FARCOT , Etienne

The purpose of this report is to investigate some dynamical properties common to several biological systems. A model is chosen, which consists of a system of piecewise affine differential equations. Such a model has been previously studied in the context of gene regulation and neural networks, as well as biochemical kinetics. Unlike most of...

The goal of this paper is to present and experiment the computer aided analysis of phase portraits of some ordinary differential equations. The latter are piecewise affine, and have been primitively introduced as coarse-grained models of gene regulatory networks. Their simple formulation allows for numerical investigation, but their typical...

This article introduces preliminary results on the control of gene networks, in the context of piecewise-affine models. We propose an extension of this well-documented class of models, where some input variables can affect the main terms of the equations, with a special focus on the case of affine dependence on inputs. This class is illustrated...

This article introduces results on the control of gene networks, in the context of piecewise-affine models. We propose an extension of this well-documented class of models, where some input variables can affect the main terms of the equations, with a special focus on the case of affine dependence on inputs. Some generic control problems are...

In this paper the existence and unicity of a stable periodic orbit is proven, for a class of piecewise affine differential equations in dimension 3 or more, provided their interaction structure is a negative feedback loop. It is also shown that the same systems converge toward a unique stable equilibrium point in dimension 2. This extends a...

In this article, we consider piecewise affine differential equations modelling gene networks. We work with arbitrary decay rates, and under a local hypothesis expressed as an alignment condition of successive focal points. The interaction graph of the system may be rather complex (multiple intricate loops of any sign, multiple thresholds,...

Piecewise affine (PWA) systems are often used to model gene regulatory networks. In this paper we elaborate on previous work about control problems for this class of models, using also some recent results guaranteeing the existence and uniqueness of limit cycles, based solely on a discrete abstraction of the system and its interaction...

This paper concerns periodic solutions of a class of equations that model gene regulatory networks. Unlike the vast majority of previous studies, it is not assumed that all decay rates are identical. To handle this more general situation, we rely on monotonicity properties of these systems. Under an alternative assumption, it is shown that a...

In this paper we consider piecewise affine differential equations modeling gene networks. We work with arbitrary decay rates, and under a local hypothesis expressed as an alignment condition of successive focal points. The interaction graph of the system may be rather complex (multiple intricate loops of any sign, multiple thresholds...). Our...

The use of hybrid dynamical systems to model gene regulation is impelled by the switch-like behaviour of the latter. Piecewise affine differential equations is one of the most extensively studied among such kind of models. We propose an extension of this class, introducing some input variables. A special focus is given to degradation and...

Hybrid systems, and especially piecewise affine (PWA) systems, are often used to model gene regulatory networks. In this paper we elaborate on previous work about control problems for this class of models, using also some recent results guaranteeing the existence and uniqueness of limit cycles, based solely on a discrete abstraction of the...

We consider patterns formed by active transport of auxin in a tissue, where the accumulation of transporters is activated by local fluxes of auxin. We characterize the steady states for which auxin is homogeneous in the tissue. Under a condition of regularity of the dependence of transporters to the flux, we can prove that one of these steady...

This chapter presents models of the processes involved in floral initiation and development. It begins by briefy presenting models of hormonal transport. The focus is on two key aspects of floral development, namely floral initiation, due to the periodic local accumulation of auxin (a plant hormone) near the plant apex, and the genetic...

Chaotic dynamics have been observed in example piecewise-affine models of gene regulatory networks. Here we show how the underlying Poincaré maps can be explicitly constructed. To do this, we proceed in two steps. First, we consider a limit case, where some parameters tend to ∞, and then consider the case with finite parameters as a...

Piecewise affine models provide a qualitative description of the dynamics of a system, and are often used to study genetic regulatory networks. The state space of a piecewise affine system is partitioned into hyperrectangles, which can be represented as nodes in a directed graph, so that the system's trajectories follow a path in a transition...

In the piecewise affine framework, trajectories evolve among hyperrectangles in the state space. A qualitative description of the dynamics - useful for models of genetic networks - can be obtained by viewing each hyperrectangle as a node in a discrete system, so that trajectories follow a path in a transition graph. In this paper, a...

In this chapter we present models of processes involved in the initiation and development of a flower. In the first section, we briefly present models of hormonal transport. We focus on two key aspects of flower development, namely the initiation, due to the periodic local accumulation of auxin (a plant hormone) near at the plant apex, and the...

Recent years have seen an impressive increase in our knowledge of the topology of plant hormone signaling networks. The complexity of these topologies has motivated the development of models for several hormones to aid understanding of how signaling networks process hormonal inputs. Such work has generated essential insights into the mechanisms...

We now have unprecedented capability to generate large datasets on the myriad of genes and molecular players that regulate plant development. Networks of interactions between systems components can be derived from that data in various ways and can be used to develop mathematical models of various degrees of sophistication. Here we discuss why,...

Growth and morphogenesis in plants require controlled transport of the plant hormone auxin. An important participant is the auxin effluxing protein PIN, whose polarized subcellular localization allows it to effectively transport auxin large distances through tissues. The flux-based model, in which auxin flux through a wall stimulates PIN...

Vascular plants produce new organs at the tip of the stem in a very organized fashion. This patterning process occurs in small groups of stem cells, the so-called shoot apical meristems (SAM), and generates regular patterns called phyllotaxis. The phyllotaxis of the model plant Arabidopsis thaliana follows a Fibonacci spiral, the most frequent...

Phyllotaxis is the geometric arrangement of organs in plants, and is known to be highly regular. However, experimental data (from [i]Arabidopsis thaliana[/i]) show that this regularity is in fact subject to specific patterns of permutations. In this paper we introduce a model for these patterns, as well as algorithms designed to identify these...