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

A dynamic model of filament eruptions and two ribbon flares

Two basically different models for the filament equilibrium by Kippenhahn and Schluter (1957) and Kuperus and Raadu (1974) have appeared in the literature. A further analyses by van Tend and Kuperus (1978) added the force due to the horizontal component of the background field to the Kuperus and Raadu model. In order to obtain a better model which actually describes these phenomena, the evolution of the filament has to be considered in detail. A first attempt was recently presented by Kaastra. Kaastra did not formulate the precise energy balance equations for the problem, as is done in the present work. In the present model not only the force balance, but also the energy balance of the filament is taken into account. Thus a fully closed system of equations is obtained, that describes the evolution of the filament, first in force equilibrium during the current build-up phase, then in the non-equilibrium phase before the eruption, and the eruption itself. A neutral point appears above the photospheric surface in the non-equilibrium phase, but long before the eruption. It was found that although the filament itself may be in non-equilibrium, the evolution may still be slow up to the height where the eruption takes place. The eruption of the filament itself causes a large induced electric field at the neutral point which leads to the observed flare phenomena

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

The multipliers of periodic points in one-dimensional dynamics

It will be shown that the smooth conjugacy class of an $S-$unimodal map which does not have a periodic attractor neither a Cantor attractor is determined by the multipliers of the periodic orbits. This generalizes a result by M.Shub and D.Sullivan for smooth expanding maps of the circle

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

No elliptic islands for the universal area-preserving map

A renormalization approach has been used in \cite{EKW1} and \cite{EKW2} to prove the existence of a \textit{universal area-preserving map}, a map with hyperbolic orbits of all binary periods. The existence of a horseshoe, with positive Hausdorff dimension, in its domain was demonstrated in \cite{GJ1}. In this paper the coexistence problem is studied, and a computer-aided proof is given that no elliptic islands with period less than 20 exist in the domain. It is also shown that less than 1.5% of the measure of the domain consists of elliptic islands. This is proven by showing that the measure of initial conditions that escape to infinity is at least 98.5% of the measure of the domain, and we conjecture that the escaping set has full measure. This is highly unexpected, since generically it is believed that for conservative systems hyperbolicity and ellipticity coexist

The Haroche-Ramsey experiment as a generalized measurement

A number of atomic beam experiments, related to the Ramsey experiment and a recent experiment by Brune et al., are studied with respect to the question of complementarity. Three different procedures for obtaining information on the state of the incoming atom are compared. Positive operator-valued measures are explicitly calculated. It is demonstrated that, in principle, it is possible to choose the experimental arrangement so as to admit an interpretation as a joint non-ideal measurement yielding interference and ``which-way'' information. Comparison of the different measurements gives insight into the question of which information is provided by a (generalized) quantum mechanical measurement. For this purpose the subspaces of Hilbert-Schmidt space, spanned by the operators of the POVM, are determined for different measurement arrangements and different values of the parameters.Comment: REVTeX, 22 pages, 5 figure