On the nature of the barlens component in barred galaxies: what do boxy/peanut bulges look like when viewed face-on?

Barred galaxies have interesting morphological features whose presence and properties set constraints on galactic evolution. Here we examine barlenses, i.e. lens-like components whose extent along the bar major axis is shorter than that of the bar and whose outline is oval or circular. We identify and analyse barlenses in $N$-body plus SPH simulations, compare them extensively with those from the NIRS0S (Near-IR S0 galaxy survey) and the S$^4$G samples (Spitzer Survey of Stellar Structure in Galaxies) and find very good agreement. We observe barlenses in our simulations from different viewing angles. This reveals that barlenses are the vertically thick part of the bar seen face-on, i.e. a barlens seen edge-on is a boxy/peanut/X bulge. In morphological studies, and in the absence of kinematics or photometry, a barlens, or part of it, may be mistaken for a classical bulge. Thus the true importance of classical bulges, both in numbers and mass, is smaller than currently assumed, which has implications for galaxy formation studies. Finally, using the shape of the isodensity curves, we propose a rule of thumb for measuring the barlens extent along the bar major axis of moderately inclined galaxies, thus providing an estimate of which part of the bar is thicker.Comment: 21 pages, 11 figures, revised version as published in MNRA

Mathematical Morphology for Quantification in Biological & Medical Image Analysis

Mathematical morphology is an established field of image processing first introduced as an application of set and lattice theories. Originally used to characterise particle distributions, mathematical morphology has gone on to be a core tool required for such important analysis methods as skeletonisation and the watershed transform. In this thesis, I introduce a selection of new image analysis techniques based on mathematical morphology. Utilising assumptions of shape, I propose a new approach for the enhancement of vessel-like objects in images: the bowler-hat transform. Built upon morphological operations, this approach is successful at challenges such as junctions and robust against noise. The bowler-hat transform is shown to give better results than competitor methods on challenging data such as retinal/fundus imagery. Building further on morphological operations, I introduce two novel methods for particle and blob detection. The first of which is developed in the context of colocalisation, a standard biological assay, and the second, which is based on Hilbert-Edge Detection And Ranging (HEDAR), with regard to nuclei detection and counting in fluorescent microscopy. These methods are shown to produce accurate and informative results for sub-pixel and supra-pixel object counting in complex and noisy biological scenarios. I propose a new approach for the automated extraction and measurement of object thickness for intricate and complicated vessels, such as brain vascular in medical images. This pipeline depends on two key technologies: semi-automated segmentation by advanced level-set methods and automatic thickness calculation based on morphological operations. This approach is validated and results demonstrating the broad range of challenges posed by these images and the possible limitations of this pipeline are shown. This thesis represents a significant contribution to the field of image processing using mathematical morphology and the methods within are transferable to a range of complex challenges present across biomedical image analysis

Detecting a disk bending wave in a barred-spiral galaxy at redshift 4.4

The recent discovery of barred spiral galaxies in the early universe ($z>2$) poses questions of how these structures form and how they influence galaxy properties in the early universe. In this study, we investigate the morphology and kinematics of the far infrared (FIR) continuum and [CII] emission in BRI1335-0417 at $z\approx 4.4$ from ALMA observations. The variations in position angle and ellipticity of the isophotes show the characteristic signature of a barred galaxy. The bar, $3.3^{+0.2}_{-0.2}$ kpc long in radius and bridging the previously identified two-armed spiral, is evident in both [CII] and FIR images, driving the galaxy's rapid evolution by channelling gas towards the nucleus. Fourier analysis of the [CII] velocity field reveals an unambiguous $m=2$ mode with a line-of-sight velocity amplitude of up to $\sim30-40$ km s$^{-1}$; the plausible explanation is the disk's vertical bending mode triggered by external perturbation, which presumably induced the high star formation rate and the bar/spiral structure. The bar identified in [CII] and FIR images of the gas-rich disk galaxy ($\gtrsim 70$\% of the total mass within radius $R\approx 2.2$ disk scale lengths) suggests a new perspective of early bar formation -- a gravitationally unstable gas-rich disk creating a star-forming gaseous bar, rather than a stellar bar emerging from a pre-existing stellar disk.Comment: Submitted to MNRAS. We welcome comments

