Switching Dynamics in Reaction Networks Induced by Molecular Discreteness

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.Comment: 11 pages, 5 figure

Synergetics in multiple exciton generation effect in quantum dots

We present detailed analysis of the non-Poissonian population of excitons produced by MEG effect in quantum dots on the base of statistic theory of MEG and synergetic approach for chemical reactions. From the analysis we can conclude that a non-Poissonian distribution of exciton population is evidence of non-linear and non-equilibrium character of the process of multiple generation of excitons in quantum dots at a single photon absorptio

Self-organized patterns of coexistence out of a predator-prey cellular automaton

We present a stochastic approach to modeling the dynamics of coexistence of prey and predator populations. It is assumed that the space of coexistence is explicitly subdivided in a grid of cells. Each cell can be occupied by only one individual of each species or can be empty. The system evolves in time according to a probabilistic cellular automaton composed by a set of local rules which describe interactions between species individuals and mimic the process of birth, death and predation. By performing computational simulations, we found that, depending on the values of the parameters of the model, the following states can be reached: a prey absorbing state and active states of two types. In one of them both species coexist in a stationary regime with population densities constant in time. The other kind of active state is characterized by local coupled time oscillations of prey and predator populations. We focus on the self-organized structures arising from spatio-temporal dynamics of the coexistence. We identify distinct spatial patterns of prey and predators and verify that they are intimally connected to the time coexistence behavior of the species. The occurrence of a prey percolating cluster on the spatial patterns of the active states is also examined.Comment: 19 pages, 11 figure

Stochastic thermodynamics of chemical reaction networks

For chemical reaction networks described by a master equation, we define energy and entropy on a stochastic trajectory and develop a consistent nonequilibrium thermodynamic description along a single stochastic trajectory of reaction events. A first-law like energy balance relates internal energy, applied (chemical) work and dissipated heat for every single reaction. Entropy production along a single trajectory involves a sum over changes in the entropy of the network itself and the entropy of the medium. The latter is given by the exchanged heat identified through the first law. Total entropy production is constrained by an integral fluctuation theorem for networks arbitrarily driven by time-dependent rates and a detailed fluctuation theorem for networks in the steady state. Further exact relations like a generalized Jarzynski relation and a generalized Clausius inequality are discussed. We illustrate these results for a three-species cyclic reaction network which exhibits nonequilibrium steady states as well as transitions between different steady states.Comment: 14 pages, 2 figures, accepted for publication in J. Chem. Phy

Reentrance effect in the lane formation of driven colloids

Recently it has been shown that a strongly interacting colloidal mixture consisting of oppositely driven particles, undergoes a nonequilibrium transition towards lane formation provided the driving strength exceeds a threshold value. We predict here a reentrance effect in lane formation: for fixed high driving force and increasing particle densities, there is first a transition towards lane formation which is followed by another transition back to a state with no lanes. Our result is obtained both by Brownian dynamics computer simulations and by a phenomenological dynamical density functional theory.Comment: 4 pages, 2 figure

Classical Stability of the Galileon

We consider the classical equations of motion for a single Galileon field with generic parameters in the presence of non-relativistic sources. We introduce the concept of absolute stability of a theory: if one can show that a field at a single point---like infinity for instance---in spacetime is stable, then stability of the field over the rest of spacetime is guaranteed for any positive energy source configuration. The Dvali-Gabadadze-Porrati (DGP) model is stable in this manner, and previous studies of spherically symmetric solutions suggest that certain classes of the single field Galileon (of which the DGP model is a subclass) may have this property as well. We find, however, that when general solutions are considered this is not the case. In fact, when considering generic solutions there are no choices of free parameters in the Galileon theory that will lead to absolute stability except the DGP choice. Our analysis indicates that the DGP model is an exceptional choice among the large class of possible single field Galileon theories. This implies that if general solutions (non-spherically symmetric) exist they may be unstable. Given astrophysical motivation for the Galileon, further investigation into these unstable solutions may prove fruitful.Comment: 23 pages, 3 figure

Random paths and current fluctuations in nonequilibrium statistical mechanics

An overview is given of recent advances in nonequilibrium statistical mechanics about the statistics of random paths and current fluctuations. Although statistics is carried out in space for equilibrium statistical mechanics, statistics is considered in time or spacetime for nonequilibrium systems. In this approach, relationships have been established between nonequilibrium properties such as the transport coefficients, the thermodynamic entropy production, or the affinities, and quantities characterizing the microscopic Hamiltonian dynamics and the chaos or fluctuations it may generate. This overview presents results for classical systems in the escape-rate formalism, stochastic processes, and open quantum systems

The dissipative effect of thermal radiation loss in high-temperature dense plasmas

A dynamical model based on the two-fluid dynamical equations with energy generation and loss is obtained and used to investigate the self-generated magnetic fields in high-temperature dense plasmas such as the solar core. The self-generation of magnetic fields might be looked at as a self-organization-type behavior of stochastic thermal radiation fields, as expected for an open dissipative system according to Prigogine's theory of dissipative structures.Comment: 4 pages, 1 postscript figure included; RevTeX3.0, epsf.tex neede

Classical Duals, Legendre Transforms and the Vainshtein Mechanism

We show how to generalize the classical duals found by Gabadadze {\it et al} to a very large class of self-interacting theories. This enables one to adopt a perturbative description beyond the scale at which classical perturbation theory breaks down in the original theory. This is particularly relevant if we want to test modified gravity scenarios that exhibit Vainshtein screening on solar system scales. We recognise the duals as being related to the Legendre transform of the original Lagrangian, and present a practical method for finding the dual in general; our methods can also be applied to self-interacting theories with a hierarchy of strong coupling scales, and with multiple fields. We find the classical dual of the full quintic galileon theory as an example.Comment: 16 page