Implementing vertex dynamics models of cell populations in biology within a consistent computational framework

The dynamic behaviour of epithelial cell sheets plays a central role during development, growth, disease and wound healing. These processes occur as a result of cell adhesion, migration, division, differentiation and death, and involve multiple processes acting at the cellular and molecular level. Computational models offer a useful means by which to investigate and test hypotheses about these processes, and have played a key role in the study of cell–cell interactions. However, the necessarily complex nature of such models means that it is difficult to make accurate comparison between different models, since it is often impossible to distinguish between differences in behaviour that are due to the underlying model assumptions, and those due to differences in the in silico implementation of the model. In this work, an approach is described for the implementation of vertex dynamics models, a discrete approach that represents each cell by a polygon (or polyhedron) whose vertices may move in response to forces. The implementation is undertaken in a consistent manner within a single open source computational framework, Chaste, which comprises fully tested, industrial-grade software that has been developed using an agile approach. This framework allows one to easily change assumptions regarding force generation and cell rearrangement processes within these models. The versatility and generality of this framework is illustrated using a number of biological examples. In each case we provide full details of all technical aspects of our model implementations, and in some cases provide extensions to make the models more generally applicable

A dispersive wave pattern on Jupiter's fastest retrograde jet at 20∘20^\circS

A compact wave pattern has been identified on Jupiter's fastest retrograding jet at 20S (the SEBs) on the southern edge of the South Equatorial Belt. The wave has been identified in both reflected sunlight from amateur observations between 2010 and 2015, thermal infrared imaging from the Very Large Telescope and near infrared imaging from the Infrared Telescope Facility. The wave pattern is present when the SEB is relatively quiescent and lacking large-scale disturbances, and is particularly notable when the belt has undergone a fade (whitening). It is generally not present when the SEB exhibits its usual large-scale convective activity ('rifts'). Tracking of the wave pattern and associated white ovals on its southern edge over several epochs have permitted a measure of the dispersion relationship, showing a strong correlation between the phase speed (-43.2 to -21.2 m/s) and the longitudinal wavelength, which varied from 4.4-10.0 deg. longitude over the course of the observations. Infrared imaging sensing low pressures in the upper troposphere suggest that the wave is confined to near the cloud tops. The wave is moving westward at a phase speed slower (i.e., less negative) than the peak retrograde wind speed (-62 m/s), and is therefore moving east with respect to the SEBs jet peak. Unlike the retrograde NEBn jet near 17N, which is a location of strong vertical wind shear that sometimes hosts Rossby wave activity, the SEBs jet remains retrograde throughout the upper troposphere, suggesting the SEBs pattern cannot be interpreted as a classical Rossby wave. Cassini-derived windspeeds and temperatures reveal that the vorticity gradient is dominated by the baroclinic term and becomes negative (changes sign) in a region near the cloud-top level (400-700 mbar) associated with the SEBs, suggesting a baroclinic origin for this meandering wave pattern. [Abr]Comment: 19 pages, 11 figures, article accepted for publication in Icaru

Geometric approach to Fletcher's ideal penalty function

Original article can be found at: www.springerlink.com Copyright Springer. [Originally produced as UH Technical Report 280, 1993]In this note, we derive a geometric formulation of an ideal penalty function for equality constrained problems. This differentiable penalty function requires no parameter estimation or adjustment, has numerical conditioning similar to that of the target function from which it is constructed, and also has the desirable property that the strict second-order constrained minima of the target function are precisely those strict second-order unconstrained minima of the penalty function which satisfy the constraints. Such a penalty function can be used to establish termination properties for algorithms which avoid ill-conditioned steps. Numerical values for the penalty function and its derivatives can be calculated efficiently using automatic differentiation techniques.Peer reviewe

Constraining the Atmospheric Composition of the Day-Night Terminators of HD 189733b : Atmospheric Retrieval with Aerosols

