Inference of Probabilities over a Stochastic IL-System by Quantifier Elimination

An algebraic approach based on quantifier elimination is proposed for the inference of probabilistic parameters over stochastic Lindenmayer systems with interaction, IL-systems. We are concerned with a multi-cellular organism as an instance of a stochastic IL system. The organism starts with one or a few cells, and develops different types of cells with distinct functions. We have constructed a simple model with cell-type order conservation and have assessed conditions for high cell-type diversity. This model is based on the stochastic IL-system for three types of cells. The cell-type order conservation corresponds to interaction terms in the IL-system. In our model, we have successfully inferred algebraic relations between the probabilities for cell-type diversity by using a symbolic method, quantifier elimination (QE). Surprisingly, three modes for the proliferation and transition rates emerged for various ratios of the initial cells to the developed cells. Furthermore, we have found that the high cell-type diversity pattern originates from the cell-type order conservation. Thus, QE has yielded analysis of the IL-system, which has revealed that, during the developing process of multi-cellular organisms, complex but explicit relations exist between cell-type diversity patterns and developmental rates.      

Algebraic Approaches to Stability Analysis of Biological Systems

In this paper, we improve and extend the approach of Wang and Xia for stability analysis of biological systems by making use of Gr?bner bases, (CAD-based) quantifier elimination, and discriminant varieties, as well as the stability criterion of Liénard and Chipart, and showing how to analyze the stability of Hopf bifurcation points. The stability and bifurcations for a class of self-assembling micelle systems with chemical sinks are analyzed in detail. We provide experimental results with comparisons for 15 biological models taken from the literature.      

Algebraic properties of separated power series

We study the commutative algebra of rings of separated power series over a ring E and that of their extensions: rings of separated (and more specifically convergent) power series from a field K with a separated E-analytic structure. Both of these collections of rings already play an important role in the model theory of non-Archimedean valued fields and we establish their algebraic properties. This will make a study of the analytic geometry over such fields through the classical methods of algebraic geometry possible.     

Stability Analysis for Discrete Biological Models Using Algebraic Methods

This paper is concerned with stability analysis of biological networks modeled as discrete and finite dynamical systems. We show how to use algebraic methods based on quantifier elimination, real solution classification and discriminant varieties to detect steady states and to analyze their stability and bifurcations for discrete dynamical systems. For finite dynamical systems, methods based on Gr?bner bases and triangular sets are applied to detect steady states. The feasibility of our approach is demonstrated by the analysis of stability and bifurcations of several discrete biological models using implementations of algebraic methods.     

An Intuitionistic Axiomatisation of Real Closed Fields

We give an intuitionistic axiomatisation of real closed fields which has the constructive reals as a model. The main result is that this axiomatisation together with just the decidability of the order relation gives the classical theory of real closed fields. To establish this we rely on the quantifier elimination theorem for real closed fields due to Tarski, and a conservation theorem of classical logic over intuitionistic logic for geometric theories.     

A Dynamical Tikhonov Regularization for Solving Ill-posed Linear Algebraic Systems

The Tikhonov method is a famous technique for regularizing ill-posed linear problems, wherein a regularization parameter needs to be determined. This article, based on an invariant-manifold method, presents an adaptive Tikhonov method to solve ill-posed linear algebraic problems. The new method consists in building a numerical minimizing vector sequence that remains on an invariant manifold, and then the Tikhonov parameter can be optimally computed at each iteration by minimizing a proper merit function. In the optimal vector method (OVM) three concepts of optimal vector, slow manifold and Hopf bifurcation are introduced. Numerical illustrations on well known ill-posed linear problems point out the computational efficiency and accuracy of the present OVM as compared with classical ones.     

Algebraic limit cycles of degree 4 for quadratic systems

Yablonskii (Differential Equations 2 (1996) 335) and Filipstov (Differential Equations 9 (1973) 983) proved the existence of two different families of algebraic limit cycles of degree 4 in the class of quadratic systems. It was an open problem to know if these two algebraic limit cycles where all the algebraic limit cycles of degree 4 for quadratic systems. Chavarriga (A new example of a quartic algebraic limit cycle for quadratic sytems, Universitat de Lleida, Preprint 1999) found a third family of this kind of algebraic limit cycles. Here, we prove that quadratic systems have exactly four different families of algebraic limit cycles. The proof provides new tools based on the index theory for algebraic solutions of polynomial vector fields.     

