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

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

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

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

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

A sequence of unsharp measurements enabling a real time visualization of a quantum oscillation

The normalized state $\ket{\psi(t)}=c_1(t)\ket{1}+c_2(t)\ket{2}$ of a single two-level system performs oscillations under the influence of a resonant driving field. It is assumed that only one realization of this process is available. We show that it is possible to approximately visualize in real time the evolution of the system as far as it is given by $|c_2(t)|^2$. For this purpose we use a sequence of particular unsharp measurements separated in time. They are specified within the theory of generalized measurements in which observables are represented by positive operator valued measures (POVM). A realization of the unsharp measurements may be obtained by coupling the two-level system to a meter and performing the usual projection measurements on the meter only.Comment: 17 pages, 3 figures, accepted for publication in Phys. Rev. A. Some typographical corrections are made and a short treatmeant of the fidelity of our measurements (N-series) is adde

Exact Results for the Kuramoto Model with a Bimodal Frequency Distribution

We analyze a large system of globally coupled phase oscillators whose natural frequencies are bimodally distributed. The dynamics of this system has been the subject of long-standing interest. In 1984 Kuramoto proposed several conjectures about its behavior; ten years later, Crawford obtained the first analytical results by means of a local center manifold calculation. Nevertheless, many questions have remained open, especially about the possibility of global bifurcations. Here we derive the system's complete stability diagram for the special case where the bimodal distribution consists of two equally weighted Lorentzians. Using an ansatz recently discovered by Ott and Antonsen, we show that in this case the infinite-dimensional problem reduces exactly to a flow in four dimensions. Depending on the parameters and initial conditions, the long-term dynamics evolves to one of three states: incoherence, where all the oscillators are desynchronized; partial synchrony, where a macroscopic group of phase-locked oscillators coexists with a sea of desynchronized ones; and a standing wave state, where two counter-rotating groups of phase-locked oscillators emerge. Analytical results are presented for the bifurcation boundaries between these states. Similar results are also obtained for the case in which the bimodal distribution is given by the sum of two Gaussians.Comment: 28 pages, 7 figures; submitted to Phys. Rev. E Added comment