Natural discretizations for the divergence, gradient, and curl on logically rectangular grids

AbstractThis is the first in series of papers creating a discrete analog of vector analysis on logically rectangular, nonorthogonal, nonsmooth grids. We introduce notations for 2-D logically rectangular grids, describe both cell-valued and nodal discretizations for scalar functions, and construct the natural discretizations of vector fields, using the vector components normal and tangential to the cell boundaries. We then define natural discrete analogs of the divergence, gradient, and curl operators based on coordinate invariant definitions and interpret these formulas in terms of curvilinear coordinates, such as length of elements of coordinate lines, areas of elements of coordinate surfaces, and elementary volumes.We introduce the discrete volume integral of scalar functions, the discrete surface integral, and a discrete analog of the line integral and prove discrete versions of the main theorems relating these objects. These theorems include the following: the discrete analog of relationship div A→ = 0 if and only if A→ = curl B→; curl A→ = 0 if and only if A→ = grad ϕ; if A→ = grad ϕ, then the line integral does not depend on path; and if the line integral of a vector function is equal to zero for any closed path, then this vector is the gradient of a scalar function.Last, we define the discrete operators DIV, GRAD, and CURL in terms of primitive differencing operators (based on forward and backward differences) and primitive metric operators (related to multiplications of discrete functions by length of edges, areas of surfaces, and volumes of 3-D cells). These formulations elucidate the structure of the discrete operators and are useful when investigating the relationships between operators and their adjoints

Breakdown of antiferromagnet order in polycrystalline NiFe/NiO bilayers probed with acoustic emission

International audienc

Simulation of stellar instabilities with vastly different timescales using domain decomposition

Strange mode instabilities in the envelopes of massive stars lead to shock waves, which can oscillate on a much shorter timescale than that associated with the primary instability. The phenomenon is studied by direct numerical simulation using a, with respect to time, implicit Lagrangian scheme, which allows for the variation by several orders of magnitude of the dependent variables. The timestep for the simulation of the system is reduced appreciably by the shock oscillations and prevents its long term study. A procedure based on domain decomposition is proposed to surmount the difficulty of vastly different timescales in various regions of the stellar envelope and thus to enable the desired long term simulations. Criteria for domain decomposition are derived and the proper treatment of the resulting inner boundaries is discussed. Tests of the approach are presented and its viability is demonstrated by application to a model for the star P Cygni. In this investigation primarily the feasibility of domain decomposition for the problem considered is studied. We intend to use the results as the basis of an extension to two dimensional simulations.Comment: 15 pages, 10 figures, published in MNRA

Poly(arabitol phosphate) teichoic acid in the cell wall of Agromyces cerinus subsp. cerinus VKM Ac-1340T

AbstractOn the basis of NMR studies and analysis of the products of acid and alkaline hydrolyses the following structures were established for the repeating units of poly(arabitol phosphate) teichoic acid: α-6-deoxy-l-Talp-(1 → 3)-β-d-GIcpNAc-(1 → 2)-α-l-Rhap-(1 → 4(2)-d-Arabitol-PO4 and β-d-GlcpNAc-(1 → 2)-α-l-Rhap-(1 → 4(2)-d-arabitol-PO4. The molar ratio of these units is about 1.2:1.0, respectively. Poly(arabitol phosphate) teichoic acid is here reported in bacterial cell walls for the first time

Br, VO3, MoO4

The intersecting ЬіѴОз-КВг-ЬіКМо04 triangle in the quaternary mutual system Li, КBr, VO3, MoO4 was studied by differential thermal analysis, and the melting temperature and composition in the invariant points were determined

Capsular profiling of the Cronobacter genus and the association of specific Cronobacter sakazakii and C. malonaticus capsule types with neonatal meningitis and necrotizing enterocolitis

Background: Cronobacter sakazakii and C. malonaticus can cause serious diseases especially in infants where they are associated with rare but fatal neonatal infections such as meningitis and necrotising enterocolitis. Methods: This study used 104 whole genome sequenced strains, covering all seven species in the genus, to analyse capsule associated clusters of genes involved in the biosynthesis of the O-antigen, colanic acid, bacterial cellulose, enterobacterial common antigen (ECA), and a previously uncharacterised K-antigen. Results: Phylogeny of the gnd and galF genes flanking the O-antigen region enabled the defining of 38 subgroups which are potential serotypes. Two variants of the colanic acid synthesis gene cluster (CA1 and CA2) were found which differed with the absence of galE in CA2. Cellulose (bcs genes) were present in all species, but were absent in C. sakazakii sequence type (ST) 13 and clonal complex (CC) 100 strains. The ECA locus was found in all strains. The K-antigen capsular polysaccharide Region 1 (kpsEDCS) and Region 3 (kpsMT) genes were found in all Cronobacter strains. The highly variable Region 2 genes were assigned to 2 homology groups (K1 and K2). C. sakazakii and C. malonaticus isolates with capsular type [K2:CA2:Cell+] were associated with neonatal meningitis and necrotizing enterocolitis. Other capsular types were less associated with clinical infections. Conclusion: This study proposes a new capsular typing scheme which identifies a possible important virulence trait associated with severe neonatal infections. The various capsular polysaccharide structures warrant further investigation as they could be relevant to macrophage survival, desiccation resistance, environmental survival, and biofilm formation in the hospital environment, including neonatal enteral feeding tubes

