The genotype-phenotype relationship in multicellular pattern-generating models - the neglected role of pattern descriptors

Background: A deep understanding of what causes the phenotypic variation arising from biological patterning processes, cannot be claimed before we are able to recreate this variation by mathematical models capable of generating genotype-phenotype maps in a causally cohesive way. However, the concept of pattern in a multicellular context implies that what matters is not the state of every single cell, but certain emergent qualities of the total cell aggregate. Thus, in order to set up a genotype-phenotype map in such a spatiotemporal pattern setting one is actually forced to establish new pattern descriptors and derive their relations to parameters of the original model. A pattern descriptor is a variable that describes and quantifies a certain qualitative feature of the pattern, for example the degree to which certain macroscopic structures are present. There is today no general procedure for how to relate a set of patterns and their characteristic features to the functional relationships, parameter values and initial values of an original pattern-generating model. Here we present a new, generic approach for explorative analysis of complex patterning models which focuses on the essential pattern features and their relations to the model parameters. The approach is illustrated on an existing model for Delta-Notch lateral inhibition over a two-dimensional lattice. Results: By combining computer simulations according to a succession of statistical experimental designs, computer graphics, automatic image analysis, human sensory descriptive analysis and multivariate data modelling, we derive a pattern descriptor model of those macroscopic, emergent aspects of the patterns that we consider of interest. The pattern descriptor model relates the values of the new, dedicated pattern descriptors to the parameter values of the original model, for example by predicting the parameter values leading to particular patterns, and provides insights that would have been hard to obtain by traditional methods. Conclusion: The results suggest that our approach may qualify as a general procedure for how to discover and relate relevant features and characteristics of emergent patterns to the functional relationships, parameter values and initial values of an underlying pattern-generating mathematical model

Solvable Model of Spiral Wave Chimeras

Spiral waves are ubiquitous in two-dimensional systems of chemical or biological oscillators coupled locally by diffusion. At the center of such spirals is a phase singularity, a topological defect where the oscillator amplitude drops to zero. But if the coupling is nonlocal, a new kind of spiral can occur, with a circular core consisting of desynchronized oscillators running at full amplitude. Here we provide the first analytical description of such a spiral wave chimera, and use perturbation theory to calculate its rotation speed and the size of its incoherent core.Comment: 4 pages, 4 figures; added reference, figure, further numerical test

Tensile Properties of Five Low-Alloy and Stainless Steels Under High-Heating-Rate and Constant-Temperature Conditions

Tensile properties of five low-alloy and stainless steels under high heating rate and constant temperatur

A German employee network and union renewal: the Siemenskonflikt

The paper shows how redundancies were resisted by Hi-Tech workers in a large German company. It details an employee network’s emergence to provide support to individuals and to pursue legal cases against the company, and analyzes the network’s norms and operation. The network operated in complementary ways to the union and works council, to achieve a favourable outcome. The case is used to test theoretical propositions derived from literature on Hi-Tech workers, union renewal and mobilization theory and it is suggested that mobilization theory requires further extension in several directions

Stably non-synchronizable maps of the plane

Pecora and Carroll presented a notion of synchronization where an (n-1)-dimensional nonautonomous system is constructed from a given $n$-dimensional dynamical system by imposing the evolution of one coordinate. They noticed that the resulting dynamics may be contracting even if the original dynamics are not. It is easy to construct flows or maps such that no coordinate has synchronizing properties, but this cannot be done in an open set of linear maps or flows in $\R^n$, $n\geq 2$. In this paper we give examples of real analytic homeomorphisms of $\R^2$ such that the non-synchronizability is stable in the sense that in a full $C^0$ neighborhood of the given map, no homeomorphism is synchronizable

