A user guide for the EMTAC-MZ CFD code

The computer code (EMTAC-MZ) was applied to investigate the flow field over a variety of very complex three-dimensional (3-D) configurations across the Mach number range (subsonic, transonic, supersonic, and hypersonic flow). In the code, a finite volume, multizone implementation of high accuracy, total variation diminishing (TVD) formulation (based on Roe's scheme) is used to solve the unsteady Euler equations. In the supersonic regions of the flow, an infinitely large time step and a space-marching scheme is employed. A finite time step and a relaxation or 3-D approximate factorization method is used in subsonic flow regions. The multizone technique allows very complicated configurations to be modeled without geometry modifications, and can easily handle combined internal and external flow problems. An elliptic grid generation package is built into the EMTAC-MZ code. To generate the computational grid, only the surface geometry data are required. Results obtained for a variety of configurations, such as fighter-like configurations (F-14, AVSTOL), flow through inlet, multi-bodies (shuttle with external tank and SRBs), are reported and shown to be in good agreement with available experimental data

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques

Three-dimensional MHD Simulations of Radiatively Inefficient Accretion Flows

We present three-dimensional MHD simulations of rotating radiatively inefficient accretion flows onto black holes. In the simulations, we continuously inject magnetized matter into the computational domain near the outer boundary, and we run the calculations long enough for the resulting accretion flow to reach a quasi-steady state. We have studied two limiting cases for the geometry of the injected magnetic field: pure toroidal field and pure poloidal field. In the case of toroidal field injection, the accreting matter forms a nearly axisymmetric, geometrically-thick, turbulent accretion disk. The disk resembles in many respects the convection-dominated accretion flows found in previous numerical and analytical investigations of viscous hydrodynamic flows. Models with poloidal field injection evolve through two distinct phases. In an initial transient phase, the flow forms a relatively flattened, quasi-Keplerian disk with a hot corona and a bipolar outflow. However, when the flow later achieves steady state, it changes in character completely. The magnetized accreting gas becomes two-phase, with most of the volume being dominated by a strong dipolar magnetic field from which a thermal low-density wind flows out. Accretion occurs mainly via narrow slowly-rotating radial streams which `diffuse' through the magnetic field with the help of magnetic reconnection events.Comment: 35 pages including 3 built-in plots and 14 separate jpg-plots; version accepted by Ap

Phurbas: An Adaptive, Lagrangian, Meshless, Magnetohydrodynamics Code. II. Implementation and Tests

We present an algorithm for simulating the equations of ideal magnetohydrodynamics and other systems of differential equations on an unstructured set of points represented by sample particles. The particles move with the fluid, so the time step is not limited by the Eulerian Courant-Friedrichs-Lewy condition. Full spatial adaptivity is required to ensure the particles fill the computational volume, and gives the algorithm substantial flexibility and power. A target resolution is specified for each point in space, with particles being added and deleted as needed to meet this target. We have parallelized the code by adapting the framework provided by GADGET-2. A set of standard test problems, including 1e-6 amplitude linear MHD waves, magnetized shock tubes, and Kelvin-Helmholtz instabilities is presented. Finally we demonstrate good agreement with analytic predictions of linear growth rates for magnetorotational instability in a cylindrical geometry. This paper documents the Phurbas algorithm as implemented in Phurbas version 1.1.Comment: 14 pages, 14 figures, ApJS accepted, revised in accordance with changes to paper I (arXiv:1110.0835

A Moving Boundary Flux Stabilization Method for Cartesian Cut-Cell Grids using Directional Operator Splitting

