V. Petrov

Dynamic properties of a delayed protein cross talk model.

In this paper we investigate how the inclusion of time delay alters the dynamical properties of the Jacob-Monod model, describing the control of the beta-galactosidase synthesis by the lac repressor protein in E. coli. The consequences of a time delay on the dynamics of this system are analysed using Hopfs theorem and Lyapunov-Andronovs theory applied to the original mathematical model and to an approximated version. Our analytical calculations predict that time delay acts as a key bifurcation parameter. This is confirmed by numerical simulations. A critical value of time delay, which depends on the values of the model parameters, is analytically established. Around this critical value, the properties of the system change drastically, allowing under certain conditions the emergence of stable limit cycles, that is self-sustained oscillations. In addition, the features of the end product repression play an essential role in the characterisation of these limit cycles: if cooperativity is considered in the end product repression, time delay higher than the mentioned critical value induce differentiated responses during the oscillations, provoking cycles of all-or-nothing response in the concentration of the species.

NEW RESULTS ABOUT ROUTE TO CHAOS IN ROSSLER SYSTEM

In this paper, the theory of Lyapunov–Andronov is applied to investigate the route to chaos in Rossler system. On the base of a new analytical formula for the first Lyapunov value at the boundary of stability region, we make a detailed bifurcation analysis of this system. From the obtained results the following new conclusions are made: Transition to chaos in the Rosslers system takes place at soft stability loss in the form of a cascade of periodic self-oscillations. Then the occurrence of chaotic self-oscillations in this system takes place under hard stability loss.

TIME DELAY MODEL OF RNA SILENCING

RNA silencing (also known as RNA interference) suppresses the expression of genes posttranscriptionally. We propose a time delay model of RNA silencing through a system consisting of double-stranded RNA (dsRNA), RNA-induced silencing complex (RISC), messenger RNA (mRNA), and RISC–mRNA complex. The time delay model is based on the consideration that the regeneration (or degradation) of the RISC–mRNA complex needs a finite time τ. The model equations are analyzed using nonlinear dynamics methods, in particular the Hopf bifurcation theorem, and they are solved numerically. From the accomplished analytical and numerical calculations, it becomes clear that time delay τ is a key factor in the behavior of the model. In this case, it has a destabilizing effect on the silencing process.

BISTABILITY AND SELF-OSCILLATIONS IN CELL CYCLE CONTROL

A qualitative model of cell cycle control is presented and its transition from bistability to limit cycle oscillations and vice versa is discussed. The origin of this model is the two-dimensional system of kinetic equations introduced by Novak–Tyson which is illustrated computationally and analytically. For this purpose a qualitative model is numerically reconstructed from the steady state behavior of the dynamical variables including the bifurcation parameter. Then, the reconstructed cubic polynomial model is generalized to an appropriate canonical form and is analyzed in terms of Lyapunov values. On this basis, the relationship between bistability and self-oscillatory behavior of mitotic cell cycle is approached qualitatively.

RECONSTRUCTING DIFFERENTIAL EQUATION FROM A TIME SERIES

This paper treats a problem of reconstructing ordinary differential equation from a single analytic time series with observational noise. We suppose that the noise is Gaussian (white). The investigation is presented in terms of classical theory of dynamical systems and modern time series analysis. We restrict our considerations on time series obtained as a numerical analytic solution of autonomous ordinary differential equation, solved with respect to the highest derivative and with polynomial right-hand side. In case of an approximate numerical solution with a rather small error, we propose a geometrical basis and a mathematical algorithm to reconstruct a low-order and low-power polynomial differential equation. To reduce the noise the given time series is smoothed at every point by moving polynomial averages using the least-squares method. Then a specific form of the least-squares method is applied to reconstruct the polynomial right-hand side of the unknown equation. We demonstrate for monotonous, periodic and chaotic solutions that this technique is very efficient.

INTEGRATING MECHANICAL CONTROL THEORY INTO MODELS OF BIOLOGICAL DEVELOPMENT — ANALYTICAL REVIEW

This paper presents both a general review on developmental biomechanics and a concrete proposition for the computation of a symmetry breaking instability of a model of biological development in terms of self-organization theory. The necessary biological and physical facts taken from the literature are described and discussed in the context of a unified statement of the problems for mathematical modeling of pattern formation. This is then applied to planar cell polarization (PCP) of the Drosophila wing. In this way, the process is modeled by an elastopolarization equation. In terms of this statement, the mechanical specificity (interaction with basal plate) of wing PCP is characterized. Some aspects of modeling somite formation as well as other developmental processes are also concerned.

ONE-DIMENSIONAL MODEL OF SOMITIC CELLS POLARIZATION IN A BISTABILITY WINDOW OF EMBRYONIC MESODERM

The considerations are based on the understanding that somitic cells polarization in bistability window of embryonic (pre-somitic) mesoderm is a dynamical process. It occurs in the form of a polarization wavefront of somite cells spread in anterior–posterior direction of the embryonic mesoderm. It is assumed that a macroscopic cell polarization has a bistable behavior corresponding to the molecular mechanism of bistability window formation. Moreover this type of polarization is supposed to be transmittable to the other cells by contact interaction. At the end, a volume of polarized cells is taken, which is able to create mechanical tension in the volume of nonpolarized neighbor cells and to inhibit their polarization. On this basis we explore the leading aspect of somitogenesis robustness by considering a simple wavefront model of polarization and analyzing its propagation in terms of the standard methods of qualitative theory of differential equations. The obtained theoretical results are interpreted in the context of their possible experimental verification.

Reaction-diffusion modeling ERK- and STAT-interaction dynamics

The modeling of the dynamics of interaction between ERK and STAT signaling pathways in the cell needs to establish the biochemical diagram of the corresponding proteins interactions as well as the corresponding reaction-diffusion scheme. Starting from the verbal description available in the literature of the cross talk between the two pathways, a simple diagram of interaction between ERK and STAT5a proteins is chosen to write corresponding kinetic equations. The dynamics of interaction is modeled in a form of two-dimensional nonlinear dynamical system for ERK—and STAT5a —protein concentrations. Then the spatial modeling of the interaction is accomplished by introducing an appropriate diffusion-reaction scheme. The obtained system of partial differential equations is analyzed and it is argued that the possibility of Turing bifurcation is presented by loss of stability of the homogeneous steady state and forms dissipative structures in the ERK and STAT interaction process. In these terms, a possible scaffolding effect in the protein interaction is related to the process of stabilization and destabilization of the dissipative structures (pattern formation) inherent to the model of ERK and STAT cross talk.