High-resolution ab initio three-dimensional X-ray diffraction microscopy

Coherent X-ray diffraction microscopy is a method of imaging non-periodic isolated objects at resolutions only limited, in principle, by the largest scattering angles recorded. We demonstrate X-ray diffraction imaging with high resolution in all three dimensions, as determined by a quantitative analysis of the reconstructed volume images. These images are retrieved from the 3D diffraction data using no a priori knowledge about the shape or composition of the object, which has never before been demonstrated on a non-periodic object. We also construct 2D images of thick objects with infinite depth of focus (without loss of transverse spatial resolution). These methods can be used to image biological and materials science samples at high resolution using X-ray undulator radiation, and establishes the techniques to be used in atomic-resolution ultrafast imaging at X-ray free-electron laser sources.Comment: 22 pages, 11 figures, submitte

Disentangling the Cosmic Web I: Morphology of Isodensity Contours

We apply Minkowski functionals and various derived measures to decipher the morphological properties of large-scale structure seen in simulations of gravitational evolution. Minkowski functionals of isodensity contours serve as tools to test global properties of the density field. Furthermore, we identify coherent objects at various threshold levels and calculate their partial Minkowski functionals. We propose a set of two derived dimensionless quantities, planarity and filamentarity, which reduce the morphological information in a simple and intuitive way. Several simulations of the gravitational evolution of initial power-law spectra provide a framework for systematic tests of our method.Comment: 26 pages including 12 figures. Accepted for publication in Ap

On the reliability of initial conditions for dissipationless cosmological simulations

We present the study of ten random realizations of a density field characterized by a cosmological power spectrum P(k) at redshift z=50. The reliability of such initial conditions for n-body simulations are tested with respect to their correlation properties. The power spectrum P(k), and the mass variance sigmaM(r) do not show detectable deviations from the desired behavior in the intermediate range of scales between the mean interparticle distance and the simulation volume. The estimator for xi(r) is too noisy to detect any reliable signal at the initial redshift z=50. The particle distributions are then evolved forward until z=0. This allows us to explore the cosmic variance stemming from the random nature of the initial conditions. With cosmic variance we mean the fact that a simulation represents a single realization of the stochastic initial conditions whereas the real Universe contains many realizations of regions of the size of the box; this problem affects most importantly the scales at about the fundamental mode. We study morphological descriptors of the matter distribution such as the genus, as well as the internal properties of the largest object(s) forming in the box. We find that the scatter is at least comparable to the scatter in the fundamental mode.Comment: 22 pages, 12 figures, replaced with major revision to previous submission, PASA in pres

Extending Continuum Models for Atom Probe Simulation

This work describes extensions to existing level-set algorithms developed for application within the field of Atom Probe Tomography (APT). We present a new simulation tool for the simulation of 3D tomographic volumes, using advanced level set methods. By combining narrow-band, B-Tree and particle-tracing approaches from level-set methods, we demonstrate a practical tool for simulating shape changes to APT samples under applied electrostatic fields, in three dimensions. This work builds upon our previous studies by allowing for non-axially symmetric solutions, with minimal loss in computational speed, whilst retaining numerical accuracy

The Area Distribution of Solar Magnetic Bright Points

Magnetic Bright Points (MBPs) are among the smallest observable objects on the solar photosphere. A combination of G-band observations and numerical simulations is used to determine their area distribution. An automatic detection algorithm, employing 1-dimensional intensity profiling, is utilized to identify these structures in the observed and simulated datasets. Both distributions peak at an area of $\approx$45000 km$^2$, with a sharp decrease towards smaller areas. The distributions conform with log-normal statistics, which suggests that flux fragmentation dominates over flux convergence. Radiative magneto-convection simulations indicate an independence in the MBP area distribution for differing magnetic flux densities. The most commonly occurring bright point size corresponds to the typical width of intergranular lanes.Comment: Astrophysical Journal, accepte