A New Spherical Harmonics Scheme for Multi-Dimensional Radiation Transport I: Static Matter Configurations

Recent work by McClarren & Hauck [29] suggests that the filtered spherical harmonics method represents an efficient, robust, and accurate method for radiation transport, at least in the two-dimensional (2D) case. We extend their work to the three-dimensional (3D) case and find that all of the advantages of the filtering approach identified in 2D are present also in the 3D case. We reformulate the filter operation in a way that is independent of the timestep and of the spatial discretization. We also explore different second- and fourth-order filters and find that the second-order ones yield significantly better results. Overall, our findings suggest that the filtered spherical harmonics approach represents a very promising method for 3D radiation transport calculations.Comment: 29 pages, 13 figures. Version matching the one in Journal of Computational Physic

A pseudospectral matrix method for time-dependent tensor fields on a spherical shell

We construct a pseudospectral method for the solution of time-dependent, non-linear partial differential equations on a three-dimensional spherical shell. The problem we address is the treatment of tensor fields on the sphere. As a test case we consider the evolution of a single black hole in numerical general relativity. A natural strategy would be the expansion in tensor spherical harmonics in spherical coordinates. Instead, we consider the simpler and potentially more efficient possibility of a double Fourier expansion on the sphere for tensors in Cartesian coordinates. As usual for the double Fourier method, we employ a filter to address time-step limitations and certain stability issues. We find that a tensor filter based on spin-weighted spherical harmonics is successful, while two simplified, non-spin-weighted filters do not lead to stable evolutions. The derivatives and the filter are implemented by matrix multiplication for efficiency. A key technical point is the construction of a matrix multiplication method for the spin-weighted spherical harmonic filter. As example for the efficient parallelization of the double Fourier, spin-weighted filter method we discuss an implementation on a GPU, which achieves a speed-up of up to a factor of 20 compared to a single core CPU implementation.Comment: 33 pages, 9 figure

3D time series analysis of cell shape using Laplacian approaches

Background: Fundamental cellular processes such as cell movement, division or food uptake critically depend on cells being able to change shape. Fast acquisition of three-dimensional image time series has now become possible, but we lack efficient tools for analysing shape deformations in order to understand the real three-dimensional nature of shape changes. Results: We present a framework for 3D+time cell shape analysis. The main contribution is three-fold: First, we develop a fast, automatic random walker method for cell segmentation. Second, a novel topology fixing method is proposed to fix segmented binary volumes without spherical topology. Third, we show that algorithms used for each individual step of the analysis pipeline (cell segmentation, topology fixing, spherical parameterization, and shape representation) are closely related to the Laplacian operator. The framework is applied to the shape analysis of neutrophil cells. Conclusions: The method we propose for cell segmentation is faster than the traditional random walker method or the level set method, and performs better on 3D time-series of neutrophil cells, which are comparatively noisy as stacks have to be acquired fast enough to account for cell motion. Our method for topology fixing outperforms the tools provided by SPHARM-MAT and SPHARM-PDM in terms of their successful fixing rates. The different tasks in the presented pipeline for 3D+time shape analysis of cells can be solved using Laplacian approaches, opening the possibility of eventually combining individual steps in order to speed up computations

The periodic standing-wave approximation: nonlinear scalar fields, adapted coordinates, and the eigenspectral method

The periodic standing wave (PSW) method for the binary inspiral of black holes and neutron stars computes exact numerical solutions for periodic standing wave spacetimes and then extracts approximate solutions of the physical problem, with outgoing waves. The method requires solution of a boundary value problem with a mixed (hyperbolic and elliptic) character. We present here a new numerical method for such problems, based on three innovations: (i) a coordinate system adapted to the geometry of the problem, (ii) an expansion in multipole moments of these coordinates and a filtering out of higher moments, and (iii) the replacement of the continuum multipole moments with their analogs for a discrete grid. We illustrate the efficiency and accuracy of this method with nonlinear scalar model problems. Finally, we take advantage of the ability of this method to handle highly nonlinear models to demonstrate that the outgoing approximations extracted from the standing wave solutions are highly accurate even in the presence of strong nonlinearities.Comment: RevTex, 32 pages, 13 figures, 6 table