Gipsy 3D: Analysis, Visualization and Vo-Tools

The scientific goals of the AMIGA project are based on the analysis of a significant amount of spectroscopic 3D data. In order to perform this work we present an initiative to develop a new VO compliant package, including present core applications and tasks offered by the Groningen Image Processing System (GIPSY), and new ones based on use cases elaborated in collaboration with ad- vanced users. One of the main goals is to provide local interoperability between GIPSY (visualization and data analysis) and other VO software. The connectivity with the Virtual Observatory environment will provide general access to 3D data VO archives and services, maximizing the potential for scientific discovery.Comment: 2 pages, 1 figure, to appear in the proceedings of the "Multi-wavelength Astronomy and Virtual Observatory" Workshop held at ESAC 1-3 Dec 200

The AMIGA sample of isolated galaxies: VIII. The rate of asymmetric HI profiles in spiral galaxies

(abridged) Measures of the HI properties of a galaxy are among the most sensitive interaction diagnostic at our disposal. We report here on a study of HI profile asymmetries (e.g., lopsidedness) in a sample of some of the most isolated galaxies in the local Universe. This presents us with an excellent opportunity to quantify the range of intrinsic HI asymmetries and provides us with a zero-point calibration for evaluating these measurements in less isolated samples. We characterize the HI profile asymmetries and search for correlations between HI asymmetry and their environments, as well as their optical and far infrared (FIR) properties. We use high signal-to-noise global HI profiles for galaxies in the AMIGA project (http://amiga.iaa.csic.es). We restrict our study to N=166 galaxies with accurate measures of the HI shape properties. We quantify asymmetries using a flux ratio parameter. The asymmetry parameter distribution of our isolated sample is well described by a Gaussian model. The width of the distribution is sigma=0.13, and could be even smaller (sigma=0.11) if instrumental errors are reduced. Only 2% of our carefully vetted isolated galaxies sample show an asymmetry in excess of 3sigma. By using this sample we minimize environmental effects as confirmed by the lack of correlation between HI asymmetry and tidal force (one-on-one interactions) and neighbor galaxy number density. On the other hand, field galaxy samples show wider distributions and deviate from a Gaussian curve. As a result we find higher asymmetry rates (~10-20%) in such samples. We find evidence that the spiral arm strength is inversely correlated with the HI asymmetry. We also find an excess of FIR luminous galaxies with larger HI asymmetries that may be spirals associated with hidden accretion events. Our sample presents the smallest fraction of asymmetric HI profiles compared with any other yet studied.Comment: 18 pages, 17 figures, accepted for publication in A&

Modelling the Fluid Mechanics of Cilia and Flagella in Reproduction and Development

Cilia and flagella are actively bending slender organelles, performing functions such as motility, feeding and embryonic symmetry breaking. We review the mechanics of viscous-dominated microscale flow, including time-reversal symmetry, drag anisotropy of slender bodies, and wall effects. We focus on the fundamental force singularity, higher order multipoles, and the method of images, providing physical insight and forming a basis for computational approaches. Two biological problems are then considered in more detail: (1) left-right symmetry breaking flow in the node, a microscopic structure in developing vertebrate embryos, and (2) motility of microswimmers through non-Newtonian fluids. Our model of the embryonic node reveals how particle transport associated with morphogenesis is modulated by the gradual emergence of cilium posterior tilt. Our model of swimming makes use of force distributions within a body-conforming finite element framework, allowing the solution of nonlinear inertialess Carreau flow. We find that a three-sphere model swimmer and a model sperm are similarly affected by shear-thinning; in both cases swimming due to a prescribed beat is enhanced by shear-thinning, with optimal Deborah number around 0.8. The sperm exhibits an almost perfect linear relationship between velocity and the logarithm of the ratio of zero to infinite shear viscosity, with shear-thickening hindering cell progress.Comment: 20 pages, 24 figure

