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Register a new userDiscreteness-induced Stochastic Steady State in Reaction Diffusion Systems: Self-consistent Analysis and Stochastic Simulations
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A self-consistent equation to derive a discreteness-induced stochastic steady state is presented for reaction-diffusion systems. For this formalism, we use the so-called Kuramoto length, a typical distance over which a molecule diffuses in its lifetime, as was originally introduced to determine if local fluctuations influence globally the whole system. We show that this Kuramoto length is also relevant to determine whether the discreteness of molecules is significant or not. If the number of molecules of a certain species within the Kuramoto length is small and discrete, localization of some other chemicals is brought about, which can accelerate certain reactions. When this acceleration influences the concentration of the original molecule species, it is shown that a novel, stochastic steady state is induced that does not appear in the continuum limit. A theory to obtain and characterize this state is introduced, based on the self-consistent equation for chemical concentrations. This stochastic steady state is confirmed by numerical simulations on a certain reaction model, which agrees well with the theoretical estimation. Formation and coexistence of domains with different stochastic states are also reported, which is maintained by the discreteness. Relevance of our result to intracellular reactions is briefly discussed.
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Similarity solutions play an important role in many fields of science: we consider here similarity in stochastic dynamics. Important issues are not only the existence of stochastic similarity, but also whether a similarity solution is dynamically attractive, and if it is, to what particular solution does the system evolve. By recasting a class of stochastic PDEs in a form to which stochastic centre manifold theory may be applied we resolve these issues in this class. For definiteness, a first example of self-similarity of the Burgers equation driven by some stochastic forced is studied. Under suitable assumptions, a stationary solution is constructed which yields the existence of a stochastic self-similar solution for the stochastic Burgers equation. Furthermore, the asymptotic convergence to the self-similar solution is proved. Second, in more general stochastic reaction-diffusion systems stochastic centre manifold theory provides a framework to construct the similarity solution, confirm its relevance, and determines the correct solution for any compact initial condition. Third, we argue that dynamically moving the spatial origin and dynamically stretching time improves the description of the stochastic similarity. Lastly, an application to an extremely simple model of turbulent mixing shows how anomalous fluctuations may arise in eddy diffusivities. The techniques and results we discuss should be applicable to a wide range of stochastic similarity problems.
In many biological situations, a species arriving from a remote source diffuses in a domain confined between two parallel surfaces until it finds a binding partner. Since such a geometric shape falls in between two- and three-dimensional settings, the behavior of the macroscopic reaction rate and its dependence on geometric parameters are not yet understood. Modeling the geometric setup by a capped cylinder with a concentric disk-like reactive region on one of the lateral surfaces, we provide an exact semi-analytical solution of the steady-state diffusion equation and compute the diffusive flux onto the reactive region. We explore the dependence of the macroscopic reaction rate on the geometric parameters and derive asymptotic results in several limits. Using the self-consistent approximation, we also obtain a simple fully explicit formula for the reaction rate that exhibits a transition from two-dimensional to three-dimensional behavior as the separation distance between lateral surfaces increases. Biological implications of these results are discussed.
To study the dynamics of chemical processes, we often adopt rate equations to observe the change in chemical concentrations. However, when the number of the molecules is small, the fluctuations cannot be neglected. We often study the effects of fluctuations with the help of stochastic differential equations. Chemicals are composed of molecules on a microscopic level. In principle, the number of molecules must be an integer, which must only change discretely. However, in analysis using stochastic differential equations, the fluctuations are regarded as continuous changes. This approximation can only be valid if applied to fluctuations that involve a sufficiently large number of molecules. In the case of extremely rare chemical species, the actual discreteness of the molecules may critically affect the dynamics of the system. To elucidate the effects of the discreteness, we study an autocatalytic system consisting of several interacting chemical species with a small number of molecules through stochastic particle simulations. We found novel states, which were characterized as an extinction of molecule species, due to the discrete nature of the molecules. We also observed a strong dependence of the chemical concentrations on the size of the system, which was caused by transitions to the novel states.
To study the fluctuations and dynamics in chemical reaction processes, stochastic differential equations based on the rate equation involving chemical concentrations are often adopted. When the number of molecules is very small, however, the discreteness in the number of molecules cannot be neglected since the number of molecules must be an integer. This discreteness can be important in biochemical reactions, where the total number of molecules is not significantly larger than the number of chemical species. To elucidate the effects of such discreteness, we study autocatalytic reaction systems comprising several chemical species through stochastic particle simulations. The generation of novel states is observed; it is caused by the extinction of some molecular species due to the discreteness in their number. We demonstrate that the reaction dynamics are switched by a single molecule, which leads to the reconstruction of the acting network structure. We also show the strong dependence of the chemical concentrations on the system size, which is caused by transitions to discreteness-induced novel states.
The occurrence of stochastic resonance in bistable systems undergoing anomalous diffusions, which arise from density-dependent fluctuations, is investigated with emphasis on the analytical formulation of the problem as well as a possible analytical derivation of key quantifiers of stochastic resonance. The nonlinear Fokker-Planck equation describing the system dynamics, together with the corresponding Ito-Langevin equation, are formulated. In the linear-response regime analytical expressions of the spectral amplification, of the signal-to-noise ratio and of the hysteresis loop area are derived as quantifiers of stochastic resonance. These quantifiers are found to be strongly dependent on the parameters controlling the type of diffusion, in particular the peak characterizing the signal-to-noise ratio occurs only in close ranges of parameters. Results introduce the relevant information that taking into consideration the interactions of anomalous diffusive systems with a periodic signal, can provide a better understanding of the physics of stochastic resonance in bistable systems driven by periodic forces.
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