Using machine learning to optimise chameleon fifth force experiments

The chameleon is a theorised scalar field that couples to matter and possess a screening mechanism, which weakens observational constraints from experiments performed in regions of higher matter density. One consequence of this screening mechanism is that the force induced by the field is dependent on the shape of the source mass (a property that distinguishes it from gravity). Therefore an optimal shape must exist for which the chameleon force is maximised. Such a shape would allow experiments to improve their sensitivity by simply changing the shape of the source mass. In this work we use a combination of genetic algorithms and the chameleon solving software SELCIE to find shapes that optimise the force at a single point in an idealised experimental environment. We note that the method we used is easily customised, and so could be used to optimise a more realistic experiment involving particle trajectories or the force acting on an extended body. We find the shapes outputted by the genetic algorithm possess common characteristics, such as a preference for smaller source masses, and that the largest fifth forces are produced by small `umbrella'-like shapes with a thickness such that the source is unscreened but the field reaches its minimum inside the source. This remains the optimal shape even as we change the chameleon potential, and the distance from the source, and across a wide range of chameleon parameters. We find that by optimising the shape in this way the fifth force can be increased by $2.45$ times when compared to a sphere, centred at the origin, of the same volume and mass.Comment: 28 pages, 17 figures, The SELCIE code is available at: https://github.com/C-Briddon/SELCI

Bar Diagnostics in Edge-On Spiral Galaxies. I. The Periodic Orbits Approach

We develop diagnostics to detect the presence and orientation of a bar in an edge-on disk, using its kinematical signature in the position-velocity diagram (PVD) of a spiral galaxy observed edge-on. Using a well-studied barred spiral galaxy mass model, we briefly review the orbital properties of two-dimensional non-axisymmetric disks and identify the main families of periodic orbits. We use those families as building blocks to model real galaxies and calculate the PVDs obtained for various realistic combinations of periodic orbit families and for a number of viewing angles with respect to the bar. We show that the global structure of the PVD is a reliable bar diagnostic in edge-on disks. Specifically, the presence of a gap between the signatures of the families of periodic orbits in the PVD follows directly from the non-homogeneous distribution of the orbits in a barred galaxy. Similarly, material in the two so-called forbidden quadrants of the PVD results from the elongated shape of the orbits. We show how the shape of the signatures of the dominant x1 and x2 families of periodic orbits in the PVD can be used efficiently to determine the viewing angle with respect to the bar and, to a lesser extent, to constrain the mass distribution of an observed galaxy. We also address the limitations of the models when interpreting observational data.Comment: 22 pages, 9 figures (AASTeX, aaspp4.sty). Accepted for publication in The Astrophysical Journa

