Qualitative analysis of the dynamics of the time delayed Chua's circuit

IEEE TRANS. CIRCUITS SYST.

Tropical geometries and dynamics of biochemical networks. Application to hybrid cell cycle models

We use the Litvinov-Maslov correspondence principle to reduce and hybridize networks of biochemical reactions. We apply this method to a cell cycle oscillator model. The reduced and hybridized model can be used as a hybrid model for the cell cycle. We also propose a practical recipe for detecting quasi-equilibrium QE reactions and quasi-steady state QSS species in biochemical models with rational rate functions and use this recipe for model reduction. Interestingly, the QE/QSS invariant manifold of the smooth model and the reduced dynamics along this manifold can be put into correspondence to the tropical variety of the hybridization and to sliding modes along this variety, respectivelyComment: conference SASB 2011, to be published in Electronic Notes in Theoretical Computer Scienc

Effects of Transport Memory and Nonlinear Damping in a Generalized Fisher's Equation

Memory effects in transport require, for their incorporation into reaction diffusion investigations, a generalization of traditional equations. The well-known Fisher's equation, which combines diffusion with a logistic nonlinearity, is generalized to include memory effects and traveling wave solutions of the equation are found. Comparison is made with alternate generalization procedures.Comment: 6 pages, 4 figures, RevTeX

Lorenz-like systems and classical dynamical equations with memory forcing: a new point of view for singling out the origin of chaos

A novel view for the emergence of chaos in Lorenz-like systems is presented. For such purpose, the Lorenz problem is reformulated in a classical mechanical form and it turns out to be equivalent to the problem of a damped and forced one dimensional motion of a particle in a two-well potential, with a forcing term depending on the ``memory'' of the particle past motion. The dynamics of the original Lorenz system in the new particle phase space can then be rewritten in terms of an one-dimensional first-exit-time problem. The emergence of chaos turns out to be due to the discontinuous solutions of the transcendental equation ruling the time for the particle to cross the intermediate potential wall. The whole problem is tackled analytically deriving a piecewise linearized Lorenz-like system which preserves all the essential properties of the original model.Comment: 48 pages, 25 figure

Reduction of dynamical biochemical reaction networks in computational biology

Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multi-scaleness is another property of these networks, that can be used to get past some of these obstacles. Networks with many well separated time scales, can be reduced to simpler networks, in a way that depends only on the orders of magnitude and not on the exact values of the kinetic parameters. The main idea used for such robust simplifications of networks is the concept of dominance among model elements, allowing hierarchical organization of these elements according to their effects on the network dynamics. This concept finds a natural formulation in tropical geometry. We revisit, in the light of these new ideas, the main approaches to model reduction of reaction networks, such as quasi-steady state and quasi-equilibrium approximations, and provide practical recipes for model reduction of linear and nonlinear networks. We also discuss the application of model reduction to backward pruning machine learning techniques