95 research outputs found
Entropy production and coarse-graining in Markov processes
We study the large time fluctuations of entropy production in Markov
processes. In particular, we consider the effect of a coarse-graining procedure
which decimates {\em fast states} with respect to a given time threshold. Our
results provide strong evidence that entropy production is not directly
affected by this decimation, provided that it does not entirely remove loops
carrying a net probability current. After the study of some examples of random
walks on simple graphs, we apply our analysis to a network model for the
kinesin cycle, which is an important biomolecular motor. A tentative general
theory of these facts, based on Schnakenberg's network theory, is proposed.Comment: 18 pages, 13 figures, submitted for publicatio
Entropy production and coarse-graining in Markov processes
We study the large time fluctuations of entropy production in Markov
processes. In particular, we consider the effect of a coarse-graining procedure
which decimates {\em fast states} with respect to a given time threshold. Our
results provide strong evidence that entropy production is not directly
affected by this decimation, provided that it does not entirely remove loops
carrying a net probability current. After the study of some examples of random
walks on simple graphs, we apply our analysis to a network model for the
kinesin cycle, which is an important biomolecular motor. A tentative general
theory of these facts, based on Schnakenberg's network theory, is proposed.Comment: 18 pages, 13 figures, submitted for publicatio
Species lifetime distribution for simple models of ecologies
Interpretation of empirical results based on a taxa's lifetime distribution
shows apparently conflicting results. Species' lifetime is reported to be
exponentially distributed, whereas higher order taxa, such as families or
genera, follow a broader distribution, compatible with power law decay. We show
that both these evidences are consistent with a simple evolutionary model that
does not require specific assumptions on species interaction. The model
provides a zero-order description of the dynamics of ecological communities and
its species lifetime distribution can be computed exactly. Different behaviors
are found: an initial power law, emerging from a random walk type of
dynamics, which crosses over to a steeper branching process-like
regime and finally is cutoff by an exponential decay which becomes weaker and
weaker as the total population increases. Sampling effects can also be taken
into account and shown to be relevant: if species in the fossil record were
sampled according to the Fisher log-series distribution, lifetime should be
distributed according to a power law. Such variability of behaviors in
a simple model, combined with the scarcity of data available, cast serious
doubts on the possibility to validate theories of evolution on the basis of
species lifetime data.Comment: 19 pages, 2 figure
Coarse-Grained Probabilistic Automata Mimicking Chaotic Systems
Discretization of phase space usually nullifies chaos in dynamical systems.
We show that if randomness is associated with discretization dynamical chaos
may survive and be indistinguishable from that of the original chaotic system,
when an entropic, coarse-grained analysis is performed. Relevance of this
phenomenon to the problem of quantum chaos is discussed.Comment: 4 pages, 4 figure
Oscillations and temporal signalling in cells
The development of new techniques to quantitatively measure gene expression
in cells has shed light on a number of systems that display oscillations in
protein concentration. Here we review the different mechanisms which can
produce oscillations in gene expression or protein concentration, using a
framework of simple mathematical models. We focus on three eukaryotic genetic
regulatory networks which show "ultradian" oscillations, with time period of
the order of hours, and involve, respectively, proteins important for
development (Hes1), apoptosis (p53) and immune response (NFkB). We argue that
underlying all three is a common design consisting of a negative feedback loop
with time delay which is responsible for the oscillatory behaviour
Anomalies, absence of local equilibrium and universality in 1-d particles systems
One dimensional systems are under intense investigation, both from
theoretical and experimental points of view, since they have rather peculiar
characteristics which are of both conceptual and technological interest. We
analyze the dependence of the behaviour of one dimensional, time reversal
invariant, nonequilibrium systems on the parameters defining their microscopic
dynamics. In particular, we consider chains of identical oscillators
interacting via hard core elastic collisions and harmonic potentials, driven by
boundary Nos\'e-Hoover thermostats. Their behaviour mirrors qualitatively that
of stochastically driven systems, showing that anomalous properties are typical
of physics in one dimension. Chaos, by itslef, does not lead to standard
behaviour, since it does not guarantee local thermodynamic equilibrium. A
linear relation is found between density fluctuations and temperature profiles.
