963 research outputs found
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
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