A New Godunov Scheme for MHD, with Application to the MRI in disks

We describe a new numerical scheme for MHD which combines a higher order Godunov method (PPM) with Constrained Transport. The results from a selection of multidimensional test problems are presented. The complete test suite used to validate the method, as well as implementations of the algorithm in both F90 and C, are available from the web. A fully three-dimensional version of the algorithm has been developed, and is being applied to a variety of astrophysical problems including the decay of supersonic MHD turbulence, the nonlinear evolution of the MHD Rayleigh-Taylor instability, and the saturation of the magnetorotational instability in the shearing box. Our new simulations of the MRI represent the first time that a higher-order Godunov scheme has been applied to this problem, providing a quantitative check on the accuracy of previous results computed with ZEUS; the latter are found to be reliable.Comment: 11 pages, style files included, Conference Proceedings: "Magnetic Fields in the Universe: from Laboratory and Stars to Primordial Structures", More information on Athena can be found at http://www.astro.princeton.edu/~jstone/athena.htm

Nonlinear Evolution of the Magnetohydrodynamic Rayleigh-Taylor Instability

We study the nonlinear evolution of the magnetic Rayleigh-Taylor instability using three-dimensional MHD simulations. We consider the idealized case of two inviscid, perfectly conducting fluids of constant density separated by a contact discontinuity perpendicular to the effective gravity g, with a uniform magnetic field B parallel to the interface. Modes parallel to the field with wavelengths smaller than l_c = [B B/(d_h - d_l) g] are suppressed (where d_h and d_l are the densities of the heavy and light fluids respectively), whereas modes perpendicular to B are unaffected. We study strong fields with l_c varying between 0.01 and 0.36 of the horizontal extent of the computational domain. Even a weak field produces tension forces on small scales that are significant enough to reduce shear (as measured by the distribution of the amplitude of vorticity), which in turn reduces the mixing between fluids, and increases the rate at which bubbles and finger are displaced from the interface compared to the purely hydrodynamic case. For strong fields, the highly anisotropic nature of unstable modes produces ropes and filaments. However, at late time flow along field lines produces large scale bubbles. The kinetic and magnetic energies transverse to gravity remain in rough equipartition and increase as t^4 at early times. The growth deviates from this form once the magnetic energy in the vertical field becomes larger than the energy in the initial field. We comment on the implications of our results to Z-pinch experiments, and a variety of astrophysical systems.Comment: 25 pages, accepted by Physics of Fluids, online version of journal has high resolution figure

The Magnetic Rayleigh-Taylor Instability in Three Dimensions

We study the magnetic Rayleigh-Taylor instability in three dimensions, with focus on the nonlinear structure and evolution that results from different initial field configurations. We study strong fields in the sense that the critical wavelength l_c at which perturbations along the field are stable is a large fraction of the size of the computational domain. We consider magnetic fields which are initially parallel to the interface, but have a variety of configurations, including uniform everywhere, uniform in the light fluid only, and fields which change direction at the interface. Strong magnetic fields do not suppress instability, in fact by inhibiting secondary shear instabilities, they reduce mixing between the heavy and light fluid, and cause the rate of growth of bubbles and fingers to increase in comparison to hydrodynamics. Fields parallel to, but whose direction changes at, the interface produce long, isolated fingers separated by the critical wavelength l_c, which may be relevant to the morphology of the optical filaments in the Crab nebula.Comment: 14 pages, 9 pages, accepted by Ap

Fourier's Law for Quasi One--Dimensional Chaotic Quantum Systems

We derive Fourier's law for a completely coherent quasi one--dimensional chaotic quantum system coupled locally to two heat baths at different temperatures. We solve the master equation to first order in the temperature difference. We show that the heat conductance can be expressed as a thermodynamic equilibrium coefficient taken at some intermediate temperature. We use that expression to show that for temperatures large compared to the mean level spacing of the system, the heat conductance is inversely proportional to the level density and, thus, inversely proportional to the length of the system

Target search on a dynamic DNA molecule

We study a protein-DNA target search model with explicit DNA dynamics applicable to in vitro experiments. We show that the DNA dynamics plays a crucial role for the effectiveness of protein "jumps" between sites distant along the DNA contour but close in 3D space. A strongly binding protein that searches by 1D sliding and jumping alone, explores the search space less redundantly when the DNA dynamics is fast on the timescale of protein jumps than in the opposite "frozen DNA" limit. We characterize the crossover between these limits using simulations and scaling theory. We also rationalize the slow exploration in the frozen limit as a subtle interplay between long jumps and long trapping times of the protein in "islands" within random DNA configurations in solution.Comment: manuscript and supplementary material combined into a single documen

An Unsplit Godunov Method for Ideal MHD via Constrained Transport in Three Dimensions

We present a single step, second-order accurate Godunov scheme for ideal MHD which is an extension of the method described by Gardiner & Stone (2005) to three dimensions. This algorithm combines the corner transport upwind (CTU) method of Colella for multidimensional integration, and the constrained transport (CT) algorithm for preserving the divergence-free constraint on the magnetic field. We describe the calculation of the PPM interface states for 3D ideal MHD which must include multidimensional ``MHD source terms'' and naturally respect the balance implicit in these terms by the ${\bf\nabla\cdot B}=0$ condition. We compare two different forms for the CTU integration algorithm which require either 6- or 12-solutions of the Riemann problem per cell per time-step, and present a detailed description of the 6-solve algorithm. Finally, we present solutions for test problems to demonstrate the accuracy and robustness of the algorithm.Comment: Extended version of the paper accepted for publication in JC