A new dimension to Turing patterns

It is well known that simple reaction-diffusion systems can display very rich pattern formation behavior. Here we have studied two examples of such systems in three dimensions. First we investigate the morphology and stability of a generic Turing system in three dimensions and then the well-known Gray-Scott model. In the latter case, we added a small number of morphogen sources in the system in order to study its robustness and the formation of connections between the sources. Our results raise the question of whether Turing patterning can produce an inductive signaling mechanism for neuronal growth.Comment: Movies available here at http://www.lce.hut.fi/research/polymer/turing.shtm

Hyperbolic character of the angular moment equations of radiative transfer and numerical methods

We study the mathematical character of the angular moment equations of radiative transfer in spherical symmetry and conclude that the system is hyperbolic for general forms of the closure relation found in the literature. Hyperbolicity and causality preservation lead to mathematical conditions allowing to establish a useful characterization of the closure relations. We apply numerical methods specifically designed to solve hyperbolic systems of conservation laws (the so-called Godunov-type methods), to calculate numerical solutions of the radiation transport equations in a static background. The feasibility of the method in any kind of regime, from diffusion to free-streaming, is demonstrated by a number of numerical tests and the effect of the choice of the closure relation on the results is discussed.Comment: 37 pags, 12 figures, accepted for publication in MNRA

A hybridizable discontinuous Galerkin method for electromagnetics with a view on subsurface applications

Two Hybridizable Discontinuous Galerkin (HDG) schemes for the solution of Maxwell's equations in the time domain are presented. The first method is based on an electromagnetic diffusion equation, while the second is based on Faraday's and Maxwell--Amp\`ere's laws. Both formulations include the diffusive term depending on the conductivity of the medium. The three-dimensional formulation of the electromagnetic diffusion equation in the framework of HDG methods, the introduction of the conduction current term and the choice of the electric field as hybrid variable in a mixed formulation are the key points of the current study. Numerical results are provided for validation purposes and convergence studies of spatial and temporal discretizations are carried out. The test cases include both simulation in dielectric and conductive media

A Two-moment Radiation Hydrodynamics Module in Athena Using a Time-explicit Godunov Method

We describe a module for the Athena code that solves the gray equations of radiation hydrodynamics (RHD), based on the first two moments of the radiative transfer equation. We use a combination of explicit Godunov methods to advance the gas and radiation variables including the non-stiff source terms, and a local implicit method to integrate the stiff source terms. We adopt the M1 closure relation and include all leading source terms. We employ the reduced speed of light approximation (RSLA) with subcycling of the radiation variables in order to reduce computational costs. Our code is dimensionally unsplit in one, two, and three space dimensions and is parallelized using MPI. The streaming and diffusion limits are well-described by the M1 closure model, and our implementation shows excellent behavior for a problem with a concentrated radiation source containing both regimes simultaneously. Our operator-split method is ideally suited for problems with a slowly varying radiation field and dynamical gas flows, in which the effect of the RSLA is minimal. We present an analysis of the dispersion relation of RHD linear waves highlighting the conditions of applicability for the RSLA. To demonstrate the accuracy of our method, we utilize a suite of radiation and RHD tests covering a broad range of regimes, including RHD waves, shocks, and equilibria, which show second-order convergence in most cases. As an application, we investigate radiation-driven ejection of a dusty, optically thick shell in the interstellar medium (ISM). Finally, we compare the timing of our method with other well-known iterative schemes for the RHD equations. Our code implementation, Hyperion, is suitable for a wide variety of astrophysical applications and will be made freely available on the Web.Comment: 30 pages, 29 figures, accepted for publication in ApJ

Stochastic collective dynamics of charged--particle beams in the stability regime

We introduce a description of the collective transverse dynamics of charged (proton) beams in the stability regime by suitable classical stochastic fluctuations. In this scheme, the collective beam dynamics is described by time--reversal invariant diffusion processes deduced by stochastic variational principles (Nelson processes). By general arguments, we show that the diffusion coefficient, expressed in units of length, is given by $\lambda_c\sqrt{N}$, where $N$ is the number of particles in the beam and $\lambda_c$ the Compton wavelength of a single constituent. This diffusion coefficient represents an effective unit of beam emittance. The hydrodynamic equations of the stochastic dynamics can be easily recast in the form of a Schr\"odinger equation, with the unit of emittance replacing the Planck action constant. This fact provides a natural connection to the so--called ``quantum--like approaches'' to beam dynamics. The transition probabilities associated to Nelson processes can be exploited to model evolutions suitable to control the transverse beam dynamics. In particular we show how to control, in the quadrupole approximation to the beam--field interaction, both the focusing and the transverse oscillations of the beam, either together or independently.Comment: 15 pages, 9 figure