Periodic pattern formation in reaction-diffusion systems -an introduction for numerical simulation

The aim of the present review is to provide a comprehensive explanation of Turing reaction–diffusion systems in sufficient detail to allow readers to perform numerical calculations themselves. The reaction–diffusion model is widely studied in the field of mathematical biology, serves as a powerful paradigm model for self-organization and is beginning to be applied to actual experimental systems in developmental biology. Despite the increase in current interest, the model is not well understood among experimental biologists, partly because appropriate introductory texts are lacking. In the present review, we provide a detailed description of the definition of the Turing reaction–diffusion model that is comprehensible without a special mathematical background, then illustrate a method for reproducing numerical calculations with Microsoft Excel. We then show some examples of the patterns generated by the model. Finally, we discuss future prospects for the interdisciplinary field of research involving mathematical approaches in developmental biology

Possible Magnetic Behavior in Oxygen-deficient {\beta}-PtO2

We studied the electronic properties of beta-platinum dioxide ({\beta}-PtO2), a catalytic material, based on density functional theory. Using the GGA+U method which reproduces the GW band structures and the experimental structural parameters, we found that the creation of an oxygen vacancy will induce local magnetic moment on the neighboring Pt and O atoms. The magnetism originates not only from the unpaired electrons that occupy the vacancy induced gap state, but also from the itinerant valence electrons. Because of antiferromagnetic (AF) coupling and the localized nature of gap states, the total magnetic moment is zero for charge-neutral state (V_o^0) and is ~ 1 \mu B for singly-charged states (V_o^\mu). Calculation of grand potential shows that, the three charge states (V_o^0, V_o^\pm) are of the same stability within a small region, and the negatively charged state (V_o^-) is energetically favored within a wide range of the band gap. On this basis we discussed the implication on catalytic behavior.Comment: 45 pages, 11 figures, 3 table

Rubidium in Metal-Deficient Disk and Halo Stars

We report the first extensive study of stellar Rb abundances. High-resolution spectra have been used to determine, or set upper limits on, the abundances of this heavy element and the associated elements Y, Zr, and Ba in 44 dwarfs and giants with metallicities spanning the range -2.0 <[Fe/H] < 0.0. In metal-deficient stars Rb is systematically overabundant relative to Fe; we find an average [Rb/Fe] of +0.21 for the 32 stars with [Fe/H] < -0.5 and measured Rb. This behavior contrasts with that of Y, Zr, and Ba, which, with the exception of three new CH stars (HD 23439A and B and BD +5 3640), are consistently slightly deficient relative to Fe in the same stars; excluding the three CH stars, we find the stars with [Fe/H] < -0.5 have average [Y/Fe], [Zr/Fe], and [Ba/Fe] of --0.19 (24 stars), --0.12 (28 stars), and --0.06 (29 stars), respectively. The different behavior of Rb on the one hand and Y, Zr, and Ba on the other can be attributed in part to the fact that in the Sun and in these stars Rb has a large r-process component while Y, Zr, and Ba are mostly s-process elements with only small r-process components. In addition, the Rb s-process abundance is dependent on the neutron density at the s-processing site. Published observations of Rb in s-process enriched red giants indicate a higher neutron density in the metal-poor giants. These observations imply a higher s-process abundance for Rb in metal-poor stars. The calculated combination of the Rb r-process abundance, as estimated for the stellar Eu abundances, and the s-process abundance as estimated for red giants accounts satisfactorily for the observed run of [Rb/Fe] with [Fe/H].Comment: 23 pages, 5 tables, 7 figure

The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform, and new ontologies being created, on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved in the future

Nonlinear electrochemical relaxation around conductors

We analyze the simplest problem of electrochemical relaxation in more than one dimension - the response of an uncharged, ideally polarizable metallic sphere (or cylinder) in a symmetric, binary electrolyte to a uniform electric field. In order to go beyond the circuit approximation for thin double layers, our analysis is based on the Poisson-Nernst-Planck (PNP) equations of dilute solution theory. Unlike most previous studies, however, we focus on the nonlinear regime, where the applied voltage across the conductor is larger than the thermal voltage. In such strong electric fields, the classical model predicts that the double layer adsorbs enough ions to produce bulk concentration gradients and surface conduction. Our analysis begins with a general derivation of surface conservation laws in the thin double-layer limit, which provide effective boundary conditions on the quasi-neutral bulk. We solve the resulting nonlinear partial differential equations numerically for strong fields and also perform a time-dependent asymptotic analysis for weaker fields, where bulk diffusion and surface conduction arise as first-order corrections. We also derive various dimensionless parameters comparing surface to bulk transport processes, which generalize the Bikerman-Dukhin number. Our results have basic relevance for double-layer charging dynamics and nonlinear electrokinetics in the ubiquitous PNP approximation.Comment: 25 pages, 17 figures, 4 table