A comparison of predicted and observed ocean tidal loading in Alaska

We investigate the elastic and anelastic response of the crust and upper mantle across Alaska to mass loading by ocean tides. GPS-inferred surface displacements recorded by the Plate Boundary Observatory network are compared with predictions of deformation associated with the redistribution of ocean water due to the tides. We process more than 5 yr of GPS data from 131 stations using a kinematic precise point positioning algorithm and estimate tidal contributions using harmonic analysis. We also forward calculate load-induced surface displacements by convolving ocean-tide models with load Green’s functions derived from spherically symmetric Earth models. We make the comparisons for dominant tidal harmonics in three frequency bands: semidiurnal (M₂), diurnal (O₁) and fortnightly (M_f). Vector differences between predicted and observed ocean tidal loading (OTL) displacements are predominantly sub-mm in magnitude in all three frequency bands and spatial components across the network, with larger residuals of up to several mm in some coastal areas. Accounting for the effects of anelastic dispersion in the upper mantle using estimates of Q from standard Earth models reduces the residuals for the M₂ harmonic by an average of 0.1–0.2 mm across the network and by more than 1 mm at some individual stations. For the relatively small M_f tide, the effects of anelastic dispersion (<0.03 mm) are undetectable within current measurement error. Incorporating a local ocean-tide model for the northeastern Pacific Ocean reduces the M₂ vertical residuals by an average of 0.2 mm, with improvements of up to 5 mm at some coastal stations. Estimated RMS observational uncertainties in the vertical component for the M₂ and O₁ tides are approximately ±0.08 mm at the two-sigma level (±0.03 mm in the horizontal components), and ±0.21 mm for the M_f harmonic (±0.07 mm in the horizontal components). For the M₂ harmonic, discrepancies between predicted and observed OTL displacements exceed observational uncertainties by about one order of magnitude. None of the ocean tide and Earth model combinations is found to reduce the M₂ residuals below the observational uncertainty, and no single forward model provides a best fit to the observed displacements across all tidal harmonics and spatial components. For the O₁ harmonic, discrepancies between predicted and observed displacements are generally several-fold larger than the observational uncertainties. For the M_f harmonic, the discrepancies are roughly within a factor of two of the observational uncertainties. We find that discrepancies between predicted and observed OTL displacements can be significantly reduced by removing a network-uniform tidal-harmonic displacement, and that the remaining discrepancies exhibit some regional-scale spatial coherency, particularly for the M₂ harmonic. We suggest that the remaining discrepancies for the M₂, O₁ and M_f tides cannot be fully explained by measurement error and instead convey information about deficiencies in ocean-tide models and deviations from spherically symmetric Earth structure

A quantitative evaluation of metallic conduction in conjugated polymers

As the periodicity in crystalline materials creates the optimal condition for electronic delocalization, one might expect that in partially crystalline conjugated polymers delocalization is impeded by intergrain transport. However, for the best conducting polymers this presumption fails. Delocalization is obstructed by interchain rather than intergrain charge transfer and we propose a model of weakly coupled disordered chains to describe the physics near the metal-insulator transition. Our quantitative calculations match the outcome of recent broad-band optical experiments and provide a consistent explanation of metallic conduction in polymers.Comment: 4 pages incl. 3 figure

Entropic particle transport: higher order corrections to the Fick-Jacobs diffusion equation

Transport of point-size Brownian particles under the influence of a constant and uniform force field through a three-dimensional channel with smoothly varying periodic cross-section is investigated. Here, we employ an asymptotic analysis in the ratio between the difference of the widest and the most narrow constriction divided through the period length of the channel geometry. We demonstrate that the leading order term is equivalent to the Fick-Jacobs approximation. By use of the higher order corrections to the probability density we derive an expression for the spatially dependent diffusion coefficient D(x) which substitutes the constant diffusion coefficient present in the common Fick-Jacobs equation. In addition, we show that in the diffusion dominated regime the average transport velocity is obtained as the product of the zeroth-order Fick-Jacobs result and the expectation value of the spatially dependent diffusion coefficient . The analytic findings are corroborated with the precise numerical results of a finite element calculation of the Smoluchowski diffusive particle dynamics occurring in a reflection symmetric sinusoidal-shaped channel.Comment: 9 pages, 3 figure