K19 capsular polysaccharide of acinetobacter baumannii is produced via a Wzy polymerase encoded in a small genomic island rather than the KL19 capsule gene cluster

© 2016 The Authors.Polymerization of the oligosaccharides (K units) of complex capsular polysaccharides (CPSs) requires a Wzy polymerase, which is usually encoded in the gene cluster that directs K unit synthesis. Here, a gene cluster at the Acinetobacter K locus (KL) that lacks a wzy gene, KL19, was found in Acinetobacter baumannii ST111 isolates 28 and RBH2 recovered from hospitals in the Russian Federation and Australia, respectively. However, these isolates produced long-chain capsule, and a wzy gene was found in a 6.1 kb genomic island (GI) located adjacent to the cpn60 gene. The GI also includes an acetyltransferase gene, atr25, which is interrupted by an insertion sequence (IS) in RBH2. The capsule structure from both strains was→3)-α-D-GalpNAc-(1→4)-α-D-GalpNAcA-(1→3)-β-D-QuipNAc4NAc-(1→, determined using NMR spectroscopy. Biosynthesis of the K unit was inferred to be initiated with QuiNAc4NAc, and hence the Wzy forms the β-(1→3) linkage between QuipNAc4NAc and GalpNAc. The GalpNAc residue is 6-O-acetylated in isolate 28 only, showing that atr25 is responsible for this acetylation. The same GI with or without an IS in atr25 was found in draft genomes of other KL19 isolates, as well as ones carrying a closely related CPS gene cluster, KL39, which differs from KL19 only in a gene for an acyltransferase in the QuiNAc4NR synthesis pathway. Isolates carrying a KL1 variant with the wzy and atr genes each interrupted by an ISAba125 also have this GI. To our knowledge, this study is the first report of genes involved in capsule biosynthesis normally found at the KL located elsewhere in A. baumannii genomes

Measurement of electrodynamics characteristics of higher order modes for harmonic cavity at 2400 MHz

In the frameworks of the High Luminosity Large Hadron Collider (HL-LHC) upgrade program an application of additional superconducting harmonic cavities operating at 800 MHz is currently under discussion. As a possible candidate, an assembly of two cavities with grooved beam pipes connected by a drift tube and housed in a common cryomodule, was proposed. In this article we discuss measurements of loaded Q-factors of higher order modes (HOM) performed on a scaled aluminium single cell cavity prototype with the fundamental frequency of 2400 MHz and on an array of two such cavities connected by a narrow beam pipe. The measurements were performed for the system with and without the matching load in the drift tube.

Structure of the capsular polysaccharide of Acinetobacter baumannii 1053 having the KL91 capsule biosynthesis gene locus

© 2014 Elsevier Ltd. All rights reserved. Acinetobacter baumannii 1053 is the type strain for the maintenance of specific bacteriophage AP22, which infects a fairly broad range of A. baumannii strains circulating in Russian clinics and hospitals. A capsular polysaccharide (CPS) was isolated from cells of strain 1053 and studied by sugar analysis along with 1D and 2D 1H and 13C NMR spectroscopy. The following structure of the linear trisaccharide repeating unit was established: →4)-β-D-ManpNAcA-(1→4)-β-D-ManpNAcA-(1→3)-α-D-FucpNAc-(1→ where ManNAcA and FucNAc indicate 2-acetamido-2-deoxymannuronic acid and 2-acetamido-2,6-dideoxygalactose, respectively. A polysaccharide having the same repeating unit but a shorter chain was isolated by the phenol-water extraction of bacterial cells. Sequencing of the CPS biosynthesis gene locus showed that A. baumannii 1053 belongs to a new group designated KL91. The gene functions assigned putatively by a comparison with available databases were in agreement with the CPS structure established

Production of the K16 capsular polysaccharide by Acinetobacter baumannii ST25 isolate D4 involves a novel glycosyltransferase encoded in the KL16 gene cluster

A new capsular polysaccharide (CPS) biosynthesis gene cluster, KL16, was found in the genome sequence of a clinical Acinetobacter baumannii ST25 isolate, D4. The variable part of KL16 contains a module of genes for synthesis of 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic acid (5,7-di-N-acetylpseudaminic acid, Pse5Ac7Ac), a gene encoding ItrA3 that initiates the CPS synthesis with d-GlcpNAc, and two glycosyltransferase (Gtr) genes. The K16 CPS was studied by sugar analysis and Smith degradation along with 1D and 2D H and C NMR spectroscopy, and shown to be built up of linear trisaccharide repeats containing d-galactose (d-Gal), N-acetyl-d-glucosamine (d-GlcNAc), and Pse5Ac7Ac. The d-Galp residue is linked to the d-GlcpNAc initiating sugar via a β-(1 → 3) linkage evidently formed by a Gtr5 variant, Gtr5, encoded in KL16. This reveals an altered or relaxed substrate specificity of this variant as the majority of Gtr5-type glycosyltransferases have previously been shown to form a β-d-Galp-(1 → 3)-d-GalpNAc linkage. The β-Psep5Ac7Ac-(2 → 4)-d-Galp linkage is predicted to be formed by the other glycosyltransferase, Gtr37, which does not match members of any known glycosyltransferase family