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

Bulk-fragment and tube-like structures of AuN (N=2-26)

Using the relativistic all-electron density-functional calculations on the AuN (N=2-26) in the generalized gradient approximation, combined with the guided simulated annealing, we have found that the two- to three-dimensional structural transition for AuN occurs between N=13 and 15, and the AuN (16<= N <=25) prefer also the pyramid-based bulk fragment structures in addition to the Au20. More importantly, the tubelike structures are found to be the most stable for Au24 and Au26, offering another powerful structure competitor with other isomers, e.g., amorphous, bulk fragment, and gold fullerene. The mechanism to cause these unusual AuN may be attributed to the stronger s-d hybridization and the d-d interaction enhanced by the relativistic effects.Comment: 12 pages and 3 figure

Same traits, different variance : Item-Level Variation Within Personality Measures

© 2014 the Author(s). This article has been published under the terms of the Creative Commons Attribution License. Without requesting permission from the Author or SAGE, you may further copy, distribute, transmit, and adapt the article, with the condition that the Author and SAGE Open are in each case credited as the source of the article. The version of record, Jamie S. Churcyard, Karen J. Pine, Shivani Sharma, Ben (C) Fletcher, ' Same Traits, Difference Variance: Item-Level Variation Within Personality Measures', SAGE Open, 2014, is available online via doi: 10.1177/2158244014522634Personality trait questionnaires are regularly used in individual differences research to examine personality scores between participants, although trait researchers tend to place little value on intra-individual variation in item ratings within a measured trait. The few studies that examine variability indices have not considered how they are related to a selection of psychological outcomes, so we recruited 160 participants (age M = 24.16, SD = 9.54) who completed the IPIP-HEXACO personality questionnaire and several outcome measures. Heterogenous within-subject differences in item ratings were found for every trait/facet measured, with measurement error that remained stable across the questionnaire. Within-subject standard deviations, calculated as measures of individual variation in specific item ratings within a trait/facet, were related to outcomes including life satisfaction and depression. This suggests these indices represent valid constructs of variability, and that researchers administering behavior statement trait questionnaires with outcome measures should also apply item-level variability indices.Peer reviewedFinal Published versio

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

Observations of Reconnection Flows in a Flare on the Solar Disk

Magnetic reconnection is a well-accepted part of the theory of solar eruptive events, though the evidence is still circumstantial. Intrinsic to the reconnection picture of a solar eruptive event, particularly in the standard model for two-ribbon flares ("CSHKP" model), are an advective flow of magnetized plasma into the reconnection region, expansion of field above the reconnection region as a flux rope erupts, retraction of heated post-reconnection loops, and downflows of cooling plasma along those loops. We report on a unique set of SDO/AIA imaging and Hinode/EIS spectroscopic observations of the disk flare SOL2016-03-23T03:54 in which all four flows are present simultaneously. This includes spectroscopic evidence for a plasma upflow in association with large-scale expanding closed inflow field. The reconnection inflows are symmetric, and consistent with fast reconnection, and the post-reconnection loops show a clear cooling and deceleration as they retract. Observations of coronal reconnection flows are still rare, and most events are observed at the solar limb, obscured by complex foregrounds, making their relationship to the flare ribbons, cusp field and arcades formed in the lower atmosphere difficult to interpret. The disk location and favorable perspective of this event have removed these ambiguities giving a clear picture of the reconnection dynamics.Comment: 9 pages, 5 figures, and 1 table. Accepted for publication in ApJ

A polynomial training algorithm for calculating perceptrons of optimal stability

Recomi (REpeated COrrelation Matrix Inversion) is a polynomially fast algorithm for searching optimally stable solutions of the perceptron learning problem. For random unbiased and biased patterns it is shown that the algorithm is able to find optimal solutions, if any exist, in at worst O(N^4) floating point operations. Even beyond the critical storage capacity alpha_c the algorithm is able to find locally stable solutions (with negative stability) at the same speed. There are no divergent time scales in the learning process. A full proof of convergence cannot yet be given, only major constituents of a proof are shown.Comment: 11 pages, Latex, 4 EPS figure