s-Process Nucleosynthesis in Carbon Stars

We present the first detailed and homogeneous analysis of the s-element content in Galactic carbon stars of N-type. Abundances of Sr,Y, Zr (low-mass s-elements, or ls) and of Ba, La, Nd, Sm and Ce (high-mass s-elements, hs) are derived using the spectral synthesis technique from high-resolution spectra. The N-stars analyzed are of nearly solar metallicity and show moderate s-element enhancements, similar to those found in S stars, but smaller than those found in the only previous similar study (Utsumi 1985), and also smaller than those found in supergiant post-AGB stars. This is in agreement with the present understanding of the envelope s-element enrichment in giant stars, which is increasing along the spectral sequence M-->MS-->S-->SC-->C during the AGB phase. We compare the observational data with recent $s$-process nucleosynthesis models for different metallicities and stellar masses. Good agreement is obtained between low mass AGB star models (M < 3 M_o) and s-elements observations. In low mass AGB stars, the 13C(alpha, n)16O reaction is the main source of neutrons for the s-process; a moderate spread, however, must exist in the abundance of 13C that is burnt in different stars. By combining information deriving from the detection of Tc, the infrared colours and the theoretical relations between stellar mass, metallicity and the final C/O ratio, we conclude that most (or maybe all) of the N-stars studied in this work are intrinsic, thermally-pulsing AGB stars; their abundances are the consequence of the operation of third dredge-up and are not to be ascribed to mass transfer in binary systems.Comment: 31 pages, 10 figures, 6 tables. Accepted in Ap

ASCR/HEP Exascale Requirements Review Report

This draft report summarizes and details the findings, results, and recommendations derived from the ASCR/HEP Exascale Requirements Review meeting held in June, 2015. The main conclusions are as follows. 1) Larger, more capable computing and data facilities are needed to support HEP science goals in all three frontiers: Energy, Intensity, and Cosmic. The expected scale of the demand at the 2025 timescale is at least two orders of magnitude -- and in some cases greater -- than that available currently. 2) The growth rate of data produced by simulations is overwhelming the current ability, of both facilities and researchers, to store and analyze it. Additional resources and new techniques for data analysis are urgently needed. 3) Data rates and volumes from HEP experimental facilities are also straining the ability to store and analyze large and complex data volumes. Appropriately configured leadership-class facilities can play a transformational role in enabling scientific discovery from these datasets. 4) A close integration of HPC simulation and data analysis will aid greatly in interpreting results from HEP experiments. Such an integration will minimize data movement and facilitate interdependent workflows. 5) Long-range planning between HEP and ASCR will be required to meet HEP's research needs. To best use ASCR HPC resources the experimental HEP program needs a) an established long-term plan for access to ASCR computational and data resources, b) an ability to map workflows onto HPC resources, c) the ability for ASCR facilities to accommodate workflows run by collaborations that can have thousands of individual members, d) to transition codes to the next-generation HPC platforms that will be available at ASCR facilities, e) to build up and train a workforce capable of developing and using simulations and analysis to support HEP scientific research on next-generation systems.Comment: 77 pages, 13 Figures; draft report, subject to further revisio

The SOFG Anatomy Entry List (SAEL):an annotation tool for functional genomics data

A great deal of data in functional genomics studies needs to be annotated with low-resolution anatomical terms. For example, gene expression assays based on manually dissected samples (microarray, SAGE, etc.) need high-level anatomical terms to describe sample origin. First-pass annotation in high-throughput assays (e.g. large-scale in situ gene expression screens or phenotype screens) and bibliographic applications, such as selection of keywords, would also benefit from a minimum set of standard anatomical terms. Although only simple terms are required, the researcher faces serious practical problems of inconsistency and confusion, given the different aims and the range of complexity of existing anatomy ontologies. A Standards and Ontologies for Functional Genomics (SOFG) group therefore initiated discussions between several of the major anatomical ontologies for higher vertebrates. As we report here, one result of these discussions is a simple, accessible, controlled vocabulary of gross anatomical terms, the SOFG Anatomy Entry List (SAEL). The SAEL is available from http://www.sofg.org and is intended as a resource for biologists, curators, bioinformaticians and developers of software supporting functional genomics. It can be used directly for annotation in the contexts described above. Importantly, each term is linked to the corresponding term in each of the major anatomy ontologies. Where the simple list does not provide enough detail or sophistication, therefore, the researcher can use the SAEL to choose the appropriate ontology and move directly to the relevant term as an entry point. The SAEL links will also be used to support computational access to the respective ontologies