Generalized Hopf Bifurcation for Planar Filippov Systems Continuous at the Origin

In this paper, we study the existence of periodic orbits bifurcating from stationary solutions of a planar dynamical system of Filippov type. This phenomenon is interpreted as a generalized Hopf bifurcation. In the case of smoothness, Hopf bifurcation is characterized by a pair of complex conjugate eigenvalues crossing through the imaginary axis. This method does not carry over to nonsmooth systems, due to the lack of linearization at the origin which is located on the line of discontinuity. In fact, generalized Hopf bifurcation is determined by interactions between the discontinuity of the system and the eigen-structures of all subsystems. With the help of geometrical observations for a corresponding piecewise linear system, we derive an analytical method to investigate the existence of periodic orbits that are obtained by searching for the fixed points of return maps.     

HOPF BIFURCATION ANALYSIS OF A 3D CHAOTIC SYSTEM

In this paper,a 3D chaotic system with multi-parameters is introduced. The dynamical systems of the original ADVP circuit and the modified ADVP model are regarded as special examples to the system.Some basic dynamical behaviors such as the stability of equilibria,the existence of Hopf bifurcation are investigated.We analyse the Hopf bifurcation of the system comprehensively using the first Lyapunov coefficient by precise symbolic computation.As a result,in fact we have studied the further dynamical behaviors.     

On the period of the limit cycles appearing in one-parameter bifurcations

The generic isolated bifurcations for one-parameter families of smooth planar vector fields {X_μ} which give rise to periodic orbits are: the Andronov-Hopf bifurcation, the bifurcation from a semi-stable periodic orbit, the saddle-node loop bifurcation and the saddle loop bifurcation. In this paper we obtain the dominant term of the asymptotic behaviour of the period of the limit cycles appearing in each of these bifurcations in terms of μ when we are near the bifurcation. The method used to study the first two bifurcations is also used to solve the same problem in another two situations: a generalization of the Andronov-Hopf bifurcation to vector fields starting with a special monodromic jet; and the Hopf bifurcation at infinity for families of polynomial vector fields.     

一类非线性系统的周期扰动Hopf分支

研究了小周期扰动对一类存在Hopf分支的非线性系统的影响.特别是应用平均法讨论了扰动频率与Hopf分支固有频率在共振及二阶次调和共振的情形周期解分支的存在性.表明了在某些参数区域内,系统存在调和解分支和次调和解分支,并进一步讨论了二阶次调和分支周期解的稳定性.     

Cylindrical Algebraic Sub-Decompositions

Cylindrical algebraic decompositions (CADs) are a key tool in real algebraic geometry, used primarily for eliminating quantifiers over the reals and studying semi-algebraic sets. In this paper we introduce cylindrical algebraic sub-decompositions (sub-CADs), which are subsets of CADs containing all the information needed to specify a solution for a given problem. We define two new types of sub-CAD: variety sub-CADs which are those cells in a CAD lying on a designated variety; and layered sub-CADs which have only those cells of dimension higher than a specified value. We present algorithms to produce these and describe how the two approaches may be combined with each other and the recent theory of truth-table invariant CAD. We give a complexity analysis showing that these techniques can offer substantial theoretical savings, which is supported by experimentation using an implementation in Maple.     

Algebraic density property of homogeneous spaces

Let X be an affine algebraic variety with a transitive action of the algebraic automorphism group. Suppose that X is equipped with several fixed point free nondegenerate SL₂-actions satisfying some mild additional assumption. Then we prove that the Lie algebra generated by completely integrable algebraic vector fields on X coincides with the space of all algebraic vector fields. In particular, we show that apart from a few exceptions this fact is true for any homogeneous space of form G/R where G is a linear algebraic group and R is a closed proper reductive subgroup of G.     

