Phase appearance or disappearance in two-phase flows

This paper is devoted to the treatment of specific numerical problems which appear when phase appearance or disappearance occurs in models of two-phase flows. Such models have crucial importance in many industrial areas such as nuclear power plant safety studies. In this paper, two outstanding problems are identified: first, the loss of hyperbolicity of the system when a phase appears or disappears and second, the lack of positivity of standard shock capturing schemes such as the Roe scheme. After an asymptotic study of the model, this paper proposes accurate and robust numerical methods adapted to the simulation of phase appearance or disappearance. Polynomial solvers are developed to avoid the use of eigenvectors which are needed in usual shock capturing schemes, and a method based on an adaptive numerical diffusion is designed to treat the positivity problems. An alternate method, based on the use of the hyperbolic tangent function instead of a polynomial, is also considered. Numerical results are presented which demonstrate the efficiency of the proposed solutions

Correlated Gravitational Wave and Neutrino Signals from General-Relativistic Rapidly Rotating Iron Core Collapse

We present results from a new set of 3D general-relativistic hydrodynamic simulations of rotating iron core collapse. We assume octant symmetry and focus on axisymmetric collapse, bounce, the early postbounce evolution, and the associated gravitational wave (GW) and neutrino signals. We employ a finite-temperature nuclear equation of state, parameterized electron capture in the collapse phase, and a multi-species neutrino leakage scheme after bounce. The latter captures the important effects of deleptonization, neutrino cooling and heating and enables approximate predictions for the neutrino luminosities in the early evolution after core bounce. We consider 12-solar-mass and 40-solar-mass presupernova models and systematically study the effects of (i) rotation, (ii) progenitor structure, and (iii) postbounce neutrino leakage on dynamics, GW, and, neutrino signals. We demonstrate, that the GW signal of rapidly rotating core collapse is practically independent of progenitor mass and precollapse structure. Moreover, we show that the effects of neutrino leakage on the GW signal are strong only in nonrotating or slowly rotating models in which GW emission is not dominated by inner core dynamics. In rapidly rotating cores, core bounce of the centrifugally-deformed inner core excites the fundamental quadrupole pulsation mode of the nascent protoneutron star. The ensuing global oscillations (f~700-800 Hz) lead to pronounced oscillations in the GW signal and correlated strong variations in the rising luminosities of antineutrino and heavy-lepton neutrinos. We find these features in cores that collapse to protoneutron stars with spin periods <~ 2.5 ms and rotational energies sufficient to drive hyper-energetic core-collapse supernova explosions. Hence, joint GW + neutrino observations of a core collapse event could deliver strong evidence for or against rapid core rotation. [abridged]Comment: 29 pages, 14 figures. Replaced with version matching published versio

Numerical simulations of shocks encountering clumpy regions

We present numerical simulations of the adiabatic interaction of a shock with a clumpy region containing many individual clouds. Our work incorporates a sub-grid turbulence model which for the first time makes this investigation feasible. We vary the Mach number of the shock, the density contrast of the clouds, and the ratio of total cloud mass to inter-cloud mass within the clumpy region. Cloud material becomes incorporated into the flow. This "mass-loading" reduces the Mach number of the shock, and leads to the formation of a dense shell. In cases in which the mass-loading is sufficient the flow slows enough that the shock degenerates into a wave. The interaction evolves through up to four stages: initially the shock decelerates; then its speed is nearly constant; next the shock accelerates as it leaves the clumpy region; finally it moves at a constant speed close to its initial speed. Turbulence is generated in the post-shock flow as the shock sweeps through the clumpy region. Clouds exposed to turbulence can be destroyed more rapidly than a similar cloud in an "isolated" environment. The lifetime of a downstream cloud decreases with increasing cloud-to-intercloud mass ratio. We briefly discuss the significance of these results for starburst superwinds and galaxy evolution.Comment: 17 pages, 19 figures, accepted for publication in MNRA

The impact of viscosity on the morphology of gaseous flows in semidetached binary systems

Results of 3D gas dynamical simulation of mass transfer in binaries are presented for systems with various values of viscosity. Analysis of obtained solutions shows that in the systems with low value of viscosity the flow structure is qualitatively similar to one for systems with high viscosity. Presented calculations confirm that there is no shock interaction between the stream from L1 and the forming accretion disk (`hot spot') at any value of viscosity.Comment: LaTeX, 18 pages, 15 eps-figures, Astron. Reports, in pres

Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq

Embryonic stem cells (ESCs) can differentiate into any given cell type and therefore represent a versatile model to study the link between gene regulation and differentiation. To quantitatively assess the dynamics of enhancer activity during the early stages of murine ESC differentiation, we analyzed accessible genomic regions using STARR-seq, a massively parallel reporter assay. This resulted in a genome-wide quantitative map of active mESC enhancers, in pluripotency and during the early stages of differentiation. We find that only a minority of accessible regions is active and that such regions are enriched near promoters, characterized by specific chromatin marks, enriched for distinct sequence motifs, and modeling shows that active regions can be predicted from sequence alone. Regions that change their activity upon retinoic acid-induced differentiation are more prevalent at distal intergenic regions when compared to constitutively active enhancers. Further, analysis of differentially active enhancers verified the contribution of individual TF motifs toward activity and inducibility as well as their role in regulating endogenous genes. Notably, the activity of retinoic acid receptor alpha (RARα) occupied regions can either increase or decrease upon the addition of its ligand, retinoic acid, with the direction of the change correlating with spacing and orientation of the RARα consensus motif and the co-occurrence of additional sequence motifs. Together, our genome-wide enhancer activity map elucidates features associated with enhancer activity levels, identifies regulatory regions disregarded by computational prediction tools, and provides a resource for future studies into regulatory elements in mESCs

