Pattern Formation by Boundary Forcing in Convectively Unstable, Oscillatory Media With and Without Differential Transport

Motivated by recent experiments and models of biological segmentation, we analyze the exicitation of pattern-forming instabilities of convectively unstable reaction-diffusion-advection (RDA) systems, occuring by means of constant or periodic forcing at the upstream boundary. Such boundary-controlled pattern selection is a generalization of the flow-distributed oscillation (FDO) mechanism that can include Turing or differential flow instability (DIFI) modes. Our goal is to clarify the relationships among these mechanisms in the general case where there is differential flow as well as differential diffusion. We do so by analyzing the dispersion relation for linear perturbations and showing how its solutions are affected by differential transport. We find a close relationship between DIFI and FDO, while the Turing mechanism gives rise to a distinct set of unstable modes. Finally, we illustrate the relevance of the dispersion relations using nonlinear simulations and we discuss the experimental implications of our results.Comment: Revised version with added content (new section and figures added), changes to wording and organizatio

Hybrid Local-Order Mechanism for Inversion Symmetry Breaking

Using classical Monte Carlo simulations, we study a simple statistical mechanical model of relevance to the emergence of polarisation from local displacements on the square and cubic lattices. Our model contains two key ingredients: a Kitaev-like orientation-dependent interaction between nearest neighbours, and a steric term that acts between next-nearest neighbours. Taken by themselves, each of these two ingredients is incapable of driving long-range symmetry breaking, despite the presence of a broad feature in the corresponding heat capacity functions. Instead each component results in a "hidden" transition on cooling to a manifold of degenerate states, the two manifolds are different in the sense that they reflect distinct types of local order. Remarkably, their intersection---\emph{i.e.} the ground state when both interaction terms are included in the Hamiltonian---supports a spontaneous polarisation. In this way, our study demonstrates how local ordering mechanisms might be combined to break global inversion symmetry in a manner conceptually similar to that operating in the "hybrid" improper ferroelectrics. We discuss the relevance of our analysis to the emergence of spontaneous polarisation in well-studied ferroelectrics such as BaTiO$_3$ and KNbO$_3$.Comment: 8 pages, 8 figure

Bagging ensemble selection for regression

Bagging ensemble selection (BES) is a relatively new ensemble learning strategy. The strategy can be seen as an ensemble of the ensemble selection from libraries of models (ES) strategy. Previous experimental results on binary classification problems have shown that using random trees as base classifiers, BES-OOB (the most successful variant of BES) is competitive with (and in many cases, superior to) other ensemble learning strategies, for instance, the original ES algorithm, stacking with linear regression, random forests or boosting. Motivated by the promising results in classification, this paper examines the predictive performance of the BES-OOB strategy for regression problems. Our results show that the BES-OOB strategy outperforms Stochastic Gradient Boosting and Bagging when using regression trees as the base learners. Our results also suggest that the advantage of using a diverse model library becomes clear when the model library size is relatively large. We also present encouraging results indicating that the non negative least squares algorithm is a viable approach for pruning an ensemble of ensembles

An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients

Although >450 different topologies can achieve the same multicellular patterning function, they can be grouped into six main classes, which operate using different underlying dynamics.Alternative designs for the same functions can therefore split into two types: (a) topology alterations that retain the same underlying dynamics and (b) alterations that utilize a completely different underlying dynamical mechanism.This segregation of networks into distinct dynamical mechanisms can be revealed by the shape of the topology atlas itself.Cell–cell communication is not usually part of the causal mechanism underlying a band-pass response during morphogen interpretation, but it can tune the result or increase robustness

A sense of place, many times over - pattern formation and evolution of repetitive morphological structures

