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Gene expression is an inherently stochastic process that depends on the structure of the biochemical regulatory network in which the gene is embedded. Here we study the dynamical consequences of the interplay between stochastic gene switching and the widespread negative feedback regulatory loop in a simple model of a biochemical regulatory network. Using a simplified hybrid simulation approach, in which only the gene activation is modeled stochastically, we find that stochasticity in gene switching by itself can induce pulses in the system, providing also analytical insights into their origin. Furthermore, we find that this simple network is able to reproduce both exponential and peaked distributions of gene active and inactive times similar to those that have been observed experimentally. This simplified hybrid simulation approach also allows us to link these patterns to the dynamics of the system for each gene state. [ABSTRACT FROM AUTHOR]

In this paper we make a thorough exploration of the technique of partial control of chaotic systems. This control technique allows one to keep the trajectories of a dynamical system close to a chaotic saddle even if the control applied is smaller than the effects of environmental noise in the system, provided that the chaotic saddle is due to the existence of a horseshoelike mapping in phase space. We state this here in a mathematically precise way using the Conley-Moser conditions, and we prove that they imply that our partial control strategy can be applied. We also give an upper bound of the control-noise ratio needed to achieve this goal, and we describe how this technique can be applied for large noise values. Finally, we study in detail the effect of imperfect targeting in our control technique. All these results are illustrated numerically with the paradigmatic Hénon map.

In this paper we study how to avoid escapes in open dynamical systems in the presence of dissipation and forcing, as it occurs in realistic physical situations. We use as a prototype model the Helmholtz oscillator, which is the simplest nonlinear oscillator with escapes. For some parameter values, this oscillator presents a critical value of the forcing for which all particles escape from its single well. By using the phase control technique, weakly changing the shape of the potential via a periodic perturbation of suitable phase varphi , we avoid the escapes in different regions of the phase space. We provide numerical evidence, heuristic arguments, and an experimental implementation in an electronic circuit of this phenomenon. Finally, we expect that this method might be useful for avoiding escapes in more complicated physical situations.

In a region in phase space where there is a chaotic saddle, all initial conditions will escape from it after a transient with the exception of a set of points of zero Lebesgue measure. The action of an external noise makes all trajectories escape faster. Attempting to avoid those escapes by applying a control smaller than noise seems to be an impossible task. Here we show, however, that this goal is indeed possible, based on a geometrical property found typically in this situation: the existence of a horseshoe. The horseshoe implies that there exist what we call safe sets, which assures that there is a general strategy that allows one to keep trajectories inside that region with control smaller than noise. We call this type of control partial control of chaos.

We present a nonfeedback method to tame or enhance crisis-induced intermittency in dynamical systems. By adding a small harmonic perturbation to a parameter of the system, the intermittent behavior can be suppressed or enhanced depending on the value of the phase difference between the main driving and the perturbation. The validity of the method is shown both in the model and in an experiment with a CO2 laser. An analysis of this scheme applied to the quadratic map near crisis illustrates the role of phase control in nonlinear dynamical systems.