Journal Staff

A time-dependent coordinate transformation of a constant coeffcient hyperbolic equation which results in a variable coeffcient problem is considered. By using the energy method, we derive well-posed boundary conditions for the continuous problem. It is shown that the number of boundary conditions depend on the coordinate transformation. By using Summation-by-Parts (SBP) operators for the space discretization and weak boundary conditions, an energy stable finite dieffrence scheme is obtained. We also show how to construct a time-dependent penalty formulation that automatically imposes the right number of boundary conditions. Numerical calculations corroborate the stability and accuracy of the approximations

Higher order finite difference schemes for the magnetic induction equations

We describe high order accurate and stable finite difference schemes for the initial-boundary value problem associated with the magnetic induction equations. These equations model the evolution of a magnetic field due to a given velocity field. The finite difference schemes are based on Summation by Parts (SBP) operators for spatial derivatives and a Simultaneous Approximation Term (SAT) technique for imposing boundary conditions. We present various numerical experiments that demonstrate both the stability as well as high order of accuracy of the schemes.Comment: 20 page

New, efficient, and accurate high order derivative and dissipation operators satisfying summation by parts, and applications in three-dimensional multi-block evolutions

We construct new, efficient, and accurate high-order finite differencing operators which satisfy summation by parts. Since these operators are not uniquely defined, we consider several optimization criteria: minimizing the bandwidth, the truncation error on the boundary points, the spectral radius, or a combination of these. We examine in detail a set of operators that are up to tenth order accurate in the interior, and we surprisingly find that a combination of these optimizations can improve the operators' spectral radius and accuracy by orders of magnitude in certain cases. We also construct high-order dissipation operators that are compatible with these new finite difference operators and which are semi-definite with respect to the appropriate summation by parts scalar product. We test the stability and accuracy of these new difference and dissipation operators by evolving a three-dimensional scalar wave equation on a spherical domain consisting of seven blocks, each discretized with a structured grid, and connected through penalty boundary conditions.Comment: 16 pages, 9 figures. The files with the coefficients for the derivative and dissipation operators can be accessed by downloading the source code for the document. The files are located in the "coeffs" subdirector

Demarcating the Right to Gather News: A Sequential Interpretation of the First Amendment

In this paper we construct well-posed boundary conditions for the compressible Euler and Navier-Stokes equations in two space dimensions. When also considering the dual equations, we show how to construct the boundary conditions so that both the primal and dual problems are well-posed. By considering the primal and dual problems simultaneously, we construct energy stable and dual consistent finite difference schemes on summation-by-  parts form with weak imposition of the boundary conditions. According to linear theory, the stable and dual consistent discretization can be used to compute linear integral functionals from the solution at a superconvergent rate. Here we evaluate numerically the superconvergence property for the non-linear Euler and Navier{ Stokes equations with linear and non-linear integral functionals

Towards Verification of Unstructured-Grid Solvers

New methodology for verification of computational methods using unstructured grids is presented. The discretization order properties are studied in computational windows, easily constructed within a collection of grids or a single grid. The windows can be adjusted to isolate the interior discretization, the boundary discretization, or singularities. A major component of the methodology is the downscaling test, introduced previously for studying the convergence rates of truncation and discretization errors of finite-volume discretization schemes on general unstructured grids. Demonstrations of the method are shown, including a comparative accuracy assessment of commonly-used schemes on general mixed grids and the identification of local accuracy deterioration at intersections of tangency and inflow/outflow boundaries. Recommendations for the use of the methodology in large-scale computational simulations are given

A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution

BACKGROUND: Comparative genomic studies of the mitochondrion-lacking protist group Diplomonadida (diplomonads) has been lacking, although Giardia lamblia has been intensively studied. We have performed a sequence survey project resulting in 2341 expressed sequence tags (EST) corresponding to 853 unique clones, 5275 genome survey sequences (GSS), and eleven finished contigs from the diplomonad fish parasite Spironucleus salmonicida (previously described as S. barkhanus). RESULTS: The analyses revealed a compact genome with few, if any, introns and very short 3' untranslated regions. Strikingly different patterns of codon usage were observed in genes corresponding to frequently sampled ESTs versus genes poorly sampled, indicating that translational selection is influencing the codon usage of highly expressed genes. Rigorous phylogenomic analyses identified 84 genes – mostly encoding metabolic proteins – that have been acquired by diplomonads or their relatively close ancestors via lateral gene transfer (LGT). Although most acquisitions were from prokaryotes, more than a dozen represent likely transfers of genes between eukaryotic lineages. Many genes that provide novel insights into the genetic basis of the biology and pathogenicity of this parasitic protist were identified including 149 that putatively encode variant-surface cysteine-rich proteins which are candidate virulence factors. A number of genomic properties that distinguish S. salmonicida from its human parasitic relative G. lamblia were identified such as nineteen putative lineage-specific gene acquisitions, distinct mutational biases and codon usage and distinct polyadenylation signals. CONCLUSION: Our results highlight the power of comparative genomic studies to yield insights into the biology of parasitic protists and the evolution of their genomes, and suggest that genetic exchange between distantly-related protist lineages may be occurring at an appreciable rate in eukaryote genome evolution