Numerical Simulation and Characterisation of the Packing of Granular Materials

The scientific problems related to granular matter are ubiquitous. It is currently an active area of research for physicists and earth scientists, with a wide range of applications within the industrial community. Simple analogue experiments exhibit behaviour that is neither predicted nor described by any current theory. The work presented here consists of modelling granular media using a two-dimensional combined Finite-Discrete Element Method (FEM-DEM). While computationally expensive, as well as modelling accurately the dynamic interactions between independent and arbitrarily shaped grains, this method allows for a complete description of the stress state within individual grains during their transient motion. After a detailed description of FEM-DEM principles, this computational approach is used to investigate the packing of elliptical particles. The work is aimed at understanding the influence of the particle shape (the ellipse aspect ratio) on the emergent properties of the granular matrix such as the particle coordination number and the packing density. The diff erences in microstructure of the resultant packing are analysed using pair correlation functions, particle orientations and pore size distributions. A comparison between frictional and frictionless systems is carried out. It shows great diff erences not only in the calculated porosity and coordination number, but also in terms of structural arrangement and stress distribution. The results suggest that the particle's shape a ffects the structural order of the particle assemblage, which itself controls the stress distribution between the pseudo-static grains. The study then focuses on describing the stress patterns or \force chains" naturally generated in a frictional system. An algorithm based on the analysis of the contact force network is proposed and applied to various packs in order to identify the force chains. A statistical analysis of the force chains looking at their orientation, length and proportion of the particles that support the loads is then performed. It is observed that force chains propagate less efficiently and more heterogeneously through granular systems made of elliptical particles than through systems of discs and it is proposed that structural diff erences due to the particle shape lead to a signifi cant reduction in the length of the stress path that propagates across connected particles. Finally, the e ffect of compression on the granular packing, the emergent properties and the contact force distribution is examined. Results show that the force network evolves towards a more randomly distributed system (from an exponential to a Gaussian distribution), and it confi rms the observations made from simulations using discs. To conclude, the combined finite-discrete element method applied to the study of granular systems provides an attractive modelling strategy to improve the knowledge of granular matter. This is due to the wide range of static and dynamic problems that can be treated with a rigorous physical basis. The applicability of the method was demonstrated through to a variety of problems that involve di fferent physical processes modelled with the FEM-DEM (internal deformations, fracture, and complex geometry). With the rapid extension of the practical limits of computational models, this work emphasizes the opportunity to move towards a modern generation of computer software to understand the complexity of the phenomena associated with discontinua

Population Genetic Structure is Unrelated to Shell Shape, Thickness and Organic Content in European Populations of the Soft-Shell Clam Mya Arenaria.

The soft-shell clam Mya arenaria is one of the most ancient invaders of European coasts and is present in many coastal ecosystems, yet little is known about its genetic structure in Europe. We collected 266 samples spanning a latitudinal cline from the Mediterranean to the North Sea and genotyped them at 12 microsatellite loci. In parallel, geometric morphometric analysis of shell outlines was used to test for associations between shell shape, latitude and genotype, and for a selection of shells we measured the thickness and organic content of the granular prismatic (PR), the crossed-lamellar (CL) and the complex crossed-lamellar (CCL) layers. Strong population structure was detected, with Bayesian cluster analysis identifying four groups located in the Mediterranean, Celtic Sea, along the continental coast of the North Sea and in Scotland. Multivariate analysis of shell shape uncovered a significant effect of collection site but no associations with any other variables. Shell thickness did not vary significantly with either latitude or genotype, although PR thickness and calcification were positively associated with latitude, while CCL thickness showed a negative association. Our study provides new insights into the population structure of this species and sheds light on factors influencing shell shape, thickness and microstructure

The evolution of dwarf galaxy satellites with different dark matter density profiles in the ErisMod simulations. I. The early infalls

We present the first simulations of tidal stirring of dwarf galaxies in the Local Group carried out in a cosmological context. We use the ErisDARK simulation of a MW-sized galaxy to identify some of the most massive subhalos ($M_{vir} > 10^8 M_{\odot}$) that fall into the main host before $z=2$. Subhalos are replaced before infall with high-resolution models of dwarf galaxies comprising a faint stellar disk embedded in a dark matter halo. The set of models contains cuspy halos as well as halos with "cored" profiles (with asymptotic inner slope $\gamma = 0.6$). The simulations are then run to $z=0$ with as many as 54 million particles and resolution as small as $\sim 4$ pc using the N-Body code ChaNGa. The stellar components of all satellites are significantly affected by tidal stirring, losing stellar mass and undergoing a morphological transformation towards a pressure supported spheroidal system. However, while some remnants with cuspy halos maintain significant rotational flattening and disk-like features, all the shallow halo models achieve $v/\sigma < 0.5$ and round shapes typical of dSph satellites of the MW and M31. Mass loss is also enhanced in the latter, and remnants can reach luminosities and velocity dispersions as low as those of Ultra Faint Dwarfs (UFDs). We argue that cuspy progenitors must be the exception rather than the rule among satellites of the MW since all the MW and M31 satellites in the luminosity range of our remnants are dSphs, a result matched only in the simulation with "cored" models