Ordering in the dilute weakly-anisotropic antiferromagnet Mn(0.35)Zn(0.65)F2

The highly diluted antiferromagnet Mn(0.35)Zn(0.65)F2 has been investigated by neutron scattering in zero field. The Bragg peaks observed below the Neel temperature TN (approximately 10.9 K) indicate stable antiferromagnetic long-range ordering at low temperature. The critical behavior is governed by random-exchange Ising model critical exponents (nu approximately 0.69 and gamma approximately 1.31), as reported for Mn(x)Zn(1-x)F2 with higher x and for the isostructural compound Fe(x)Zn(1-x)F2. However, in addition to the Bragg peaks, unusual scattering behavior appears for |q|>0 below a glassy temperature Tg approximately 7.0 K. The glassy region T<Tg corresponds to that of noticeable frequency dependence in earlier zero-field ac susceptibility measurements on this sample. These results indicate that long-range order coexists with short-range nonequilibrium clusters in this highly diluted magnet.Comment: 7 pages, 5 figure

Efficient Implementation of Elastohydrodynamics via Integral Operators

The dynamics of geometrically non-linear flexible filaments play an important role in a host of biological processes, from flagella-driven cell transport to the polymeric structure of complex fluids. Such problems have historically been computationally expensive due to numerical stiffness associated with the inextensibility constraint, as well as the often non-trivial boundary conditions on the governing high-order PDEs. Formulating the problem for the evolving shape of a filament via an integral equation in the tangent angle has recently been found to greatly alleviate this numerical stiffness. The contribution of the present manuscript is to enable the simulation of non-local interactions of multiple filaments in a computationally efficient manner using the method of regularized stokeslets within this framework. The proposed method is benchmarked against a non-local bead and link model, and recent code utilizing a local drag velocity law. Systems of multiple filaments (1) in a background fluid flow, (2) under a constant body force, and (3) undergoing active self-motility are modeled efficiently. Buckling instabilities are analyzed by examining the evolving filament curvature, as well as by coarse-graining the body frame tangent angles using a Chebyshev approximation for various choices of the relevant non-dimensional parameters. From these experiments, insight is gained into how filament-filament interactions can promote buckling, and further reveal the complex fluid dynamics resulting from arrays of these interacting fibers. By examining active moment-driven filaments, we investigate the speed of worm- and sperm-like swimmers for different governing parameters. The MATLAB(R) implementation is made available as an open-source library, enabling flexible extension for alternate discretizations and different surrounding flows.Comment: 37 pages, 17 figure

Physics of Rheologically-Enhanced Propulsion: Different Strokes in Generalized Stokes

Shear-thinning is an important rheological property of many biological fluids, such as mucus, whereby the apparent viscosity of the fluid decreases with shear. Certain microscopic swimmers have been shown to progress more rapidly through shear-thinning fluids, but is this behavior generic to all microscopic swimmers, and what are the physics through which shear-thinning rheology affects a swimmer's propulsion? We examine swimmers employing prescribed stroke kinematics in two-dimensional, inertialess Carreau fluid: shear-thinning "Generalized Stokes" flow. Swimmers are modeled, using the method of femlets, by a set of immersed, regularized forces. The equations governing the fluid dynamics are then discretized over a body-fitted mesh and solved with the finite element method. We analyze the locomotion of three distinct classes of microswimmer: (1) conceptual swimmers comprising sliding spheres employing both one- and two-dimensional strokes, (2) slip-velocity envelope models of ciliates commonly referred to as "squirmers" and (3) monoflagellate pushers, such as sperm. We find that morphologically identical swimmers with different strokes may swim either faster or slower in shear-thinning fluids than in Newtonian fluids. We explain this kinematic sensitivity by considering differences in the viscosity of the fluid surrounding propulsive and payload elements of the swimmer, and using this insight suggest two reciprocal sliding sphere swimmers which violate Purcell's Scallop theorem in shear-thinning fluids. We also show that an increased flow decay rate arising from shear-thinning rheology is associated with a reduction in the swimming speed of slip-velocity squirmers. For sperm-like swimmers, a gradient of thick to thin fluid along the flagellum alters the force it exerts upon the fluid, flattening trajectories and increasing instantaneous swimming speed.Comment: 22 pages, 28 figure

