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

Streaming Tree Transducers

Theory of tree transducers provides a foundation for understanding expressiveness and complexity of analysis problems for specification languages for transforming hierarchically structured data such as XML documents. We introduce streaming tree transducers as an analyzable, executable, and expressive model for transforming unranked ordered trees in a single pass. Given a linear encoding of the input tree, the transducer makes a single left-to-right pass through the input, and computes the output in linear time using a finite-state control, a visibly pushdown stack, and a finite number of variables that store output chunks that can be combined using the operations of string-concatenation and tree-insertion. We prove that the expressiveness of the model coincides with transductions definable using monadic second-order logic (MSO). Existing models of tree transducers either cannot implement all MSO-definable transformations, or require regular look ahead that prohibits single-pass implementation. We show a variety of analysis problems such as type-checking and checking functional equivalence are solvable for our model.Comment: 40 page

Automated Driving and its Effect on the Safety Ecosystem: How do Compatibility Issues Affect the Transition Period?

AbstractDifferent components of automated vehicles are being made available commercially as we speak. Much research has been conducted into these components and many of these have been studied with respect to their effects on safety, but the transition period from non-automated driving to fully automated vehicles raises safety related issues dealing with mixed traffic situations. More in-depth knowledge should be gained in (the safety of) the behaviour of drivers of unequipped vehicles, enabling automated vehicles to predict and adequately respond to potentially unsafe behaviour, a concept we call backwards compatibility. Also, automated vehicle system design tends to be from an optimal system performance perspective which leads to driving patterns such as driving in the centre of a lane. Other (human) road users however likely exhibit driving behaviour in line with different rationales which allow for suboptimal driving patterns. As of yet, it remains unclear whether these patterns contain indications about the intentions of a driver and if or how other road users anticipate these. This could have two consequences with regard to mixed traffic situations. First of all, other road users might miss important cues from the behaviour of the automated vehicle (what we call forward incompatibility). Secondly, the occupant of an automated vehicle might expect human-like behaviour from the automated vehicle in safety-critical situations, lowering acceptance if this does not meet expectations. The current paper considers these issues and states that we need more insight in how road users use other road users’ behaviour to anticipate safety critical events, especially in the transition period towards fully automated vehicles

Multithermal Analysis of a CDS Coronal Loop

The observations from 1998 April 20 taken with the Coronal Diagnostics Spectrometer CDS on SOHO of a coronal loop on the limb have shown that the plasma was multi-thermal along each line of sight investigated, both before and after background subtraction. The latter result relied on Emission Measure Loci plots, but in this Letter, we used a forward folding technique to produce Differential Emission Measure curves. We also calculate DEM-weighted temperatures for the chosen pixels and find a gradient in temperature along the loop as a function of height that is not compatible with the flat profiles reported by numerous authors for loops observed with EIT on SOHO and TRACE. We also find discrepancies in excess of the mathematical expectation between some of the observed and predicted CDS line intensities. We demonstrate that these differences result from well-known limitations in our knowledge of the atomic data and are to be expected. We further show that the precision of the DEM is limited by the intrinsic width of the ion emissivity functions that are used to calculate the DEM. Hence we conclude that peaks and valleys in the DEM, while in principle not impossible, cannot be confirmed from the data.Comment: 12 pages, 3 figures, Accepted by ApJ Letter

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 Phase Transition for Circle Maps and Cherry Flows

We study $C^{2}$ weakly order preserving circle maps with a flat interval. The main result of the paper is about a sharp transition from degenerate geometry to bounded geometry depending on the degree of the singularities at the boundary of the flat interval. We prove that the non-wandering set has zero Hausdorff dimension in the case of degenerate geometry and it has Hausdorff dimension strictly greater than zero in the case of bounded geometry. Our results about circle maps allow to establish a sharp phase transition in the dynamics of Cherry flows

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

Maximal Accuracy and Minimal Disturbance in the Arthurs-Kelly Simultaneous Measurement Process

The accuracy of the Arthurs-Kelly model of a simultaneous measurement of position and momentum is analysed using concepts developed by Braginsky and Khalili in the context of measurements of a single quantum observable. A distinction is made between the errors of retrodiction and prediction. It is shown that the distribution of measured values coincides with the initial state Husimi function when the retrodictive accuracy is maximised, and that it is related to the final state anti-Husimi function (the P representation of quantum optics) when the predictive accuracy is maximised. The disturbance of the system by the measurement is also discussed. A class of minimally disturbing measurements is characterised. It is shown that the distribution of measured values then coincides with one of the smoothed Wigner functions described by Cartwright.Comment: 12 pages, 0 figures. AMS-Latex. Earlier version replaced with final published versio

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

Driven Brownian transport through arrays of symmetric obstacles

We numerically investigate the transport of a suspended overdamped Brownian particle which is driven through a two-dimensional rectangular array of circular obstacles with finite radius. Two limiting cases are considered in detail, namely, when the constant drive is parallel to the principal or the diagonal array axes. This corresponds to studying the Brownian transport in periodic channels with reflecting walls of different topologies. The mobility and diffusivity of the transported particles in such channels are determined as functions of the drive and the array geometric parameters. Prominent transport features, like negative differential mobilities, excess diffusion peaks, and unconventional asymptotic behaviors, are explained in terms of two distinct lengths, the size of single obstacles (trapping length) and the lattice constant of the array (local correlation length). Local correlation effects are further analyzed by continuously rotating the drive between the two limiting orientations.Comment: 10 pages 13 figure