Efficient Parallel Simulation of Atherosclerotic Plaque Formation Using Higher Order Discontinuous Galerkin Schemes

Abstract The compact Discontinuous Galerkin 2 (CDG2) method was successfully tested for elliptic problems, scalar convection-diffusion equations and compressible Navier-Stokes equations. In this paper we use the newly developed DG method to solve a mathematical model for early stages of atherosclerotic plaque formation. Atherosclerotic plaque is mainly formed by accumulation of lipid-laden cells in the arterial walls which leads to a heart attack in case the artery is occluded or a thrombus is built through a rupture of the plaque. After describing a mathematical model and the discretization scheme, we present some benchmark tests comparing the CDG2 method to other commonly used DG methods. Furthermore, we take parallelization and higher order discretization schemes into account.

A posteriori error analysis and adaptive non-intrusive numerical schemes for systems of random conservation laws

In this article we consider one-dimensional random systems of hyperbolic conservation laws. We first establish existence and uniqueness of random entropy admissible solutions for initial value problems of conservation laws which involve random initial data and random flux functions. Based on these results we present an a posteriori error analysis for a numerical approximation of the random entropy admissible solution. For the stochastic discretization, we consider a non-intrusive approach, the Stochastic Collocation method. The spatio-temporal discretization relies on the Runge--Kutta Discontinuous Galerkin method. We derive the a posteriori estimator using continuous reconstructions of the discrete solution. Combined with the relative entropy stability framework this yields computable error bounds for the entire space-stochastic discretization error. The estimator admits a splitting into a stochastic and a deterministic (space-time) part, allowing for a novel residual-based space-stochastic adaptive mesh refinement algorithm. We conclude with various numerical examples investigating the scaling properties of the residuals and illustrating the efficiency of the proposed adaptive algorithm

General Relativistic Magnetohydrodynamic Bondi--Hoyle Accretion

In this paper we present a fully relativistic study of axisymmetric magnetohydrodynamic Bondi--Hoyle accretion onto a moving Kerr black hole. The equations of general relativistic magnetohydrodynamics are solved using high resolution shock capturing methods. In this treatment we consider the ideal MHD limit. The parameters of interest in this study are the adiabatic constant $\Gamma$, the asymptotic speed of sound $c_{s}^{\infty}$, and the plasma beta parameter $\beta_{P}$. We focus the investigation on the parameter regime in which the flow is supersonic, or when $v_\infty \ge c_{s}^{\infty}$. In some cases, subsonic asymptotic flows are considered for comparison purposes. We study the accretion rates of the total energy and momenta, as well as the hydrodynamic energy and momentum accretion rates. The models presented in this study exhibit a matter density depletion in the downstream region of the black hole which tends to vacuum $(\rho_0=0)$ in convergence tests. This feature is due to the presence of the magnetic field, more specifically the magnetic pressure, and is not seen in previous purely hydrodynamic studies.Comment: Version 2: The figures have been reformatted to fit the paper. All verbal content remains identical to version

An Unstaggered Constrained Transport Method for the 3D Ideal Magnetohydrodynamic Equations

Numerical methods for solving the ideal magnetohydrodynamic (MHD) equations in more than one space dimension must either confront the challenge of controlling errors in the discrete divergence of the magnetic field, or else be faced with nonlinear numerical instabilities. One approach for controlling the discrete divergence is through a so-called constrained transport method, which is based on first predicting a magnetic field through a standard finite volume solver, and then correcting this field through the appropriate use of a magnetic vector potential. In this work we develop a constrained transport method for the 3D ideal MHD equations that is based on a high-resolution wave propagation scheme. Our proposed scheme is the 3D extension of the 2D scheme developed by Rossmanith [SIAM J. Sci. Comp. 28, 1766 (2006)], and is based on the high-resolution wave propagation method of Langseth and LeVeque [J. Comp. Phys. 165, 126 (2000)]. In particular, in our extension we take great care to maintain the three most important properties of the 2D scheme: (1) all quantities, including all components of the magnetic field and magnetic potential, are treated as cell-centered; (2) we develop a high-resolution wave propagation scheme for evolving the magnetic potential; and (3) we develop a wave limiting approach that is applied during the vector potential evolution, which controls unphysical oscillations in the magnetic field. One of the key numerical difficulties that is novel to 3D is that the transport equation that must be solved for the magnetic vector potential is only weakly hyperbolic. In presenting our numerical algorithm we describe how to numerically handle this problem of weak hyperbolicity, as well as how to choose an appropriate gauge condition. The resulting scheme is applied to several numerical test cases.Comment: 46 pages, 12 figure

A high-order Godunov scheme for global 3D MHD accretion disks simulations. I. The linear growth regime of the magneto-rotational instability

