Nonequilibrium corrections in the pressure tensor due to an energy flux

The physical interpretation of the nonequilibrium corrections in the pressure tensor for radiation submitted to an energy flux obtained in some previous works is revisited. Such pressure tensor is shown to describe a moving equilibrium system but not a real nonequilibrium situation.Comment: 4 pages, REVTeX, Brief Report to appear in PRE Dec 9

Theory of Compton scattering by anisotropic electrons

Compton scattering plays an important role in various astrophysical objects such as accreting black holes and neutron stars, pulsars, and relativistic jets, clusters of galaxies as well as the early Universe. In most of the calculations it is assumed that the electrons have isotropic angular distribution in some frame. However, there are situations where the anisotropy may be significant due to the bulk motions, or anisotropic cooling by synchrotron radiation, or anisotropic source of seed soft photons. We develop here an analytical theory of Compton scattering by anisotropic distribution of electrons that can simplify significantly the calculations. Assuming that the electron angular distribution can be represented by a second order polynomial over cosine of some angle (dipole and quadrupole anisotropy), we integrate the exact Klein-Nishina cross-section over the angles. Exact analytical and approximate formulae valid for any photon and electron energies are derived for the redistribution functions describing Compton scattering of photons with arbitrary angular distribution by anisotropic electrons. The analytical expressions for the corresponding photon scattering cross-section on such electrons as well as the mean energy of scattered photons, its dispersion and radiation pressure force are also derived. We applied the developed formalism to the accurate calculations of the thermal and kinematic Sunyaev-Zeldovich effects for arbitrary electron distributions.Comment: 23 pages, 12 figures, ApJ Supplement Series, in pres

Link between the laws of geometrical optics and the radiative transfer equation in media with a spatially varying refractive index

We proposed in a previous paper [Opt. Commun. 228, 33 (2003)] a modified radiative transfer equation to describe radiative transfer in a medium with a spatially varying refractive index. The present paper is devoted to the demonstration that this equation perfectly works in the non-absorbing / non-scattering limit, what was contested by L. Mart\'i-L\'opez and coworkers [Opt. Commun. 266, 44 (2006)]. The assertion that this equation would imply a zero divergence of the rays is also commented.Comment: 14 pages, 3 figure

Regulation of amino-acid metabolism controls flux to lipid accumulation in <i>Yarrowia lipolytica</i>

Yarrowia lipolytica is a promising microbial cell factory for the production of lipids to be used as fuels and chemicals, but there are few studies on regulation of its metabolism. Here we performed the first integrated data analysis of Y. lipolytica grown in carbon and nitrogen limited chemostat cultures. We first reconstructed a genome-scale metabolic model and used this for integrative analysis of multilevel omics data. Metabolite profiling and lipidomics was used to quantify the cellular physiology, while regulatory changes were measured using RNAseq. Analysis of the data showed that lipid accumulation in Y. lipolytica does not involve transcriptional regulation of lipid metabolism but is associated with regulation of amino-acid biosynthesis, resulting in redirection of carbon flux during nitrogen limitation from amino acids to lipids. Lipid accumulation in Y. lipolytica at nitrogen limitation is similar to the overflow metabolism observed in many other microorganisms, e.g. ethanol production by Sacchromyces cerevisiae at nitrogen limitation

Characterization of Neurospora crassa and Fusarium graminearum mutants defective in repeat-induced point mutation