Effects of the environment on galaxies in the Catalogue of Isolated Galaxies: physical satellites and large scale structure

We aim to identify and quantify the effects of the satellite distribution around a sample of galaxies in the Catalogue of Isolated Galaxies (CIG), as well as the effects of the Large Scale Structure (LSS) using the SDSS-DR9. To recover the physically bound galaxies we focus on the satellites which are within the escape speed of each CIG galaxy. We also propose a more conservative method using the stacked Gaussian distribution of the velocity difference of the neighbours. The tidal strengths affecting the primary galaxy are estimated to quantify the effects of the local and LSS environments. We also define the projected number density parameter at the 5$^{\rm th}$ nearest neighbour to characterise the LSS around the CIG galaxies. Out of the 386 CIG galaxies considered in this study, at least 340 (88\% of the sample) have no physically linked satellite. Out of the 386 CIG galaxies, 327 (85\% of the sample) have no physical companion within a projected distance of 0.3 Mpc. The CIG galaxies are distributed following the LSS of the local Universe, although presenting a large heterogeneity in their degree of connection with it. A clear segregation appears between early-type CIG galaxies with companions and isolated late-type CIG galaxies. Isolated galaxies are in general bluer, with likely younger stellar populations and rather high star formation with respect to older, redder CIG galaxies with companions. Reciprocally, the satellites are redder and with an older stellar populations around massive early-type CIG galaxies, while they have a younger stellar content around massive late-type CIG galaxies. This suggests that the CIG is composed of a heterogeneous population of galaxies, sampling from old to more recent, dynamical systems of galaxies.Comment: 19 pages, 10 figures, 1 table, accepted for publication in Astronomy & Astrophysic

The HI Content of Compact Groups of Galaxies

The HI content of Hickson Compact Groups in the southern hemisphere is measured using data from the HI Parkes All Sky Survey (HIPASS), and dedicated observations using the narrowband filter on the Multibeam instrument on the Parkes telescope. The expected HI mass of these groups was estimated using the luminosity, diameter and morphological types of the member galaxies, calibrated from published data. Taking careful account of non-detection limits, the results show that the compact group population that has been detected by these observations has an HI content similar to that of galaxies in the reference field sample. The upper limits for the undetected groups lie within the normal range; improvement of these limits will require a large increase in sensitivity.Comment: 27 pages, 5 figures. Accepted for publication in PAS

Setting the normalcy level of HI properties in isolated galaxies

Studying the atomic gas (HI) properties of the most isolated galaxies is essential to quantify the effect that the environment exerts on this sensitive component of the interstellar medium. We observed and compiled HI data for a well defined sample of ~ 800 galaxies in the Catalog of Isolated Galaxies, as part of the AMIGA project (Analysis of the ISM in Isolated GAlaxies, http://amiga.iaa.es), which enlarges considerably previous samples used to quantify the HI deficiency in galaxies located in denser environments. By studying the shape of 182 HI profiles, we revisited the usually accepted result that, independently of the environment, more than half of the galaxies present a perturbed HI disk. In isolated galaxies this would certainly be a striking result if these are supposed to be the most relaxed systems, and has implications in the relaxation time scales of HI disks and the nature of the most frequent perturbing mechanisms in galaxies. Our sample likely exhibits the lowest HI asymmetry level in the local Universe. We found that other field samples present an excess of ~ 20% more asymmetric HI profiles than that in CIG. Still a small percentage of galaxies in our sample present large asymmetries. Follow-up high resolution VLA maps give insight into the origin of such asymmetries.Comment: 4 pages, 2 figures, Conference 'Galaxies in Isolation: Exploring Nature vs. Nurture', Granada, 12-15 May 2009. To be published in the ASP Conference Serie