5,073 research outputs found
General Iteration graphs and Boolean automata circuits
This article is set in the field of regulation networks modeled by discrete
dynamical systems. It focuses on Boolean automata networks. In such networks,
there are many ways to update the states of every element. When this is done
deterministically, at each time step of a discretised time flow and according
to a predefined order, we say that the network is updated according to
block-sequential update schedule (blocks of elements are updated sequentially
while, within each block, the elements are updated synchronously). Many
studies, for the sake of simplicity and with some biologically motivated
reasons, have concentrated on networks updated with one particular
block-sequential update schedule (more often the synchronous/parallel update
schedule or the sequential update schedules). The aim of this paper is to give
an argument formally proven and inspired by biological considerations in favour
of the fact that the choice of a particular update schedule does not matter so
much in terms of the possible and likely dynamical behaviours that networks may
display
Boolean networks synchronism sensitivity and XOR circulant networks convergence time
In this paper are presented first results of a theoretical study on the role
of non-monotone interactions in Boolean automata networks. We propose to
analyse the contribution of non-monotony to the diversity and complexity in
their dynamical behaviours according to two axes. The first one consists in
supporting the idea that non-monotony has a peculiar influence on the
sensitivity to synchronism of such networks. It leads us to the second axis
that presents preliminary results and builds an understanding of the dynamical
behaviours, in particular concerning convergence times, of specific
non-monotone Boolean automata networks called XOR circulant networks.Comment: In Proceedings AUTOMATA&JAC 2012, arXiv:1208.249
Boolean Dynamics with Random Couplings
This paper reviews a class of generic dissipative dynamical systems called
N-K models. In these models, the dynamics of N elements, defined as Boolean
variables, develop step by step, clocked by a discrete time variable. Each of
the N Boolean elements at a given time is given a value which depends upon K
elements in the previous time step.
We review the work of many authors on the behavior of the models, looking
particularly at the structure and lengths of their cycles, the sizes of their
basins of attraction, and the flow of information through the systems. In the
limit of infinite N, there is a phase transition between a chaotic and an
ordered phase, with a critical phase in between.
We argue that the behavior of this system depends significantly on the
topology of the network connections. If the elements are placed upon a lattice
with dimension d, the system shows correlations related to the standard
percolation or directed percolation phase transition on such a lattice. On the
other hand, a very different behavior is seen in the Kauffman net in which all
spins are equally likely to be coupled to a given spin. In this situation,
coupling loops are mostly suppressed, and the behavior of the system is much
more like that of a mean field theory.
We also describe possible applications of the models to, for example, genetic
networks, cell differentiation, evolution, democracy in social systems and
neural networks.Comment: 69 pages, 16 figures, Submitted to Springer Applied Mathematical
Sciences Serie
ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra
Background: Many biological systems are modeled qualitatively with discrete
models, such as probabilistic Boolean networks, logical models, Petri nets, and
agent-based models, with the goal to gain a better understanding of the system.
The computational complexity to analyze the complete dynamics of these models
grows exponentially in the number of variables, which impedes working with
complex models. Although there exist sophisticated algorithms to determine the
dynamics of discrete models, their implementations usually require
labor-intensive formatting of the model formulation, and they are oftentimes
not accessible to users without programming skills. Efficient analysis methods
are needed that are accessible to modelers and easy to use. Method: By
converting discrete models into algebraic models, tools from computational
algebra can be used to analyze their dynamics. Specifically, we propose a
method to identify attractors of a discrete model that is equivalent to solving
a system of polynomial equations, a long-studied problem in computer algebra.
Results: A method for efficiently identifying attractors, and the web-based
tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other
analysis methods for discrete models. ADAM converts several discrete model
types automatically into polynomial dynamical systems and analyzes their
dynamics using tools from computer algebra. Based on extensive experimentation
with both discrete models arising in systems biology and randomly generated
networks, we found that the algebraic algorithms presented in this manuscript
are fast for systems with the structure maintained by most biological systems,
namely sparseness, i.e., while the number of nodes in a biological network may
be quite large, each node is affected only by a small number of other nodes,
and robustness, i.e., small number of attractors
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