, 3 figures, invited talk at the 35th European Physical Society meeting on plasma physic

SVAMP: sequence variation analysis, maps and phylogeny.

SUMMARY: SVAMP is a stand-alone desktop application to visualize genomic variants (in variant call format) in the context of geographical metadata. Users of SVAMP are able to generate phylogenetic trees and perform principal coordinate analysis in real time from variant call format (VCF) and associated metadata files. Allele frequency map, geographical map of isolates, Tajima's D metric, single nucleotide polymorphism density, GC and variation density are also available for visualization in real time. We demonstrate the utility of SVAMP in tracking a methicillin-resistant Staphylococcus aureus outbreak from published next-generation sequencing data across 15 countries. We also demonstrate the scalability and accuracy of our software on 245 Plasmodium falciparum malaria isolates from three continents. AVAILABILITY AND IMPLEMENTATION: The Qt/C++ software code, binaries, user manual and example datasets are available at http://cbrc.kaust.edu.sa/svamp CONTACT: [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online