Traction force microscopy with optimized regularization and automated Bayesian parameter selection for comparing cells

Adherent cells exert traction forces on to their environment, which allows them to migrate, to maintain tissue integrity, and to form complex multicellular structures. This traction can be measured in a perturbation-free manner with traction force microscopy (TFM). In TFM, traction is usually calculated via the solution of a linear system, which is complicated by undersampled input data, acquisition noise, and large condition numbers for some methods. Therefore, standard TFM algorithms either employ data filtering or regularization. However, these approaches require a manual selection of filter- or regularization parameters and consequently exhibit a substantial degree of subjectiveness. This shortcoming is particularly serious when cells in different conditions are to be compared because optimal noise suppression needs to be adapted for every situation, which invariably results in systematic errors. Here, we systematically test the performance of new methods from computer vision and Bayesian inference for solving the inverse problem in TFM. We compare two classical schemes, L1- and L2-regularization, with three previously untested schemes, namely Elastic Net regularization, Proximal Gradient Lasso, and Proximal Gradient Elastic Net. Overall, we find that Elastic Net regularization, which combines L1 and L2 regularization, outperforms all other methods with regard to accuracy of traction reconstruction. Next, we develop two methods, Bayesian L2 regularization and Advanced Bayesian L2 regularization, for automatic, optimal L2 regularization. Using artificial data and experimental data, we show that these methods enable robust reconstruction of traction without requiring a difficult selection of regularization parameters specifically for each data set. Thus, Bayesian methods can mitigate the considerable uncertainty inherent in comparing cellular traction forces

The Shape of Dark Matter Haloes II. The Galactus HI Modelling & Fitting Tool

We present a new HI modelling tool called \textsc{Galactus}. The program has been designed to perform automated fits of disc-galaxy models to observations. It includes a treatment for the self-absorption of the gas. The software has been released into the public domain. We describe the design philosophy and inner workings of the program. After this, we model the face-on galaxy NGC2403, using both self-absorption and optically thin models, showing that self-absorption occurs even in face-on galaxies. It is shown that the maximum surface brightness plateaus seen in Paper I of this series are indeed signs of self-absorption. The apparent HI mass of an edge-on galaxy can be drastically lower compared to that same galaxy seen face-on. The Tully-Fisher relation is found to be relatively free from self-absorption issues.Comment: Accepted for publication by Monthly Notices RAS. Hi-res. version available at www.astro.rug.nl/~vdkruit/Petersetal-II.pd

I Zw 18 as morphological paradigm for rapidly assembling high-z galaxies

IZw18, ever since regarded as the prototypical blue compact dwarf (BCD) galaxy, is, quite ironically, the most atypical BCD known. This is because its large exponential low-surface brightness envelope is not due to an old stellar host but entirely due to extended nebular emission (ne) (Papaderos et al. 2002; P02). We study IZw18 and IZw18C down to an unprecedently faint surface brightness level using HST ACS data. We argue that the properties of IZw18C can be consistently accounted for by propagating star formation over the past ~100 Myr, in combination with stellar diffusion and the associated radial stellar mass filtering effect (P02). As for IZw18, we find that ne extends out to ~16 stellar scale lengths and provides at least 1/3 of the total optical emission. The case of IZw18 suggests caution in studies of distant galaxies in dominant stages of their evolution, rapidly assembling their stellar mass at high specific star formation rates (SSFRs). It calls attention to the fact that ne is not necessarily cospatial with the underlying ionizing and non-ionizing stellar background, neither has to scale with its surface density. The prodigious energetic output during dominant phases of galaxy evolution may result in large exponential ne envelopes, extending much beyond the still compact stellar component, just like in IZw18. Therefore, the morphological paradigm of IZw18, while probably unique in the nearby Universe, may be ubiquitous among high-SSFR galaxies at high redshift. Using IZw18 as reference, we show that extended ne may introduce substantial observational biases and significantly affect fundamental galaxy relations. Among others, we show that the surface brightness profiles of distant morphological analogs to IZw18 may be barely distinguishable from Sersic profiles with an exponent 2<n<5, thus mimicking the profiles of massive galaxy spheroids. (abridged)Comment: 22 pages, 15 figures, Accepted for publication in Astronomy and Astrophysic

Differential interferometry of QSO broad line regions I: improving the reverberation mapping model fits and black hole mass estimates

Reverberation mapping estimates the size and kinematics of broad line regions (BLR) in Quasars and type I AGNs. It yields size-luminosity relation, to make QSOs standard cosmological candles, and mass-luminosity relation to study the evolution of black holes and galaxies. The accuracy of these relations is limited by the unknown geometry of the BLR clouds distribution and velocities. We analyze the independent BLR structure constraints given by super-resolving differential interferometry. We developed a three-dimensional BLR model to compute all differential interferometry and reverberation mapping signals. We extrapolate realistic noises from our successful observations of the QSO 3C273 with AMBER on the VLTI. These signals and noises quantify the differential interferometry capacity to discriminate and measure BLR parameters including angular size, thickness, spatial distribution of clouds, local-to-global and radial-to-rotation velocity ratios, and finally central black hole mass and BLR distance. A Markov Chain Monte Carlo model-fit, of data simulated for various VLTI instruments, gives mass accuracies between 0.06 and 0.13 dex, to be compared to 0.44 dex for reverberation mapping mass-luminosity fits. We evaluate the number of QSOs accessible to measures with current (AMBER), upcoming (GRAVITY) and possible (OASIS with new generation fringe trackers) VLTI instruments. With available technology, the VLTI could resolve more than 60 BLRs, with a luminosity range larger than four decades, sufficient for a good calibration of RM mass-luminosity laws, from an analysis of the variation of BLR parameters with luminosity.Comment: 19 pages, 14 figures, accepted by MNRAS on December 5, 201

The SINS survey of z~2 galaxy kinematics: properties of the giant star forming clumps

We have studied the properties of giant star forming clumps in five z~2 star-forming disks with deep SINFONI AO spectroscopy at the ESO VLT. The clumps reside in disk regions where the Toomre Q-parameter is below unity, consistent with their being bound and having formed from gravitational instability. Broad H{\alpha}/[NII] line wings demonstrate that the clumps are launching sites of powerful outflows. The inferred outflow rates are comparable to or exceed the star formation rates, in one case by a factor of eight. Typical clumps may lose a fraction of their original gas by feedback in a few hundred million years, allowing them to migrate into the center. The most active clumps may lose much of their mass and disrupt in the disk. The clumps leave a modest imprint on the gas kinematics. Velocity gradients across the clumps are 10-40 km/s/kpc, similar to the galactic rotation gradients. Given beam smearing and clump sizes, these gradients may be consistent with significant rotational support in typical clumps. Extreme clumps may not be rotationally supported; either they are not virialized, or they are predominantly pressure supported. The velocity dispersion is spatially rather constant and increases only weakly with star formation surface density. The large velocity dispersions may be driven by the release of gravitational energy, either at the outer disk/accreting streams interface, and/or by the clump migration within the disk. Spatial variations in the inferred gas phase oxygen abundance are broadly consistent with inside-out growing disks, and/or with inward migration of the clumps.Comment: accepted Astrophys. Journal, February 9, 201