Mutation of repetitive DNA by repeat-induced point mutation (RIP) is a process that occurs in many filamentous fungi of the Ascomycota during the sexual cycle. Concurrently, direct DNA repeats are often deleted by homologous recombination at high frequency during the sexual cycle. Thus, the processes of RIP and deletion compete to either mutate or remove repetitive DNA from the genome of filamentous fungi during sexual cycles. Both processes contribute to genome streamlining by controlling proliferation of transposable elements and by limiting expansion of gene families. While the genetic requirements for deletion by homologous recombination are well known, the mechanism behind the specific detection and mutation of repetitive DNA by RIP has yet to be elucidated as only a single gene essential for RIP, rid, has been identified. We have developed Fusarium graminearum as a model organism for the study of RIP by showing that it mutates repetitive DNA frequently during the sexual cycle and that the mutations due to RIP are dependent on rid. Further, we have sequenced a genetic mapping strain of F. graminearum (00-676-2) and identified 62,310 single nucleotide polymorphisms (SNPs) compared to the reference strain (PH-1). The SNP map will be useful for quickly mapping new mutants by bulk segregant analysis and high-throughput sequencing for which bioinformatic tools were specifically developed. The groundwork has thus been laid for identification of novel RIP mutants in F. graminearum, which being homothallic has a major advantage for identification of recessive mutations. We used a forward genetics approach to shed light on the mechanism of RIP in Neurospora crassa. Two rrr mutants that dominantly r̲educe R̲IP and r̲ecombination were characterized and identified as different mutated alleles of the same gene, rrr-1[superscript L496P] and rrr-1[superscript G325N] by bulk segregant analysis and high-throughput sequencing. Bioinformatic characterization suggests RRR-1 belongs to a previously uncharacterized group of dynamin-like proteins, which are generally involved in membrane fission and fusion. RRR-1-GFP localizes to the nuclear membrane, but not DNA, suggesting it affects RIP and recombination frequency indirectly by altering nuclear membrane dynamics during sexual development and thereby altering temporal aspects of RIP and recombination. We used a reverse genetics approach to determine whether high frequency RIP and homologous recombination of repetitive DNA during the sexual cycle are linked mechanistically or spatio-temporally. We tested strains where genes important for deletion by homologous recombination were knocked out and found all to be completely RIP competent except mre11, which, while sterile in homozygous deletion crosses, displayed lower RIP frequency in heterozygous crosses. This suggests that mre11 has roles in homologous recombination as well as non-homologous end joining may be important for RIP. Collectively, this work developed methods for efficiently mapping mutations and identified a novel protein that reduces RIP and recombination frequency but did not identify any mechanistic link between the two processes

Similarity Properties and Scaling Laws of Radiation Hydrodynamic Flows in Laboratory Astrophysics

The spectacular recent development of modern high-energy density laboratory facilities which concentrate more and more energy in millimetric volumes allows the astrophysical community to reproduce and to explore, in millimeter-scale targets and during very short times, astrophysical phenomena where radiation and matter are strongly coupled. The astrophysical relevance of these experiments can be checked from the similarity properties and especially scaling laws establishment, which constitutes the keystone of laboratory astrophysics. From the radiating optically thin regime to the so-called optically thick radiative pressure regime, we present in this paper, for the first time, a complete analysis of the main radiating regimes that we encountered in laboratory astrophysics with the same formalism based on the Lie-group theory. The use of the Lie group method appears as systematic which allows to construct easily and orderly the scaling laws of a given problem. This powerful tool permits to unify the recent major advances on scaling laws and to identify new similarity concepts that we discuss in this paper and which opens important applications for the present and the future laboratory astrophysics experiments. All these results enable to demonstrate theoretically that astrophysical phenomena in such radiating regimes can be explored experimentally thanks to powerful facilities. Consequently the results presented here are a fundamental tool for the high-energy density laboratory astrophysics community in order to quantify the astrophysics relevance and justify laser experiments. Moreover, relying on the Lie-group theory, this paper constitutes the starting point of any analysis of the self-similar dynamics of radiating fluids.Comment: Astrophys. J. accepte

A photon transport problem with a time-dependent point source

We consider a time-dependent problem of photon transport in an interstellar cloud with a point photon source modeled by a Dirac δ functional. The existence of a unique distributional solution to this problem is established by using the theory of continuous semigroups of operators on locally convex spaces coupled with a constructive approach for producing spaces of generalized functions