EvoL: The new Padova T-SPH parallel code for cosmological simulations - I. Basic code: gravity and hydrodynamics

We present EvoL, the new release of the Padova N-body code for cosmological simulations of galaxy formation and evolution. In this paper, the basic Tree + SPH code is presented and analysed, together with an overview on the software architectures. EvoL is a flexible parallel Fortran95 code, specifically designed for simulations of cosmological structure formation on cluster, galactic and sub-galactic scales. EvoL is a fully Lagrangian self-adaptive code, based on the classical Oct-tree and on the Smoothed Particle Hydrodynamics algorithm. It includes special features such as adaptive softening lengths with correcting extra-terms, and modern formulations of SPH and artificial viscosity. It is designed to be run in parallel on multiple CPUs to optimize the performance and save computational time. We describe the code in detail, and present the results of a number of standard hydrodynamical tests.Comment: 33 pages, 49 figures, accepted on A&

Multidimensional Supernova Simulations with Approximative Neutrino Transport I. Neutron Star Kicks and the Anisotropy of Neutrino-Driven Explosions in Two Spatial Dimensions

By means of two-dimensional (2D) simulations we study hydrodynamic instabilities during the first seconds of neutrino-driven supernova explosions, using a PPM hydrodynamics code, supplemented with a gray, non-equilibrium approximation of radial neutrino transport. We consider three 15 solar mass progenitors with different structures and one rotating model, in which we replace the dense core of the newly formed neutron star (NS) by a contracting inner grid boundary, and trigger neutrino-driven explosions by systematically varying the neutrino fluxes emitted at this boundary. Confirming more idealized studies as well as supernova simulations with spectral transport, we find that random seed perturbations can grow by hydrodynamic instabilities to a globally asymmetric mass distribution, leading to a dominance of dipole (l=1) and quadrupole (l=2) modes in the explosion ejecta. Anisotropic gravitational and hydrodynamic forces are found to accelerate the NS on a timescale of 2-3 seconds. Since the explosion anisotropies develop chaotically, the magnitude of the corresponding kick varies stochastically in response to small differences in the fluid flow. Our more than 70 models separate into two groups, one with high and the other with low NS velocities and accelerations after 1s of post-bounce evolution, depending on whether the l=1 mode is dominant in the ejecta or not. This leads to a bimodality of the distribution when the NS velocities are extrapolated to their terminal values. The fast group has an average velocity of about 500 km/s and peak values in excess of 1000 km/s. Establishing a link to the measured distribution of pulsar velocities, however, requires a much larger set of calculations and ultimately 3D modeling. (abridged)Comment: 40 pages, 28 figures; significantly shortened and revised version according to referee's comments; accepted by Astronomy & Astrophysic

Simulation techniques for cosmological simulations

Modern cosmological observations allow us to study in great detail the evolution and history of the large scale structure hierarchy. The fundamental problem of accurate constraints on the cosmological parameters, within a given cosmological model, requires precise modelling of the observed structure. In this paper we briefly review the current most effective techniques of large scale structure simulations, emphasising both their advantages and shortcomings. Starting with basics of the direct N-body simulations appropriate to modelling cold dark matter evolution, we then discuss the direct-sum technique GRAPE, particle-mesh (PM) and hybrid methods, combining the PM and the tree algorithms. Simulations of baryonic matter in the Universe often use hydrodynamic codes based on both particle methods that discretise mass, and grid-based methods. We briefly describe Eulerian grid methods, and also some variants of Lagrangian smoothed particle hydrodynamics (SPH) methods.Comment: 42 pages, 16 figures, accepted for publication in Space Science Reviews, special issue "Clusters of galaxies: beyond the thermal view", Editor J.S. Kaastra, Chapter 12; work done by an international team at the International Space Science Institute (ISSI), Bern, organised by J.S. Kaastra, A.M. Bykov, S. Schindler & J.A.M. Bleeke

A New Open-Source Code for Spherically-Symmetric Stellar Collapse to Neutron Stars and Black Holes

We present the new open-source spherically-symmetric general-relativistic (GR) hydrodynamics code GR1D. It is based on the Eulerian formulation of GR hydrodynamics (GRHD) put forth by Romero-Ibanez-Gourgoulhon and employs radial-gauge, polar-slicing coordinates in which the 3+1 equations simplify substantially. We discretize the GRHD equations with a finite-volume scheme, employing piecewise-parabolic reconstruction and an approximate Riemann solver. GR1D is intended for the simulation of stellar collapse to neutron stars and black holes and will also serve as a testbed for modeling technology to be incorporated in multi-D GR codes. Its GRHD part is coupled to various finite-temperature microphysical equations of state in tabulated form that we make available with GR1D. An approximate deleptonization scheme for the collapse phase and a neutrino-leakage/heating scheme for the postbounce epoch are included and described. We also derive the equations for effective rotation in 1D and implement them in GR1D. We present an array of standard test calculations and also show how simple analytic equations of state in combination with presupernova models from stellar evolutionary calculations can be used to study qualitative aspects of black hole formation in failing rotating core-collapse supernovae. In addition, we present a simulation with microphysical EOS and neutrino leakage/heating of a failing core-collapse supernova and black hole formation in a presupernova model of a 40 solar mass zero-age main-sequence star. We find good agreement on the time of black hole formation (within 20%) and last stable protoneutron star mass (within 10%) with predictions from simulations with full Boltzmann neutrino radiation hydrodynamics.Comment: 25 pages, 6 figures, 2 appendices. Accepted for publication to the Classical and Quantum Gravity special issue for MICRA2009. Code may be downloaded from http://www.stellarcollapse.org Update: corrected title, small modifications suggested by the referees, added source term derivation in appendix