96,075 research outputs found
Analysis of parametric biological models with non-linear dynamics
In this paper we present recent results on parametric analysis of biological
models. The underlying method is based on the algorithms for computing
trajectory sets of hybrid systems with polynomial dynamics. The method is then
applied to two case studies of biological systems: one is a cardiac cell model
for studying the conditions for cardiac abnormalities, and the second is a
model of insect nest-site choice.Comment: In Proceedings HSB 2012, arXiv:1208.315
Transverse Patterns in Nonlinear Optical Resonators
The book is devoted to the formation and dynamics of localized structures
(vortices, solitons) and extended patterns (stripes, hexagons, tilted waves) in
nonlinear optical resonators such as lasers, optical parametric oscillators,
and photorefractive oscillators. The theoretical analysis is performed by
deriving order parameter equations, and also through numerical integration of
microscopic models of the systems under investigation. Experimental
observations, and possible technological implementations of transverse optical
patterns are also discussed. A comparison with patterns found in other
nonlinear systems, i.e. chemical, biological, and hydrodynamical systems, is
given. This article contains the table of contents and the introductory chapter
of the book.Comment: 37 pages, 14 figures. Table of contents and introductory chapter of
the boo
Selection theorem for systems with inheritance
The problem of finite-dimensional asymptotics of infinite-dimensional dynamic
systems is studied. A non-linear kinetic system with conservation of supports
for distributions has generically finite-dimensional asymptotics. Such systems
are apparent in many areas of biology, physics (the theory of parametric wave
interaction), chemistry and economics. This conservation of support has a
biological interpretation: inheritance. The finite-dimensional asymptotics
demonstrates effects of "natural" selection. Estimations of the asymptotic
dimension are presented. After some initial time, solution of a kinetic
equation with conservation of support becomes a finite set of narrow peaks that
become increasingly narrow over time and move increasingly slowly. It is
possible that these peaks do not tend to fixed positions, and the path covered
tends to infinity as t goes to infinity. The drift equations for peak motion
are obtained. Various types of distribution stability are studied: internal
stability (stability with respect to perturbations that do not extend the
support), external stability or uninvadability (stability with respect to
strongly small perturbations that extend the support), and stable realizability
(stability with respect to small shifts and extensions of the density peaks).
Models of self-synchronization of cell division are studied, as an example of
selection in systems with additional symmetry. Appropriate construction of the
notion of typicalness in infinite-dimensional space is discussed, and the
notion of "completely thin" sets is introduced.
Key words: Dynamics; Attractor; Evolution; Entropy; Natural selectionComment: 46 pages, the final journal versio
Feedback control architecture & the bacterial chemotaxis network
Bacteria move towards favourable and away from toxic environments by changing their swimming pattern. This response is regulated by the chemotaxis signalling pathway, which has an important feature: it uses feedback to ‘reset’ (adapt) the bacterial sensing ability, which allows the bacteria to sense a range of background environmental changes. The role of this feedback has been studied extensively in the simple chemotaxis pathway of Escherichia coli. However it has been recently found that the majority of bacteria have multiple chemotaxis homologues of the E. coli proteins, resulting in more complex pathways. In this paper we investigate the configuration and role of feedback in Rhodobacter sphaeroides, a bacterium containing multiple homologues of the chemotaxis proteins found in E. coli. Multiple proteins could produce different possible feedback configurations, each having different chemotactic performance qualities and levels of robustness to variations and uncertainties in biological parameters and to intracellular noise. We develop four models corresponding to different feedback configurations. Using a series of carefully designed experiments we discriminate between these models and invalidate three of them. When these models are examined in terms of robustness to noise and parametric uncertainties, we find that the non-invalidated model is superior to the others. Moreover, it has a ‘cascade control’ feedback architecture which is used extensively in engineering to improve system performance, including robustness. Given that the majority of bacteria are known to have multiple chemotaxis pathways, in this paper we show that some feedback architectures allow them to have better performance than others. In particular, cascade control may be an important feature in achieving robust functionality in more complex signalling pathways and in improving their performance
Entropy-based parametric estimation of spike train statistics
We consider the evolution of a network of neurons, focusing on the asymptotic
behavior of spikes dynamics instead of membrane potential dynamics. The spike
response is not sought as a deterministic response in this context, but as a
conditional probability : "Reading out the code" consists of inferring such a
probability. This probability is computed from empirical raster plots, by using
the framework of thermodynamic formalism in ergodic theory. This gives us a
parametric statistical model where the probability has the form of a Gibbs
distribution. In this respect, this approach generalizes the seminal and
profound work of Schneidman and collaborators. A minimal presentation of the
formalism is reviewed here, while a general algorithmic estimation method is
proposed yielding fast convergent implementations. It is also made explicit how
several spike observables (entropy, rate, synchronizations, correlations) are
given in closed-form from the parametric estimation. This paradigm does not
only allow us to estimate the spike statistics, given a design choice, but also
to compare different models, thus answering comparative questions about the
neural code such as : "are correlations (or time synchrony or a given set of
spike patterns, ..) significant with respect to rate coding only ?" A numerical
validation of the method is proposed and the perspectives regarding spike-train
code analysis are also discussed.Comment: 37 pages, 8 figures, submitte
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