ColDICE: a parallel Vlasov-Poisson solver using moving adaptive simplicial tessellation

Resolving numerically Vlasov-Poisson equations for initially cold systems can be reduced to following the evolution of a three-dimensional sheet evolving in six-dimensional phase-space. We describe a public parallel numerical algorithm consisting in representing the phase-space sheet with a conforming, self-adaptive simplicial tessellation of which the vertices follow the Lagrangian equations of motion. The algorithm is implemented both in six- and four-dimensional phase-space. Refinement of the tessellation mesh is performed using the bisection method and a local representation of the phase-space sheet at second order relying on additional tracers created when needed at runtime. In order to preserve in the best way the Hamiltonian nature of the system, refinement is anisotropic and constrained by measurements of local Poincar\'e invariants. Resolution of Poisson equation is performed using the fast Fourier method on a regular rectangular grid, similarly to particle in cells codes. To compute the density projected onto this grid, the intersection of the tessellation and the grid is calculated using the method of Franklin and Kankanhalli (1993) generalised to linear order. As preliminary tests of the code, we study in four dimensional phase-space the evolution of an initially small patch in a chaotic potential and the cosmological collapse of a fluctuation composed of two sinusoidal waves. We also perform a "warm" dark matter simulation in six-dimensional phase-space that we use to check the parallel scaling of the code.Comment: Code and illustration movies available at: http://www.vlasix.org/index.php?n=Main.ColDICE - Article submitted to Journal of Computational Physic

Functional role of PGAM5 multimeric assemblies and their polymerization into filaments.

PGAM5 is a mitochondrial protein phosphatase whose genetic ablation in mice results in mitochondria-related disorders, including neurodegeneration. Functions of PGAM5 include regulation of mitophagy, cell death, metabolism and aging. However, mechanisms regulating PGAM5 activation and signaling are poorly understood. Using electron cryo-microscopy, we show that PGAM5 forms dodecamers in solution. We also present a crystal structure of PGAM5 that reveals the determinants of dodecamer formation. Furthermore, we observe PGAM5 dodecamer assembly into filaments both in vitro and in cells. We find that PGAM5 oligomerization into a dodecamer is not only essential for catalytic activation, but this form also plays a structural role on mitochondrial membranes, which is independent of phosphatase activity. Together, these findings suggest that modulation of the oligomerization of PGAM5 may be a regulatory switch of potential therapeutic interest

Fast computations with the harmonic Poincaré-Steklov operators on nested refined meshes

In this paper we develop asymptotically optimal algorithms for fast computations with the discrete harmonic Poincar'e-Steklov operators in presence of nested mesh refinement. For both interior and exterior problems the matrix-vector multiplication for the finite element approximations to the Poincar'e-Steklov operators is shown to have a complexity of the order O(Nreflog3N) where Nref is the number of degrees of freedom on the polygonal boundary under consideration and N = 2-p0 · Nref, p0 ≥ 1, is the dimension of a finest quasi-uniform level. The corresponding memory needs are estimated by O(Nreflog2N). The approach is based on the multilevel interface solver (as in the case of quasi-uniform meshes, see [20]) applied to the Schur complement reduction onto the nested refined interface associated with nonmatching decomposition of a polygon by rectangular substructures

Finite elements on degenerate meshes: inverse-type inequalities and applications

In this paper we obtain a range of inverse-type inequalities which are applicable to finite-element functions on general classes of meshes, including degenerate meshes obtained by anisotropic refinement. These are obtained for Sobolev norms of positive, zero and negative order. In contrast to classical inverse estimates, negative powers of the minimum mesh diameter are avoided. We give two applications of these estimates in the context of boundary elements: (i) to the analysis of quadrature error in discrete Galerkin methods and (ii) to the analysis of the panel clustering algorithm. Our results show that degeneracy in the meshes yields no degradation in the approximation properties of these method

Hydrodynamical adaptive mesh refinement simulations of turbulent flows - I. Substructure in a wind

The problem of the resolution of turbulent flows in adaptive mesh refinement (AMR) simulations is investigated by means of 3D hydrodynamical simulations in an idealised setup, representing a moving subcluster during a merger event. AMR simulations performed with the usual refinement criteria based on local gradients of selected variables do not properly resolve the production of turbulence downstream of the cluster. Therefore we apply novel AMR criteria which are optimised to follow the evolution of a turbulent flow. We demonstrate that these criteria provide a better resolution of the flow past the subcluster, allowing us to follow the onset of the shear instability, the evolution of the turbulent wake and the subsequent back-reaction on the subcluster core morphology. We discuss some implications for the modelling of cluster cold fronts.Comment: 11 pages, 14 figures. Small changes to match the version accepted by MNRA

Ray Tracing Simulations of Weak Lensing by Large-Scale Structure

We investigate weak lensing by large-scale structure using ray tracing through N-body simulations. Photon trajectories are followed through high resolution simulations of structure formation to make simulated maps of shear and convergence on the sky. Tests with varying numerical parameters are used to calibrate the accuracy of computed lensing statistics on angular scales from about 1 arcminute to a few degrees. Various aspects of the weak lensing approximation are also tested. For fields a few degrees on a side the shear power spectrum is almost entirely in the nonlinear regime and agrees well with nonlinear analytical predictions. Sampling fluctuations in power spectrum estimates are investigated by comparing several ray tracing realizations of a given model. For survey areas smaller than a degree on a side the main source of scatter is nonlinear coupling to modes larger than the survey. We develop a method which uses this effect to estimate the mass density parameter Omega from the scatter in power spectrum estimates for subregions of a larger survey. We show that the power spectrum can be measured accurately from realistically noisy data on scales corresponding to 1-10 Mpc/h. Non-Gaussian features in the one point distribution function of the weak lensing convergence (reconstructed from the shear) are also sensitive to Omega. We suggest several techniques for estimating Omega in the presence of noise and compare their statistical power, robustness and simplicity. With realistic noise Omega can be determined to within 0.1-0.2 from a deep survey of several square degrees.Comment: 59 pages, 22 figures included. Matches version accepted for Ap

Metric-based anisotropic mesh adaptation for 3D acoustic boundary element methods

International audienceThis paper details the extension of a metric-based anisotropic mesh adaptation strategy to the boundary element method for problems of 3D acoustic wave propagation. Traditional mesh adaptation strategies for boundary element methods rely on Galerkin discretizations of the boundary integral equations, and the development of appropriate error indicators. They often require the solution of further integral equations. These methods utilise the error indicators to mark elements where the error is above a specified tolerance and then refine these elements. Such an approach cannot lead to anisotropic adaptation regardless of how these elements are refined, since the orientation and shape of current elements cannot be modified. In contrast, the method proposed here is independent of the discretization technique (e.g., collocation, Galerkin). Furthermore, it completely remeshes at each refinement step, altering the shape, size, and orientation of each element according to an optimal metric based on a numerically recovered Hessian of the boundary solution. The resulting adaptation procedure is truly anisotropic and independent of the complexity of the geometry. We show via a variety of numerical examples that it recovers optimal convergence rates for domains with geometric singularities. In particular, a faster convergence rate is recovered for scattering problems with complex geometries