Kinetic approaches to lactose operon induction and bimodality

The quasi-equilibrium approximation is acceptable when molecular interactions are fast enough compared to circuit dynamics, but is no longer allowed when cellular activities are governed by rare events. A typical example is the lactose operon (lac), one of the most famous paradigms of transcription regulation, for which several theories still coexist to describe its behaviors. The lac system is generally analyzed by using equilibrium constants, contradicting single-event hypotheses long suggested by Novick and Weiner (1957). Enzyme induction as an all-or-none phenomenon. Proc. Natl. Acad. Sci. USA 43, 553-566) and recently refined in the study of (Choi et al., 2008. A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science 322, 442-446). In the present report, a lac repressor (LacI)-mediated DNA immunoprecipitation experiment reveals that the natural LacI-lac DNA complex built in vivo is extremely tight and long-lived compared to the time scale of lac expression dynamics, which could functionally disconnect the abortive expression bursts and forbid using the standard modes of lac bistability. As alternatives, purely kinetic mechanisms are examined for their capacity to restrict induction through: (i) widely scattered derepression related to the arrival time variance of a predominantly backward asymmetric random walk and (ii) an induction threshold arising in a single window of derepression without recourse to nonlinear multimeric binding and Hill functions. Considering the complete disengagement of the lac repressor from the lac promoter as the probabilistic consequence of a transient stepwise mechanism, is sufficient to explain the sigmoidal lac responses as functions of time and of inducer concentration. This sigmoidal shape can be misleadingly interpreted as a phenomenon of equilibrium cooperativity classically used to explain bistability, but which has been reported to be weak in this system

New treatments of density fluctuations and recurrence times for re-estimating Zermelo's paradox

What is the probability that all the gas in a box accumulates in the same half of this box? Though amusing, this question underlies the fundamental problem of density fluctuations at equilibrium, which has profound implementations in many physical fields. The currently accepted solutions are derived from the studies of Brownian motion by Smoluchowski, but they are not appropriate for the directly colliding particles of gases. Two alternative theories are proposed here using self-regulatory Bernoulli distributions. A discretization of space is first introduced to develop a mechanism of matter congestion holding for high densities. In a second mechanism valid in ordinary conditions, the influence of local pressure on the location of every particle is examined using classical laws of ideal gases. This approach reveals that a negative feedback results from the reciprocal influences between individual particles and the population of particles, which strongly reduces the probability of atypical microstates. Finally, a thermodynamic quantum of time is defined to compare the recurrence times of improbable macrostates predicted through these different approaches.Comment: Le titre a \'et\'e chang\'e Ancien titre: Roles for local crowding and pressure in counteracting density fluctuations at equilibriu

Simply conceiving the Arrhenius law and absolute kinetic constants using the geometric distribution

Although first-order rate constants are basic ingredients of physical chemistry, biochemistry and systems modeling, their innermost nature is derived from complex physical chemistry mechanisms. The present study suggests that equivalent conclusions can be more straightly obtained from simple statistics. The different facets of kinetic constants are first classified and clarified with respect to time and energy and the equivalences between traditional flux rate and modern probabilistic modeling are summarized. Then, a naive but rigorous approach is proposed to concretely perceive how the Arrhenius law naturally emerges from the geometric distribution. It appears that (1) the distribution in time of chemical events as well as (2) their mean frequency, are both dictated by randomness only and as such, are accurately described by time-based and spatial exponential processes respectively

A simple asymmetric evolving random network

We introduce a new oriented evolving graph model inspired by biological networks. A node is added at each time step and is connected to the rest of the graph by random oriented edges emerging from older nodes. This leads to a statistical asymmetry between incoming and outgoing edges. We show that the model exhibits a percolation transition and discuss its universality. Below the threshold, the distribution of component sizes decreases algebraically with a continuously varying exponent depending on the average connectivity. We prove that the transition is of infinite order by deriving the exact asymptotic formula for the size of the giant component close to the threshold. We also present a thorough analysis of aging properties. We compute local-in-time profiles for the components of finite size and for the giant component, showing in particular that the giant component is always dense among the oldest nodes but invades only an exponentially small fraction of the young nodes close to the threshold.Comment: 33 pages, 3 figures, to appear in J. Stat. Phy

On Root Multiplicities of Some Hyperbolic Kac-Moody Algebras

Using the coset construction, we compute the root multiplicities at level three for some hyperbolic Kac-Moody algebras including the basic hyperbolic extension of $A_1^{(1)}$ and $E_{10}$.Comment: 10 pages, LaTe

Loewner Chains

These lecture notes on 2D growth processes are divided in two parts. The first part is a non-technical introduction to stochastic Loewner evolutions (SLEs). Their relationship with 2D critical interfaces is illustrated using numerical simulations. Schramm's argument mapping conformally invariant interfaces to SLEs is explained. The second part is a more detailed introduction to the mathematically challenging problems of 2D growth processes such as Laplacian growth, diffusion limited aggregation (DLA), etc. Their description in terms of dynamical conformal maps, with discrete or continuous time evolution, is recalled. We end with a conjecture based on possible dendritic anomalies which, if true, would imply that the Hele-Shaw problem and DLA are in different universality classes.Comment: 46 pages, 21 figure

Sailing the Deep Blue Sea of Decaying Burgers Turbulence

We study Lagrangian trajectories and scalar transport statistics in decaying Burgers turbulence. We choose velocity fields, solutions of the inviscid Burgers equation, whose probability distributions are specified by Kida's statistics. They are time-correlated, not time-reversal invariant and not Gaussian. We discuss in some details the effect of shocks on trajectories and transport equations. We derive the inviscid limit of these equations using a formalism of operators localized on shocks. We compute the probability distribution functions of the trajectories although they do not define Markov processes. As physically expected, these trajectories are statistically well-defined but collapse with probability one at infinite time. We point out that the advected scalars enjoy inverse energy cascades. We also make a few comments on the connection between our computations and persistence problems.Comment: 18 pages, one figure in eps format, Latex, published versio