Periodic travelling-wave solution of brusselator

The Hopf bifurcation Theorem requires that one at first knows all eigenvalues of the linearized system; and a difficulty in applying the Hopf Theorem is that in the general case we are unable to solve an algebraic equation of degreen (n3) with parameter coefficients.This paper firstly proves Theorem 1 which enables us to know the existence of the Hopf bifuecation by direct use of the coefficients of the characteristic equ ation of the linearized system for the case where the characteristic equation of the linearized system has degree 2, 3 or 4. Then by using Theorem 1, we gave out the condition for existing a periodic traveling-wave solution of Brusselator in diffusion by Hopf bifurcat on. Finally, we discuss the problem of bifurcation direction and the problem of stability of the bifurcation.     

Bifurcation from periodic solutions with spatiotemporal symmetry, including resonances and mode interactions

We study local bifurcation in equivariant dynamical systems from periodic solutions with a mixture of spatial and spatiotemporal symmetries.In previous work, we focused primarily on codimension one bifurcations. In this paper, we show that the techniques used in the codimension one analysis can be extended to understand also higher codimension bifurcations, including resonant bifurcations and mode interactions. In particular, we present a general reduction scheme by which we relate bifurcations from periodic solutions to bifurcations from fixed points of twisted equivariant diffeomorphisms, which in turn are linked via normal form theory to bifurcations from equilibria of equivariant vector fields.We also obtain a general theory for bifurcation from relative periodic solutions and we show how to incorporate time-reversal symmetries into our framework.     

Computational Complexity in Algebraic Systems

Computability and computational complexity were first considered over the fields of real and complex numbers and generalized to arbitrary algebraic systems. This article approaches the theory of computational complexity over an arbitrary algebraic system by taking computability over the list extension for a computational model of it. We study the resultant polynomial complexity classes and mention some NP-complete problems.     

Nonstandard Point Counting for Algebraic Varieties

For varieties over a field k, we define motivic measures with values in ordered fields, using point counting over finite fields and taking the limits with respect to ultrafilters. Some properties and problems related to such measures are discussed. We define similar measures for algebraic dynamical systems by counting periodic points, and explain how they can be used to prove certain statements, such as the non-rationality of a motivic zeta function.     

Generic bifurcation of refracted systems

In this article we discuss some qualitative and geometric aspects of non-smooth dynamical systems theory. Our goal is to study the diagram bifurcation of typical singularities that occur generically in one parameter families of certain piecewise smooth vector fields named Refracted Systems. Such systems has a codimension-one submanifold as its discontinuity set.     

Algebraic topological methods for the supercritical Q-curvature problem

We study the problem of existence of conformal metrics with prescribed Q-curvature on closed four-dimensional Riemannian manifolds. This problem has a variational structure, and in the case of interest here, it is noncompact in the sense that accumulations points of some noncompact flow lines of a pseudogradient of the associated Euler–Lagrange functional, the so-called true critical points at infinity of the associated variational problem, occur. Using the characterization of the critical points at infinity of the associated variational problem which is established in [42], combined with some arguments from Morse theory, some algebraic topological methods, and some tools from dynamical system originating from Conley's isolated invariant sets and isolated blocks theory, we derive a new kind of existence results under an algebraic topological hypothesis involving the topology of the underling manifold, stable and unstable manifolds of some of the critical points at infinity of the associated Euler–Lagrange functional.     

Local analysis near a folded saddle-node singularity

Folded saddle-nodes occur generically in one parameter families of singularly perturbed systems with two slow variables. We show that these folded singularities are the organizing centers for two main delay phenomena in singular perturbation problems: canards and delayed Hopf bifurcations. We combine techniques from geometric singular perturbation theory—the blow-up technique—and from delayed Hopf bifurcation theory—complex time path analysis—to analyze the flow near such folded saddle-nodes. In particular, we show the existence of canards as intersections of stable and unstable slow manifolds. To derive these canard results, we extend the singularly perturbed vector field into the complex domain and study it along elliptic paths. This enables us to extend the invariant slow manifolds beyond points where normal hyperbolicity is lost. Furthermore, we define a way-in/way-out function describing the maximal delay expected for generic solutions passing through a folded saddle-node singularity. Branch points associated with the change from a complex to a real eigenvalue structure in the variational equation along the critical (slow) manifold make our analysis significantly different from the classical delayed Hopf bifurcation analysis where these eigenvalues are complex only.