Discrete time piecewise affine models of genetic regulatory networks

We introduce simple models of genetic regulatory networks and we proceed to the mathematical analysis of their dynamics. The models are discrete time dynamical systems generated by piecewise affine contracting mappings whose variables represent gene expression levels. When compared to other models of regulatory networks, these models have an additional parameter which is identified as quantifying interaction delays. In spite of their simplicity, their dynamics presents a rich variety of behaviours. This phenomenology is not limited to piecewise affine model but extends to smooth nonlinear discrete time models of regulatory networks. In a first step, our analysis concerns general properties of networks on arbitrary graphs (characterisation of the attractor, symbolic dynamics, Lyapunov stability, structural stability, symmetries, etc). In a second step, focus is made on simple circuits for which the attractor and its changes with parameters are described. In the negative circuit of 2 genes, a thorough study is presented which concern stable (quasi-)periodic oscillations governed by rotations on the unit circle -- with a rotation number depending continuously and monotonically on threshold parameters. These regular oscillations exist in negative circuits with arbitrary number of genes where they are most likely to be observed in genetic systems with non-negligible delay effects.Comment: 34 page

Interacting Intersections

Intersecting p-branes can be viewed as higher-dimensional interpretations of multi-charge extremal p-branes, where some of the individual p-branes undergo diagonal dimensional oxidation, while the others oxidise vertically. Although the naive vertical oxidation of a single p-brane gives a continuum of p-branes, a more natural description arises if one considers a periodic array of p-branes in the higher dimension, implying a dependence on the compactification coordinates. This still reduces to the single lower-dimensional p-brane when viewed at distances large compared with the period. Applying the same logic to the multi-charge solutions, we are led to consider more general classes of intersecting p-brane solutions, again depending on the compactification coordinates, which turn out to be described by interacting functions rather than independent harmonic functions. These new solutions also provide a more satisfactory interpretation for the lower-dimensional multi-charge p-branes, which otherwise appear to be nothing more than the improbable coincidence of charge-centres of individual constituents with zero binding energy.Comment: 20 pages, Latex, references adde

Dynamical Anomalous Subvarieties: Structure and Bounded Height Theorems

According to Medvedev and Scanlon, a polynomial $f(x)\in \bar{\mathbb Q}[x]$ of degree $d\geq 2$ is called disintegrated if it is not linearly conjugate to $x^d$ or $\pm C_d(x)$ (where $C_d(x)$ is the Chebyshev polynomial of degree $d$). Let $n\in\mathbb{N}$, let $f_1,\ldots,f_n\in \bar{\mathbb Q}[x]$ be disintegrated polynomials of degrees at least 2, and let $\varphi=f_1\times\ldots\times f_n$ be the corresponding coordinate-wise self-map of $({\mathbb P}^1)^n$. Let $X$ be an irreducible subvariety of $({\mathbb P}^1)^n$ of dimension $r$ defined over $\bar{\mathbb Q}$. We define the \emph{$\varphi$-anomalous} locus of $X$ which is related to the \emph{$\varphi$-periodic} subvarieties of $({\mathbb P}^1)^n$. We prove that the $\varphi$-anomalous locus of $X$ is Zariski closed; this is a dynamical analogue of a theorem of Bombieri, Masser, and Zannier \cite{BMZ07}. We also prove that the points in the intersection of $X$ with the union of all irreducible $\varphi$-periodic subvarieties of $({\mathbb P}^1)^n$ of codimension $r$ have bounded height outside the $\varphi$-anomalous locus of $X$; this is a dynamical analogue of Habegger's theorem \cite{Habegger09} which was previously conjectured in \cite{BMZ07}. The slightly more general self-maps $\varphi=f_1\times\ldots\times f_n$ where each $f_i\in \bar{\mathbb Q}(x)$ is a disintegrated rational map are also treated at the end of the paper.Comment: Minor mistakes corrected, slight reorganizatio

A semi-numerical method for periodic orbits in a bisymmetrical potential

We use a semi-numerical method to find the position and period of periodic orbits in a bisymmetrical potential, made up of a two dimensional harmonic oscillator, with an additional term of a Plummer potential, in a number of resonant cases. The results are compared with the outcomes obtained by the numerical integration of the equations of motion and the agreement is good. This indicates that the semi-numerical method gives general and reliable results. Comparison with other methods of locating periodic orbits is also made.Comment: Published in Mechanics Research Communication journal, 6 pages, 5 figures and 6 table

Multidimensional extension of the Morse--Hedlund theorem

A celebrated result of Morse and Hedlund, stated in 1938, asserts that a sequence $x$ over a finite alphabet is ultimately periodic if and only if, for some $n$, the number of different factors of length $n$ appearing in $x$ is less than $n+1$. Attempts to extend this fundamental result, for example, to higher dimensions, have been considered during the last fifteen years. Let $d\ge 2$. A legitimate extension to a multidimensional setting of the notion of periodicity is to consider sets of \ZZ^d definable by a first order formula in the Presburger arithmetic . With this latter notion and using a powerful criterion due to Muchnik, we exhibit a complete extension of the Morse--Hedlund theorem to an arbitrary dimension $d$ and characterize sets of $\ZZ^d$ definable in in terms of some functions counting recurrent blocks, that is, blocks occurring infinitely often