Egg size-number trade-off and a decline in oviposition site choice quality: Female Pararge aegeria butterflies pay a cost of having males present at oviposition

Once mated, the optimal strategy for females of the monandrous butterfly, Pararge aegeria, is to avoid male contact and devote as much time as possible to ovipositing, as there is little advantage for females to engage in multiple matings. In other butterfly species the presence of males during egg laying has been shown to affect aspects of oviposition behavior and it has been suggested that repeated interference from males has the potential to reduce reproductive output. The aim of this study was to assess the effects of male presence during oviposition on reproductive output and behavior of a population of P. aegeria obtained from Madeira Island, Portugal, and maintained in the laboratory. Two experiments were performed where females were housed individually in small cages. Experiment 1 examined how social factors influenced the egg laying behavior of females. To do this the presence or absence of males was manipulated and egg size and number was measured over the first 14 days of oviposition. It was observed that when males were present during oviposition females made a trade-off between egg size and number. Experiment 2 examined how social factors affected oviposition site choice. Again, male presence/absence was manipulated, but in this experiment where the female laid her egg in relation to host quality was scored, and the size of the egg laid was measured. In the absence of males females selectively positioned their larger eggs on good quality host plants. However, selective oviposition was no longer observed when females were in the presence of males. We suggest that P. aegeria females from the Madeira Island population are adapted for a flexible oviposition strategy, governed by external cues, allowing a trade-off between egg size and number when the time available for egg laying is limiting

Interaction of laser radiation with the material during production powders and fibers

Воздействие лазерного излучения на твердое тело приводит к изменению температурного поля обрабатываемого вещества. Характер нагрева, определяющийся скоростями изменения температуры, температурных градиентов, оказывается различным в зависимости от свойств обрабатываемого материала и условий обработки. Основными физическими параметрами процесса лазерной обработки твердых тел являются удельная мощность поглощенного лазерного потока 104–109 Вт/см2 и время взаимодействия металла с лучом 10–5–10–8 с. При взаимодействии подобных импульсов излучения с поверхностью происходит мгновенное взрывоподобное плавление части материала и перевод окружающего поверхность вещества в плазменное состояние. Последующее расширение плазмы сопровождается возникновением ударной волны с пиковым давлением 1–10 ГПа, которая действует на материал, и имеет место диспергирование металла. Решена математическая задача нагрева и плавления цилиндрической пластины нормально падающим на ее поверхность световым потоком лазерного излучения, описываемая системой уравнений теплопроводности в трех сечениях нагреваемой пластины, которые характеризуются временным фактором воздействия лазерного излучения на вещество: 1) 0 ≤ t ≤ tm; 2) t > tm; 3) tm tm; 3) tm < t ≤ th (here tm, th is the time moment corresponding to the beginning of the formation of the liquid phase and the end of the melting of the plate, respectively). The calculated dependences of changes in the surface temperature of metal alloys X18N10T, X15N60 during the action of a laser radiation pulse with a duration of τ=5 ms are presented. The presence of a phase transition associated with metal melting (an inflection in the curves) leads to a temporary decrease in the rate of temperature growth. The distribution of temperature fields causes a significant heterogeneity in the distribution of temperature over the thickness of materials, which reaches 2000 °C or more depending on the thickness of the metal and the conditions of exposure. The temperature curves of the surface heating repeat the shape of the pulse, and the temperature of the rest of the metal has a nonlinear tendency to increase with the output to the asymptote. It is established that the process of explosive metal sputtering requires heating the volume of the material above the melting point at a thickness of 300–350 microns and an impact energy of 7–8 J. Reducing the level of energy impact to 5–6 J and increasing the thickness of the workpiece more than 500 microns does not provide the distribution of temperature fields required for the implementation of the spraying process