Simply Generated Trees, B-series and Wigner Processes

We consider simply generated trees and study multiplicative functions on rooted plane trees. We show that the associated generating functions satisfy differential equations or difference equations. Our approach considers B-series from Butcher's theory, the generating functions are seen as generalized Runge-Kutta methodsComment: 19 pages, 1 figur

Stationary distributions and condensation in autocatalytic CRN

We investigate a broad family of non weakly reversible stochastically modeled reaction networks (CRN), by looking at their steady-state distributions. Most known results on stationary distributions assume weak reversibility and zero deficiency. We first give explicitly product-form steady-state distributions for a class of non weakly reversible autocatalytic CRN of arbitrary deficiency. Examples of interest in statistical mechanics (inclusion process), life sciences and robotics (collective decision making in ant and robot swarms) are provided. The product-form nature of the steady-state then enables the study of condensation in particle systems that are generalizations of the inclusion process.Comment: 25 pages. Some typos corrected, shortened some part

Long time behavior of the solutions to non-linear Kraichnan equations

We consider the solution of a nonlinear Kraichnan equation $$\partial_s H(s,t)=\int_t^s H(s,u)H(u,t) k(s,u) du,\quad s\ge t$$ with a covariance kernel $k$ and boundary condition $H(t,t)=1$. We study the long time behaviour of $H$ as the time parameters $t,s$ go to infinity, according to the asymptotic behaviour of $k$. This question appears in various subjects since it is related with the analysis of the asymptotic behaviour of the trace of non-commutative processes satisfying a linear differential equation, but also naturally shows up in the study of the so-called response function and aging properties of the dynamics of some disordered spin systems.Comment: 32 page

Phenotypic diversity and population growth in fluctuating environment: a MBPRE approach

Organisms adapt to fluctuating environments by regulating their dynamics, and by adjusting their phenotypes to environmental changes. We model population growth using multitype branching processes in random environments, where the offspring distribution of some organism having trait t\in\cT in environment e\in\cE is given by some (fixed) distribution $\Upsilon_{t,e}$ on \bbN. Then, the phenotypes are attributed using a distribution (strategy) $\pi_{t,e}$ on the trait space \cT. We look for the optimal strategy $\pi_{t,e}$, t\in\cT, e\in\cE maximizing the net growth rate or Lyapounov exponent, and characterize the set of optimal strategies. This is considered for various models of interest in biology: hereditary versus non-hereditary strategies and strategies involving or not involving a sensing mechanism. Our main results are obtained in the setting of non-hereditary strategies: thanks to a reduction to simple branching processes in random environment, we derive an exact expression for the net growth rate and a characterisation of optimal strategies. We also focus on typical genealogies, that is, we consider the problem of finding the typical lineage of a randomly chosen organism.Comment: 21 page

Ultrasensitivity and sharp threshold theorems for multisite systems

We study the ultrasensitivity of multisite binding processes where ligand molecules can bind to several binding sites, considering more particularly recent models involving complex chemical reactions in phosphorylation systems such as allosteric phosphorylation processes, or substrate-catalyst chain reactions and nucleosome mediated cooperativity. New statistics based formulas for the Hill coefficient and the effective Hill coefficient are provided and necessary conditions for a system to be ultrasensitive are exhibited. We then assume that the binding process is described by a density dependent birth and death process. We provide precise large deviation results for the steady state distribution of the process, and show that switch-like ultrasensitive responses are strongly related to the multi-stability of the associated dynamical system. Ultrasensitivity occurs if and only if the entropy of the dynamical system has more than one global minimum for some critical ligand concentration. In this case, the Hill coefficient is proportional to the number of binding sites, and the systems is highly ultrasensitive. We also discuss the interpretation of an extension $I_q$ of the effective Hill coefficient $I_{0.9}$ for which we recommend the computation of a broad range of values of $q$ instead of just the standard one corresponding to the 10% to 90% variation in the dose-response. It is shown that this single choice can sometimes mislead the conclusion by not detecting ultrasensitivity. This new approach allows a better understanding of multisite ultrasensitive systems and provides new tools for the design of such systems

Strand separation in negatively supercoiled DNA

Abstract.: We consider Benham's model for strand separation in negatively supercoiled circular DNA, and study denaturation as function of the linking difference density κ<0. We propose a statistical version of this model, based on bayesian segmentation methods of current use in bioinformatics; this leads to new algorithms with priors adapted to supercoiled DNA, taking into account the random nature of the free energies needed to denature base pair