An explicit moving boundary method for the numerical solution of time-dependent hyperbolic conservation laws on grids produced by the intersection of complex geometries with a regular Cartesian grid is presented. As it employs directional operator splitting, implementation of the scheme is rather straightforward. Extending the method for static walls from Klein et al., Phil. Trans. Roy. Soc., A367, no. 1907, 4559-4575 (2009), the scheme calculates fluxes needed for a conservative update of the near-wall cut-cells as linear combinations of standard fluxes from a one-dimensional extended stencil. Here the standard fluxes are those obtained without regard to the small sub-cell problem, and the linear combination weights involve detailed information regarding the cut-cell geometry. This linear combination of standard fluxes stabilizes the updates such that the time-step yielding marginal stability for arbitrarily small cut-cells is of the same order as that for regular cells. Moreover, it renders the approach compatible with a wide range of existing numerical flux-approximation methods. The scheme is extended here to time dependent rigid boundaries by reformulating the linear combination weights of the stabilizing flux stencil to account for the time dependence of cut-cell volume and interface area fractions. The two-dimensional tests discussed include advection in a channel oriented at an oblique angle to the Cartesian computational mesh, cylinders with circular and triangular cross-section passing through a stationary shock wave, a piston moving through an open-ended shock tube, and the flow around an oscillating NACA 0012 aerofoil profile.Comment: 30 pages, 27 figures, 3 table

Mechanistic and pathological study of the genesis, growth, and rupture of abdominal aortic aneurysms

Postprint (published version

Arbitrary-Lagrangian-Eulerian discontinuous Galerkin schemes with a posteriori subcell finite volume limiting on moving unstructured meshes

We present a new family of high order accurate fully discrete one-step Discontinuous Galerkin (DG) finite element schemes on moving unstructured meshes for the solution of nonlinear hyperbolic PDE in multiple space dimensions, which may also include parabolic terms in order to model dissipative transport processes. High order piecewise polynomials are adopted to represent the discrete solution at each time level and within each spatial control volume of the computational grid, while high order of accuracy in time is achieved by the ADER approach. In our algorithm the spatial mesh configuration can be defined in two different ways: either by an isoparametric approach that generates curved control volumes, or by a piecewise linear decomposition of each spatial control volume into simplex sub-elements. Our numerical method belongs to the category of direct Arbitrary-Lagrangian-Eulerian (ALE) schemes, where a space-time conservation formulation of the governing PDE system is considered and which already takes into account the new grid geometry directly during the computation of the numerical fluxes. Our new Lagrangian-type DG scheme adopts the novel a posteriori sub-cell finite volume limiter method, in which the validity of the candidate solution produced in each cell by an unlimited ADER-DG scheme is verified against a set of physical and numerical detection criteria. Those cells which do not satisfy all of the above criteria are flagged as troubled cells and are recomputed with a second order TVD finite volume scheme. The numerical convergence rates of the new ALE ADER-DG schemes are studied up to fourth order in space and time and several test problems are simulated. Finally, an application inspired by Inertial Confinement Fusion (ICF) type flows is considered by solving the Euler equations and the PDE of viscous and resistive magnetohydrodynamics (VRMHD).Comment: 39 pages, 21 figure

A computational framework for the morpho-elastic development of molluskan shells by surface and volume growth

Mollusk shells are an ideal model system for understanding the morpho-elastic basis of morphological evolution of invertebrates' exoskeletons. During the formation of the shell, the mantle tissue secretes proteins and minerals that calcify to form a new incremental layer of the exoskeleton. Most of the existing literature on the morphology of mollusks is descriptive. The mathematical understanding of the underlying coupling between pre-existing shell morphology, de novo surface deposition and morpho-elastic volume growth is at a nascent stage, primarily limited to reduced geometric representations. Here, we propose a general, three-dimensional computational framework coupling pre-existing morphology, incremental surface growth by accretion, and morpho-elastic volume growth. We exercise this framework by applying it to explain the stepwise morphogenesis of seashells during growth: new material surfaces are laid down by accretive growth on the mantle whose form is determined by its morpho-elastic growth. Calcification of the newest surfaces extends the shell as well as creates a new scaffold that constrains the next growth step. We study the effects of surface and volumetric growth rates, and of previously deposited shell geometries on the resulting modes of mantle deformation, and therefore of the developing shell's morphology. Connections are made to a range of complex shells ornamentations.Comment: Main article is 20 pages long with 15 figures. Supplementary material is 4 pages long with 6 figures and 6 attached movies. To be published in PLOS Computational Biolog