Fifty years ago, Lewis Wolpert introduced the concept of "positional information" to explain how patterns form in a multicellular embryonic field. Using morphogen gradients, whose continuous distributions of positional values are discretized via thresholds into distinct cellular states, he provided, at the theoretical level, an elegant solution to the "French Flag problem." In the intervening years, many experimental studies have lent support to Wolpert's ideas. However, the embryonic patterning of highly repetitive morphological structures, as often occurring in nature, can reveal limitations in the strict implementation of his initial theory, given the number of distinct threshold values that would have to be specified. Here, we review how positional information is complemented to circumvent these inadequacies, to accommodate tissue growth and pattern periodicity. In particular, we focus on functional anatomical assemblies composed of such structures, like the vertebrate spine or tetrapod digits, where the resulting segmented architecture is intrinsically linked to periodic pattern formation and unidirectional growth. These systems integrate positional information and growth with additional patterning cues that, we suggest, increase robustness and evolvability. We discuss different experimental and theoretical models to study such patterning systems, and how the underlying processes are modulated over evolutionary timescales to enable morphological diversification

Geometric Aspects of the Moduli Space of Riemann Surfaces

This is a survey of our recent results on the geometry of moduli spaces and Teichmuller spaces of Riemann surfaces appeared in math.DG/0403068 and math.DG/0409220. We introduce new metrics on the moduli and the Teichmuller spaces of Riemann surfaces with very good properties, study their curvatures and boundary behaviors in great detail. Based on the careful analysis of these new metrics, we have a good understanding of the Kahler-Einstein metric from which we prove that the logarithmic cotangent bundle of the moduli space is stable. Another corolary is a proof of the equivalences of all of the known classical complete metrics to the new metrics, in particular Yau's conjectures in the early 80s on the equivalences of the Kahler-Einstein metric to the Teichmuller and the Bergman metric.Comment: Survey article of our recent results on the subject. Typoes corrrecte

Periodic pattern formation in reaction-diffusion systems -an introduction for numerical simulation

The aim of the present review is to provide a comprehensive explanation of Turing reaction–diffusion systems in sufficient detail to allow readers to perform numerical calculations themselves. The reaction–diffusion model is widely studied in the field of mathematical biology, serves as a powerful paradigm model for self-organization and is beginning to be applied to actual experimental systems in developmental biology. Despite the increase in current interest, the model is not well understood among experimental biologists, partly because appropriate introductory texts are lacking. In the present review, we provide a detailed description of the definition of the Turing reaction–diffusion model that is comprehensible without a special mathematical background, then illustrate a method for reproducing numerical calculations with Microsoft Excel. We then show some examples of the patterns generated by the model. Finally, we discuss future prospects for the interdisciplinary field of research involving mathematical approaches in developmental biology

Independent Loop Invariants for 2+1 Gravity

We identify an explicit set of complete and independent Wilson loop invariants for 2+1 gravity on a three-manifold $M=\R\times\Sigma^g$, with $\Sigma^g$ a compact oriented Riemann surface of arbitrary genus $g$. In the derivation we make use of a global cross section of the $PSU(1,1)$-principal bundle over Teichm\"uller space given in terms of Fenchel-Nielsen coordinates.Comment: 11pp, 2 figures (postscript, compressed and uu-encoded), TeX, Pennsylvania State University, CGPG-94/7-

Quantitative analysis of cell types during growth and morphogenesis in Hydra

Tissue maceration was used to determine the absolute number and the distribution of cell types in Hydra. It was shown that the total number of cells per animal as well as the distribution of cells vary depending on temperature, feeding conditions, and state of growth. During head and foot regeneration and during budding the first detectable change in the cell distribution is an increase in the number of nerve cells at the site of morphogenesis. These results and the finding that nerve cells are most concentrated in the head region, diminishing in density down the body column, are discussed in relation to tissue polarity

A mechanism for morphogen-controlled domain growth

Many developmental systems are organised via the action of graded distributions of morphogens. In the Drosophila wing disc, for example, recent experimental evidence has shown that graded expression of the morphogen Dpp controls cell proliferation and hence disc growth. Our goal is to explore a simple model for regulation of wing growth via the Dpp gradient: we use a system of reaction-diffusion equations to model the dynamics of Dpp and its receptor Tkv, with advection arising as a result of the flow generated by cell proliferation. We analyse the model both numerically and analytically, showing that uniform domain growth across the disc produces an exponentially growing wing disc