A number of observations have shown that Rayleigh scattering by aerosols dominates the transmission spectrum of HD 189733b at wavelengths shortward of 1 $\mu$m. In this study, we retrieve a range of aerosol distributions consistent with transmission spectroscopy between 0.3-24 $\mu$m that were recently re-analyzed by Pont et al. (2013). To constrain the particle size and the optical depth of the aerosol layer, we investigate the degeneracies between aerosol composition, temperature, planetary radius, and molecular abundances that prevent unique solutions for transit spectroscopy. Assuming that the aerosol is composed of MgSiO$_3$, we suggest that a vertically uniform aerosol layer over all pressures with a monodisperse particle size smaller than about 0.1 $\mu$m and an optical depth in the range 0.002-0.02 at 1 $\mu$m provides statistically meaningful solutions for the day/night terminator regions of HD 189733b. Generally, we find that a uniform aerosol layer provide adequate fits to the data if the optical depth is less than 0.1 and the particle size is smaller than 0.1 $\mu$m, irrespective of the atmospheric temperature, planetary radius, aerosol composition, and gaseous molecules. Strong constraints on the aerosol properties are provided by spectra at wavelengths shortward of 1 $\mu$m as well as longward of 8 $\mu$m, if the aerosol material has absorption features in this region. We show that these are the optimal wavelengths for quantifying the effects of aerosols, which may guide the design of future space observations. The present investigation indicates that the current data offer sufficient information to constrain some of the aerosol properties of HD189733b, but the chemistry in the terminator regions remains uncertain.Comment: Transferred to ApJ and accepted. 11 pages, 10 figures, 1 tabl

Trajectories in the Context of the Quantum Newton's Law

In this paper, we apply the one dimensional quantum law of motion, that we recently formulated in the context of the trajectory representation of quantum mechanics, to the constant potential, the linear potential and the harmonic oscillator. In the classically allowed regions, we show that to each classical trajectory there is a family of quantum trajectories which all pass through some points constituting nodes and belonging to the classical trajectory. We also discuss the generalization to any potential and give a new definition for de Broglie's wavelength in such a way as to link it with the length separating adjacent nodes. In particular, we show how quantum trajectories have as a limit when $\hbar \to 0$ the classical ones. In the classically forbidden regions, the nodal structure of the trajectories is lost and the particle velocity rapidly diverges.Comment: 17 pages, LateX, 6 eps figures, minor modifications, Title changed, to appear in Physica Script

The optical transmission spectrum of the hot Jupiter HAT-P-32b: clouds explain the absence of broad spectral features?

We report Gemini-North GMOS observations of the inflated hot Jupiter HAT-P-32b during two primary transits. We simultaneously observed two comparison stars and used differential spectro-photometry to produce multi-wavelength light curves. 'White' light curves and 29 'spectral' light curves were extracted for each transit and analysed to refine the system parameters and produce transmission spectra from 520-930nm in ~14nm bins. The light curves contain time-varying white noise as well as time-correlated noise, and we used a Gaussian process model to fit this complex noise model. Common mode corrections derived from the white light curve fits were applied to the spectral light curves which significantly improved our precision, reaching typical uncertainties in the transit depth of ~2x10^-4, corresponding to about half a pressure scale height. The low resolution transmission spectra are consistent with a featureless model, and we can confidently rule out broad features larger than about one scale height. The absence of Na/K wings or prominent TiO/VO features is most easily explained by grey absorption from clouds in the upper atmosphere, masking the spectral features. However, we cannot confidently rule out clear atmosphere models with low abundances (~10^-3 solar) of TiO, VO or even metal hydrides masking the Na and K wings. A smaller scale height or ionisation could also contribute to muted spectral features, but alone are unable to to account for the absence of features reported here.Comment: 17 pages, 11 figures, 2 tables, accepted for publication in MNRA

A Gemini ground-based transmission spectrum of WASP-29b: a featureless spectrum from 515 to 720nm

We report Gemini-South GMOS observations of the exoplanet system WASP-29 during primary transit as a test case for differential spectrophotometry. We use the multi-object spectrograph to observe the target star and a comparison star simultaneously to produce multiple light curves at varying wavelengths. The 'white' light curve and fifteen 'spectral' light curves are analysed to refine the system parameters and produce a transmission spectrum from 515 to 720nm. All light curves exhibit time-correlated noise, which we model using a variety of techniques. These include a simple noise rescaling, a Gaussian process model, and a wavelet based method. These methods all produce consistent results, although with different uncertainties. The precision of the transmission spectrum is improved by subtracting a common signal from all the spectral light curves, reaching a typical precision of ~1x10^-4 in transit depth. The transmission spectrum is free of spectral features, and given the non-detection of a pressure broadened Na feature, we can rule out the presence of a Na rich atmosphere free of clouds or hazes, although we cannot rule out a narrow Na core. This indicates that Na is not present in the atmosphere, and/or that clouds/hazes play a significant role in the atmosphere and mask the broad wings of the Na feature, although the former is a more likely explanation given WASP-29b's equilibrium temperature of ~970 K, at which Na can form various compounds. We also briefly discuss the use of Gaussian process and wavelet methods to account for time correlated noise in transit light curves.Comment: 15 pages, 9 figures, 3 tables. Published in MNRAS. Figure 2 corrected in version