69 research outputs found
Systems with inheritance: dynamics of distributions with conservation of support, natural selection and finite-dimensional asymptotics
If we find a representation of an infinite-dimensional dynamical system as a nonlinear kinetic system with {\it conservation of supports} of distributions, then (after some additional technical steps) we can state that the asymptotics is finite-dimensional. This conservation of support has a {\it quasi-biological interpretation, inheritance} (if a gene was not presented initially in a isolated population without mutations, then it cannot appear at later time). These quasi-biological models can describe various physical, chemical, and, of course, biological
systems. The finite-dimensional asymptotic demonstrates effects of {\it ``natural" selection}. The estimations of asymptotic dimension are presented. The support of an individual limit distribution is almost always small. But the union of such supports can be the whole space even for one solution. Possible are such situations: a solution is a finite set of narrow peaks getting in time more and more narrow, moving slower and slower. It is possible that these peaks do not tend to fixed positions, rather they continue moving, and the path covered tends to infinity at . The {\it drift equations} for peaks motion are obtained. Various types of stability are studied.
In example, models of cell division self-synchronization are
studied. The appropriate construction of notion of typicalness in infinite-dimensional spaces is discussed, and the ``completely thin" sets are introduced
Geometrical complexity of data approximators
There are many methods developed to approximate a cloud of vectors embedded
in high-dimensional space by simpler objects: starting from principal points
and linear manifolds to self-organizing maps, neural gas, elastic maps, various
types of principal curves and principal trees, and so on. For each type of
approximators the measure of the approximator complexity was developed too.
These measures are necessary to find the balance between accuracy and
complexity and to define the optimal approximations of a given type. We propose
a measure of complexity (geometrical complexity) which is applicable to
approximators of several types and which allows comparing data approximations
of different types.Comment: 10 pages, 3 figures, minor correction and extensio
Four basic symmetry types in the universal 7-cluster structure of 143 complete bacterial genomic sequences
Coding information is the main source of heterogeneity
(non-randomness) in the sequences of bacterial genomes. This
information can be naturally modeled by analysing cluster structures in the ``in-phase'' triplet distributions of relatively short genomic fragments (200-400bp). We found a universal 7-cluster structure in all 143 completely sequenced bacterial genomes available in Genbank in August 2004, and explained its properties.
The 7-cluster structure is responsible for the main part of sequence heterogeneity in bacterial genomes. In this sense, our 7 clusters is the basic model of bacterial genome sequence. We demonstrated that there are four basic ``pure'' types of this model, observed in nature: ``parallel triangles'', ``perpendicular triangles'',
degenerated case and the flower-like type. We show that codon usage of bacterial genomes is a multi-linear function of their genomic G+C-content with high accuracy (more precisely, by two similar functions, one for eubacterial genomes and the other one for archaea).
All 143 cluster animated 3D-scatters are collected in a database and is made available on our web-site:
http://www.ihes.fr/~zinovyev/7clusters
The finding can be readily introduced into any software for gene prediction, sequence alignment or bacterial genomes classification
Kinetic Path Summation, Multi--Sheeted Extension of Master Equation, and Evaluation of Ergodicity Coefficient
We study the Master equation with time--dependent coefficients, a linear
kinetic equation for the Markov chains or for the monomolecular chemical
kinetics. For the solution of this equation a path summation formula is proved.
This formula represents the solution as a sum of solutions for simple kinetic
schemes (kinetic paths), which are available in explicit analytical form. The
relaxation rate is studied and a family of estimates for the relaxation time
and the ergodicity coefficient is developed. To calculate the estimates we
introduce the multi--sheeted extensions of the initial kinetics. This approach
allows us to exploit the internal ("micro")structure of the extended kinetics
without perturbation of the base kinetics.Comment: The final journal versio
Dynamical robustness of biological networks with hierarchical distribution of time scales
We propose the concepts of distributed robustness and r-robustness, well
adapted to functional genetics. Then we discuss the robustness of the
relaxation time using a chemical reaction description of genetic and signalling
networks. First, we obtain the following result for linear networks: for large
multiscale systems with hierarchical distribution of time scales the variance
of the inverse relaxation time (as well as the variance of the stationary rate)
is much lower than the variance of the separate constants. Moreover, it can
tend to 0 faster than 1/n, where n is the number of reactions. We argue that
similar phenomena are valid in the nonlinear case as well. As a numerical
illustration we use a model of signalling network that can be applied to
important transcription factors such as NFkB
On the dynamics of solutions for autonomous reaction-diffusion equation in Rⁿ with multivalued nonlinearity
We consider the dynamics of solutions for autonomous reaction-diffusion equation in Rⁿ with multivalued nonlinearity. The a priory estimates for solutions are obtained. The existence of compact invariant global attractor for m-semiflow was justified
Quasichemical Models of Multicomponent Nonlinear Diffusion
Diffusion preserves the positivity of concentrations, therefore,
multicomponent diffusion should be nonlinear if there exist non-diagonal terms.
The vast variety of nonlinear multicomponent diffusion equations should be
ordered and special tools are needed to provide the systematic construction of
the nonlinear diffusion equations for multicomponent mixtures with significant
interaction between components. We develop an approach to nonlinear
multicomponent diffusion based on the idea of the reaction mechanism borrowed
from chemical kinetics.
Chemical kinetics gave rise to very seminal tools for the modeling of
processes. This is the stoichiometric algebra supplemented by the simple
kinetic law. The results of this invention are now applied in many areas of
science, from particle physics to sociology. In our work we extend the area of
applications onto nonlinear multicomponent diffusion.
We demonstrate, how the mechanism based approach to multicomponent diffusion
can be included into the general thermodynamic framework, and prove the
corresponding dissipation inequalities. To satisfy thermodynamic restrictions,
the kinetic law of an elementary process cannot have an arbitrary form. For the
general kinetic law (the generalized Mass Action Law), additional conditions
are proved. The cell--jump formalism gives an intuitively clear representation
of the elementary transport processes and, at the same time, produces kinetic
finite elements, a tool for numerical simulation.Comment: 81 pages, Bibliography 118 references, a review paper (v4: the final
published version
Asymptotology of Chemical Reaction Networks
The concept of the limiting step is extended to the asymptotology of
multiscale reaction networks. Complete theory for linear networks with well
separated reaction rate constants is developed. We present algorithms for
explicit approximations of eigenvalues and eigenvectors of kinetic matrix.
Accuracy of estimates is proven. Performance of the algorithms is demonstrated
on simple examples. Application of algorithms to nonlinear systems is
discussed.Comment: 23 pages, 8 figures, 84 refs, Corrected Journal Versio
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