This link and the temporal asymmetry of fluctuations of the main observables
are robust against modifications of thermostat parameters and against
perturbations of the dynamics.Comment: 26 pages, 16 figures, revised text, two appendices adde
Continuous coexistence or discrete species? A new review of an old question
Question: Is the coexistence of a continuum of species or ecological types possible in real-world communities? Or should one expect distinctly different species?
Mathematical methods: We study whether the coexistence of species in a continuum of ecological types is (a) dynamically stable (against changes in population densities) and (b) structurally robust (against changes in population dynamics). Since most of the reviewed investigations are based on Lotka-Volterra models, we carefully explain which of the presented conclusions are model-independent.
mathematical conclusions: Seemingly plausible models with dynamically stable continuous- coexistence solutions do exist. However, these models either depend on biologically unrealistic mathematical assumptions (e.g. non-differentiable ingredient functions) or are structurally unstable (i.e. destroyable by arbitrarily small modifications to those ingredient functions). The dynamical stability of a continuous-coexistence solution, if it exists, requires positive definiteness of the model's competition kernel.
Biological conclusions: While the classical expectation of fixed limits to similarity is mathematically naive, the fundamental discreteness of species is a natural consequence of the basic structure of ecological interactio
Oscillation patterns in negative feedback loops
Organisms are equipped with regulatory systems that display a variety of
dynamical behaviours ranging from simple stable steady states, to switching and
multistability, to oscillations. Earlier work has shown that oscillations in
protein concentrations or gene expression levels are related to the presence of
at least one negative feedback loop in the regulatory network. Here we study
the dynamics of a very general class of negative feedback loops. Our main
result is that in these systems the sequence of maxima and minima of the
concentrations is uniquely determined by the topology of the loop and the
activating/repressing nature of the interaction between pairs of variables.
This allows us to devise an algorithm to reconstruct the topology of
oscillating negative feedback loops from their time series; this method applies
even when some variables are missing from the data set, or if the time series
shows transients, like damped oscillations. We illustrate the relevance and the
limits of validity of our method with three examples: p53-Mdm2 oscillations,
circadian gene expression in cyanobacteria, and cyclic binding of cofactors at
the estrogen-sensitive pS2 promoter.Comment: 10 pages, 8 figure
Growth, competition and cooperation in spatial population genetics
We study an individual based model describing competition in space between
two different alleles. Although the model is similar in spirit to classic
models of spatial population genetics such as the stepping stone model, here
however space is continuous and the total density of competing individuals
fluctuates due to demographic stochasticity. By means of analytics and
numerical simulations, we study the behavior of fixation probabilities,
fixation times, and heterozygosity, in a neutral setting and in cases where the
two species can compete or cooperate. By concluding with examples in which
individuals are transported by fluid flows, we argue that this model is a
natural choice to describe competition in marine environments.Comment: 29 pages, 14 figures; revised version including a section with
results in the presence of fluid flow
How Gaussian competition leads to lumpy or uniform species distributions
A central model in theoretical ecology considers the competition of a range
of species for a broad spectrum of resources. Recent studies have shown that
essentially two different outcomes are possible. Either the species surviving
competition are more or less uniformly distributed over the resource spectrum,
or their distribution is 'lumped' (or 'clumped'), consisting of clusters of
species with similar resource use that are separated by gaps in resource space.
Which of these outcomes will occur crucially depends on the competition kernel,
which reflects the shape of the resource utilization pattern of the competing
species. Most models considered in the literature assume a Gaussian competition
kernel. This is unfortunate, since predictions based on such a Gaussian
assumption are not robust. In fact, Gaussian kernels are a border case
scenario, and slight deviations from this function can lead to either uniform
or lumped species distributions. Here we illustrate the non-robustness of the
Gaussian assumption by simulating different implementations of the standard
competition model with constant carrying capacity. In this scenario, lumped
species distributions can come about by secondary ecological or evolutionary
mechanisms or by details of the numerical implementation of the model. We
analyze the origin of this sensitivity and discuss it in the context of recent
applications of the model.Comment: 11 pages, 3 figures, revised versio
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