A multigroup diffusion solver using pseudo transient continuation for a radiation-hydrodynamic code with patch-based AMR

We present a scheme to solve the nonlinear multigroup radiation diffusion (MGD) equations. The method is incorporated into a massively parallel, multidimensional, Eulerian radiation-hydrodynamic code with adaptive mesh refinement (AMR). The patch-based AMR algorithm refines in both space and time creating a hierarchy of levels, coarsest to finest. The physics modules are time-advanced using operator splitting. On each level, separate level-solve packages advance the modules. Our multigroup level-solve adapts an implicit procedure which leads to a two-step iterative scheme that alternates between elliptic solves for each group with intra-cell group coupling. For robustness, we introduce pseudo transient continuation (PTC). We analyze the magnitude of the PTC parameter to ensure positivity of the resulting linear system, diagonal dominance and convergence of the two-step scheme. For AMR, a level defines a subdomain for refinement. For diffusive processes such as MGD, the refined level uses Dirichet boundary data at the coarse-fine interface and the data is derived from the coarse level solution. After advancing on the fine level, an additional procedure, the sync-solve (SS), is required in order to enforce conservation. The MGD SS reduces to an elliptic solve on a combined grid for a system of G equations, where G is the number of groups. We adapt the partial temperature scheme for the SS; hence, we reuse the infrastructure developed for scalar equations. Results are presented. (Abridged)Comment: 46 pages, 14 figures, accepted to JC

A Hybrid Godunov Method for Radiation Hydrodynamics

From a mathematical perspective, radiation hydrodynamics can be thought of as a system of hyperbolic balance laws with dual multiscale behavior (multiscale behavior associated with the hyperbolic wave speeds as well as multiscale behavior associated with source term relaxation). With this outlook in mind, this paper presents a hybrid Godunov method for one-dimensional radiation hydrodynamics that is uniformly well behaved from the photon free streaming (hyperbolic) limit through the weak equilibrium diffusion (parabolic) limit and to the strong equilibrium diffusion (hyperbolic) limit. Moreover, one finds that the technique preserves certain asymptotic limits. The method incorporates a backward Euler upwinding scheme for the radiation energy density and flux as well as a modified Godunov scheme for the material density, momentum density, and energy density. The backward Euler upwinding scheme is first-order accurate and uses an implicit HLLE flux function to temporally advance the radiation components according to the material flow scale. The modified Godunov scheme is second-order accurate and directly couples stiff source term effects to the hyperbolic structure of the system of balance laws. This Godunov technique is composed of a predictor step that is based on Duhamel's principle and a corrector step that is based on Picard iteration. The Godunov scheme is explicit on the material flow scale but is unsplit and fully couples matter and radiation without invoking a diffusion-type approximation for radiation hydrodynamics. This technique derives from earlier work by Miniati & Colella 2007. Numerical tests demonstrate that the method is stable, robust, and accurate across various parameter regimes.Comment: accepted for publication in Journal of Computational Physics; 61 pages, 15 figures, 11 table

CASTRO: A New Compressible Astrophysical Solver. II. Gray Radiation Hydrodynamics

We describe the development of a flux-limited gray radiation solver for the compressible astrophysics code, CASTRO. CASTRO uses an Eulerian grid with block-structured adaptive mesh refinement based on a nested hierarchy of logically-rectangular variable-sized grids with simultaneous refinement in both space and time. The gray radiation solver is based on a mixed-frame formulation of radiation hydrodynamics. In our approach, the system is split into two parts, one part that couples the radiation and fluid in a hyperbolic subsystem, and another parabolic part that evolves radiation diffusion and source-sink terms. The hyperbolic subsystem is solved explicitly with a high-order Godunov scheme, whereas the parabolic part is solved implicitly with a first-order backward Euler method.Comment: accepted for publication in ApJS, high-resolution version available at https://ccse.lbl.gov/Publications/wqzhang/castro2.pd