Evolution of bHLH transcription factors that control cell differentiation in plants

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Outbreak size distributions in epidemics with multiple stages

Multiple-type branching processes that model the spread of infectious diseases are investigated. In these stochastic processes, the disease goes through multiple stages before it eventually disappears. We mostly focus on the critical multistage Susceptible-Infected-Recovered (SIR) infection process. In the infinite population limit, we compute the outbreak size distributions and show that asymptotic results apply to more general multiple-type critical branching processes. Finally using heuristic arguments and simulations we establish scaling laws for a multistage SIR model in a finite population.Comment: 7 pages, 2 figures; added references, final versio

On universality in aging ferromagnets

This work is a contribution to the study of universality in out-of-equilibrium lattice models undergoing a second-order phase transition at equilibrium. The experimental protocol that we have chosen is the following: the system is prepared in its high-temperature phase and then quenched at the critical temperature $T_c$. We investigated by mean of Monte Carlo simulations two quantities that are believed to take universal values: the exponent $\lambda/z$ obtained from the decay of autocorrelation functions and the asymptotic value $X_\infty$ of the fluctuation-dissipation ratio $X(t,s)$. This protocol was applied to the Ising model, the 3-state clock model and the 4-state Potts model on square, triangular and honeycomb lattices and to the Ashkin-Teller model at the point belonging at equilibrium to the 3-state Potts model universality class and to a multispin Ising model and the Baxter-Wu model both belonging to the 4-state Potts model universality class at equilibrium.Comment: 17 page

Slow Relaxation in a Constrained Ising Spin Chain: a Toy Model for Granular Compaction

We present detailed analytical studies on the zero temperature coarsening dynamics in an Ising spin chain in presence of a dynamically induced field that favors locally the `-' phase compared to the `+' phase. We show that the presence of such a local kinetic bias drives the system into a late time state with average magnetization m=-1. However the magnetization relaxes into this final value extremely slowly in an inverse logarithmic fashion. We further map this spin model exactly onto a simple lattice model of granular compaction that includes the minimal microscopic moves needed for compaction. This toy model then predicts analytically an inverse logarithmic law for the growth of density of granular particles, as seen in recent experiments and thereby provides a new mechanism for the inverse logarithmic relaxation. Our analysis utilizes an independent interval approximation for the particle and the hole clusters and is argued to be exact at late times (supported also by numerical simulations).Comment: 9 pages RevTeX, 1 figures (.eps

Quasi-stationary regime of a branching random walk in presence of an absorbing wall

A branching random walk in presence of an absorbing wall moving at a constant velocity $v$ undergoes a phase transition as the velocity $v$ of the wall varies. Below the critical velocity $v_c$, the population has a non-zero survival probability and when the population survives its size grows exponentially. We investigate the histories of the population conditioned on having a single survivor at some final time $T$. We study the quasi-stationary regime for $v<v_c$ when $T$ is large. To do so, one can construct a modified stochastic process which is equivalent to the original process conditioned on having a single survivor at final time $T$. We then use this construction to show that the properties of the quasi-stationary regime are universal when $v\to v_c$. We also solve exactly a simple version of the problem, the exponential model, for which the study of the quasi-stationary regime can be reduced to the analysis of a single one-dimensional map.Comment: 2 figures, minor corrections, one reference adde

Autonomous multispecies reaction-diffusion systems with more-than-two-site interactions

Autonomous multispecies systems with more-than-two-neighbor interactions are studied. Conditions necessary and sufficient for closedness of the evolution equations of the $n$-point functions are obtained. The average number of the particles at each site for one species and three-site interactions, and its generalization to the more-than-three-site interactions is explicitly obtained. Generalizations of the Glauber model in different directions, using generalized rates, generalized number of states at each site, and generalized number of interacting sites, are also investigated.Comment: 9 pages, LaTeX2

Patchiness and Demographic Noise in Three Ecological Examples

Understanding the causes and effects of spatial aggregation is one of the most fundamental problems in ecology. Aggregation is an emergent phenomenon arising from the interactions between the individuals of the population, able to sense only -at most- local densities of their cohorts. Thus, taking into account the individual-level interactions and fluctuations is essential to reach a correct description of the population. Classic deterministic equations are suitable to describe some aspects of the population, but leave out features related to the stochasticity inherent to the discreteness of the individuals. Stochastic equations for the population do account for these fluctuation-generated effects by means of demographic noise terms but, owing to their complexity, they can be difficult (or, at times, impossible) to deal with. Even when they can be written in a simple form, they are still difficult to numerically integrate due to the presence of the "square-root" intrinsic noise. In this paper, we discuss a simple way to add the effect of demographic stochasticity to three classic, deterministic ecological examples where aggregation plays an important role. We study the resulting equations using a recently-introduced integration scheme especially devised to integrate numerically stochastic equations with demographic noise. Aimed at scrutinizing the ability of these stochastic examples to show aggregation, we find that the three systems not only show patchy configurations, but also undergo a phase transition belonging to the directed percolation universality class.Comment: 20 pages, 5 figures. To appear in J. Stat. Phy

The non-equilibrium response of the critical Ising model: Universal scaling properties and Local Scale Invariance

Motivated by recent numerical findings [M. Henkel, T. Enss, and M. Pleimling, J. Phys. A: Math. Gen. 39 (2006) L589] we re-examine via Monte Carlo simulations the linear response function of the two-dimensional Ising model with Glauber dynamics quenched to the critical point. At variance with the results of Henkel et al., we detect discrepancies between the actual scaling behavior of the response function and the prediction of Local Scale Invariance. Such differences are clearly visible in the impulse autoresponse function, whereas they are drastically reduced in integrated response functions. Accordingly, the scaling form predicted on the basis of Local Scale Invariance simply provides an accurate fitting form for some quantities but cannot be considered to be exact.Comment: 25 pages, 4 figure

Surface Covering of Downed Logs: Drivers of a Neglected Process in Dead Wood Ecology

Many species use coarse woody debris (CWD) and are disadvantaged by the forestry-induced loss of this resource. A neglected process affecting CWD is the covering of the surfaces of downed logs caused by sinking into the ground (increasing soil contact, mostly covering the underside of the log), and dense overgrowth by ground vegetation. Such cover is likely to profoundly influence the quality and accessibility of CWD for wood-inhabiting organisms, but the factors affecting covering are largely unknown. In a five-year experiment we determined predictors of covering rate of fresh logs in boreal forests and clear-cuts. Logs with branches were little covered because they had low longitudinal ground contact. For branchless logs, longitudinal ground contact was most strongly related to estimated peat depth (positive relation). The strongest predictor for total cover of branchless logs was longitudinal ground contact. To evaluate the effect on cover of factors other than longitudinal ground contact, we separately analyzed data from only those log sections that were in contact with the ground. Four factors were prominent predictors of percentage cover of such log sections: estimated peat depth, canopy shade (both increasing cover), potential solar radiation calculated from slope and slope aspect, and diameter of the log (both reducing cover). Peat increased cover directly through its low resistance, which allowed logs to sink and soil contact to increase. High moisture and low temperatures in pole-ward facing slopes and under a canopy favor peat formation through lowered decomposition and enhanced growth of peat-forming mosses, which also proved to rapidly overgrow logs. We found that in some boreal forests, peat and fast-growing mosses can rapidly cover logs lying on the ground. When actively introducing CWD for conservation purposes, we recommend that such rapid covering is avoided, thereby most likely improving the CWD's longevity as habitat for many species