8,532 research outputs found
Positive circuits and maximal number of fixed points in discrete dynamical systems
We consider the Cartesian product X of n finite intervals of integers and a
map F from X to itself. As main result, we establish an upper bound on the
number of fixed points for F which only depends on X and on the topology of the
positive circuits of the interaction graph associated with F. The proof uses
and strongly generalizes a theorem of Richard and Comet which corresponds to a
discrete version of the Thomas' conjecture: if the interaction graph associated
with F has no positive circuit, then F has at most one fixed point. The
obtained upper bound on the number of fixed points also strongly generalizes
the one established by Aracena et al for a particular class of Boolean
networks.Comment: 13 page
Homogeneous and Scalable Gene Expression Regulatory Networks with Random Layouts of Switching Parameters
We consider a model of large regulatory gene expression networks where the
thresholds activating the sigmoidal interactions between genes and the signs of
these interactions are shuffled randomly. Such an approach allows for a
qualitative understanding of network dynamics in a lack of empirical data
concerning the large genomes of living organisms. Local dynamics of network
nodes exhibits the multistationarity and oscillations and depends crucially
upon the global topology of a "maximal" graph (comprising of all possible
interactions between genes in the network). The long time behavior observed in
the network defined on the homogeneous "maximal" graphs is featured by the
fraction of positive interactions () allowed between genes.
There exists a critical value such that if , the
oscillations persist in the system, otherwise, when it tends to
a fixed point (which position in the phase space is determined by the initial
conditions and the certain layout of switching parameters). In networks defined
on the inhomogeneous directed graphs depleted in cycles, no oscillations arise
in the system even if the negative interactions in between genes present
therein in abundance (). For such networks, the bidirectional edges
(if occur) influence on the dynamics essentially. In particular, if a number of
edges in the "maximal" graph is bidirectional, oscillations can arise and
persist in the system at any low rate of negative interactions between genes
(). Local dynamics observed in the inhomogeneous scalable regulatory
networks is less sensitive to the choice of initial conditions. The scale free
networks demonstrate their high error tolerance.Comment: LaTeX, 30 pages, 20 picture
Dichotomy Results for Fixed-Point Existence Problems for Boolean Dynamical Systems
A complete classification of the computational complexity of the fixed-point
existence problem for boolean dynamical systems, i.e., finite discrete
dynamical systems over the domain {0, 1}, is presented. For function classes F
and graph classes G, an (F, G)-system is a boolean dynamical system such that
all local transition functions lie in F and the underlying graph lies in G. Let
F be a class of boolean functions which is closed under composition and let G
be a class of graphs which is closed under taking minors. The following
dichotomy theorems are shown: (1) If F contains the self-dual functions and G
contains the planar graphs then the fixed-point existence problem for (F,
G)-systems with local transition function given by truth-tables is NP-complete;
otherwise, it is decidable in polynomial time. (2) If F contains the self-dual
functions and G contains the graphs having vertex covers of size one then the
fixed-point existence problem for (F, G)-systems with local transition function
given by formulas or circuits is NP-complete; otherwise, it is decidable in
polynomial time.Comment: 17 pages; this version corrects an error/typo in the 2008/01/24
versio
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
Dichotomy Results for Fixed Point Counting in Boolean Dynamical Systems
We present dichotomy theorems regarding the computational complexity of
counting fixed points in boolean (discrete) dynamical systems, i.e., finite
discrete dynamical systems over the domain {0,1}. For a class F of boolean
functions and a class G of graphs, an (F,G)-system is a boolean dynamical
system with local transitions functions lying in F and graphs in G. We show
that, if local transition functions are given by lookup tables, then the
following complexity classification holds: Let F be a class of boolean
functions closed under superposition and let G be a graph class closed under
taking minors. If F contains all min-functions, all max-functions, or all
self-dual and monotone functions, and G contains all planar graphs, then it is
#P-complete to compute the number of fixed points in an (F,G)-system; otherwise
it is computable in polynomial time. We also prove a dichotomy theorem for the
case that local transition functions are given by formulas (over logical
bases). This theorem has a significantly more complicated structure than the
theorem for lookup tables. A corresponding theorem for boolean circuits
coincides with the theorem for formulas.Comment: 16 pages, extended abstract presented at 10th Italian Conference on
Theoretical Computer Science (ICTCS'2007
Dynamical complexity of discrete time regulatory networks
Genetic regulatory networks are usually modeled by systems of coupled
differential equations and by finite state models, better known as logical
networks, are also used. In this paper we consider a class of models of
regulatory networks which present both discrete and continuous aspects. Our
models consist of a network of units, whose states are quantified by a
continuous real variable. The state of each unit in the network evolves
according to a contractive transformation chosen from a finite collection of
possible transformations, according to a rule which depends on the state of the
neighboring units. As a first approximation to the complete description of the
dynamics of this networks we focus on a global characteristic, the dynamical
complexity, related to the proliferation of distinguishable temporal behaviors.
In this work we give explicit conditions under which explicit relations between
the topological structure of the regulatory network, and the growth rate of the
dynamical complexity can be established. We illustrate our results by means of
some biologically motivated examples.Comment: 28 pages, 4 figure
Bifurcations and Chaos in Time Delayed Piecewise Linear Dynamical Systems
We reinvestigate the dynamical behavior of a first order scalar nonlinear
delay differential equation with piecewise linearity and identify several
interesting features in the nature of bifurcations and chaos associated with it
as a function of the delay time and external forcing parameters. In particular,
we point out that the fixed point solution exhibits a stability island in the
two parameter space of time delay and strength of nonlinearity. Significant
role played by transients in attaining steady state solutions is pointed out.
Various routes to chaos and existence of hyperchaos even for low values of time
delay which is evidenced by multiple positive Lyapunov exponents are brought
out. The study is extended to the case of two coupled systems, one with delay
and the other one without delay.Comment: 34 Pages, 14 Figure
AND-NOT logic framework for steady state analysis of Boolean network models
Finite dynamical systems (e.g. Boolean networks and logical models) have been
used in modeling biological systems to focus attention on the qualitative
features of the system, such as the wiring diagram. Since the analysis of such
systems is hard, it is necessary to focus on subclasses that have the
properties of being general enough for modeling and simple enough for
theoretical analysis. In this paper we propose the class of AND-NOT networks
for modeling biological systems and show that it provides several advantages.
Some of the advantages include: Any finite dynamical system can be written as
an AND-NOT network with similar dynamical properties. There is a one-to-one
correspondence between AND-NOT networks, their wiring diagrams, and their
dynamics. Results about AND-NOT networks can be stated at the wiring diagram
level without losing any information. Results about AND-NOT networks are
applicable to any Boolean network. We apply our results to a Boolean model of
Th-cell differentiation
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