We employ the PLUTO code for computational astrophysics to assess and compare the validity of different numerical algorithms on simulations of the magneto-rotational instability in 3D accretion disks. In particular we stress on the importance of using a consistent upwind reconstruction of the electro-motive force (EMF) when using the constrained transport (CT) method to avoid the onset of numerical instabilities. We show that the electro-motive force (EMF) reconstruction in the classical constrained transport (CT) method for Godunov schemes drives a numerical instability. The well-studied linear growth of magneto-rotational instability (MRI) is used as a benchmark for an inter-code comparison of PLUTO and ZeusMP. We reproduce the analytical results for linear MRI growth in 3D global MHD simulations and present a robust and accurate Godunov code which can be used for 3D accretion disk simulations in curvilinear coordinate systems

MHD simulations of jet acceleration from Keplerian accretion disks: the effects of disk resistivity

Accretion disks and astrophysical jets are used to model many active astrophysical objects, viz., young stars, relativistic stars, and active galactic nuclei. In this paper we present self-consistent time-dependent simulations of supersonic jets launched from magnetized accretion disks, using high resolution numerical techniques. In particular we study the effects of the disk magnetic resistivity, parametrized through an alpha-prescription, in determining the properties of the inflow-outflow system. Moreover we analyze under which conditions steady state solutions of the type proposed in the self similar models of Blandford and Payne can be reached and maintained in a self consistent nonlinear stage. We use the resistive MHD FLASH code with adaptive mesh refinement, allowing us to follow the evolution of the structure for a time scale long enough to reach steady state. A detailed analysis of the initial configuration state is given. We obtain the expected solutions in the axisymmetric (2.5D) limit. Assuming a magnetic field around equipartition with the thermal pressure of the disk, we show how the characteristics of the disk jet system, as the ejection efficiency and the energetics, are affected by the anomalous resistivity acting inside the disk.Comment: 20 pages, 18 figures, accepted for publication in Astronomy and Astrophysic

A divergence-cleaning scheme for cosmological SPMHD simulations

In magnetohydrodynamics (MHD), the magnetic field is evolved by the induction equation and coupled to the gas dynamics by the Lorentz force. We perform numerical smoothed particle magnetohydrodynamics (Spmhd) simulations and study the influence of a numerical magnetic divergence. For instabilities arising from divergence B related errors, we find the hyperbolic/parabolic cleaning scheme suggested by Dedner et al. 2002 to give good results and prevent numerical artifacts from growing. Additionally, we demonstrate that certain current Spmhd implementations of magnetic field regularizations give rise to unphysical instabilities in long-time simulations. We also find this effect when employing Euler potentials (divergenceless by definition), which are not able to follow the winding-up process of magnetic field lines properly. Furthermore, we present cosmological simulations of galaxy cluster formation at extremely high resolution including the evolution of magnetic fields. We show synthetic Faraday rotation maps and derive structure functions to compare them with observations. Comparing all the simulations with and without divergence cleaning, we are able to confirm the results of previous simulations performed with the standard implementation of MHD in Spmhd at normal resolution. However, at extremely high resolution, a cleaning scheme is needed to prevent the growth of numerical errors at small scales.Comment: 15 pages, 19 figures, submitted to MNRA

The discontinuous Galerkin method for fractional degenerate convection-diffusion equations

We propose and study discontinuous Galerkin methods for strongly degenerate convection-diffusion equations perturbed by a fractional diffusion (L\'evy) operator. We prove various stability estimates along with convergence results toward properly defined (entropy) solutions of linear and nonlinear equations. Finally, the qualitative behavior of solutions of such equations are illustrated through numerical experiments

Modeling of Protostellar Clouds and their Observational Properties

A physical model and two-dimensional numerical method for computing the evolution and spectra of protostellar clouds are described. The physical model is based on a system of magneto-gasdynamical equations, including ohmic and ambipolar diffusion, and a scheme for calculating the thermal and ionization structure of a cloud. The dust and gas temperatures are determined during the calculations of the thermal structure of the cloud. The results of computing the dynamical and thermal structure of the cloud are used to model the radiative transfer in continuum and in molecular lines. We presented the results for clouds in hydrostatic and thermal equilibrium. The evolution of a rotating magnetic protostellar cloud starting from a quasi-static state is also considered. Spectral maps for optically thick lines of linear molecules are analyzed. We have shown that the influence of the magnetic field and rotation can lead to a redistribution of angular momentum in the cloud and the formation of a characteristic rotational velocity structure. As a result, the distribution of the velocity centroid of the molecular lines can acquire an hourglass shape. We plan to use the developed program package together with a model for the chemical evolution to interpret and model observed starless and protostellar cores.Comment: Accepted to Astronomy Report