Related papers: Switching rates of multi-step reactions
The transient response of a stationary state of a quantum particle in a step potential to an instantaneous change in the step height (a simplified model for a sudden bias switch in an electronic semiconductor device) is solved exactly by…
Cells use genetic switches to shift between alternate gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Here, we study the dynamics of switching in a generic-feedback on/off switch. Unlike…
Stochastic reaction networks are mathematical models frequently used in, but not limited to, biochemistry. These models are continuous-time Markov chains whose transition rates depend on certain parameters called rate constants, which…
The power-law TST reaction rate coefficient for an elementary bimolecular reaction is studied when the reaction takes place in a nonequilibrium system with power-law distributions. We derive a generalized TST rate coefficient, which not…
Variational perturbation theory is used to determine the decay rates of metastable states across a cubic barrier of arbitrary height. For high barriers, a variational resummation procedure is applied to the complex energy eigenvalues…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
This paper is concerned with classes of models of stochastic reaction dynamics with time-scales separation. We demonstrate that the existence of the time-scale separation naturally leads to the application of the averaging principle and…
Equilibrium rate theories play a crucial role in understanding rare, reactive events. However, they are inapplicable to a range of irreversible processes in systems driven far from thermodynamic equilibrium like active and biological…
We develop a spectral formulation and a stationary WKB approximation for calculating the probabilities of rare events (large deviations from the mean) in systems of reacting particles with infinite-range interaction, describable by a master…
We develop an analytical diffusion-equation-type approximation scheme for the one-dimensional coagulation reaction A+A->A with partial reaction probability on particle encounters which are otherwise hard-core. The new approximation…
In this paper we develop a perturbation method to predict the rate of occurrence of rare events for singularly perturbed stochastic systems using a probability density function approach. In contrast to a stochastic normal form approach, we…
The rate equation for an arbitrary mth order growth or decay reaction can be expressed in terms of the q-exponential function, with q equal to m. The analysis suggests that a wide variety of reaction rate (kinetic) processes and models, in…
A perturbation framework is developed to analyze metastable behavior in stochastic processes with random internal and external states. The process is assumed to be under weak noise conditions, and the case where the deterministic limit is…
We investigate the influence of a stochastically fluctuating step-barrier potential on bimolecular reaction rates by exact analytical theory and stochastic simulations. We demonstrate that the system exhibits a new resonant reaction…
In preliminary analysis of control charts, one may encounter multiple shifts and/or outliers especially with a large number of observations. The following paper addresses this problem. A statistical model for detecting and estimating…
We consider stochastic reaction networks modeled by continuous-time Markov chains. Such reaction networks often contain many reactions, potentially occurring at different time scales, and have unknown parameters (kinetic rates, total…
A general class of stochastic gene expression models with self regulation is considered. One or more genes randomly switch between regulatory states, each having a different mRNA transcription rate. The gene or genes are self regulating…
We calculate the probabilities to find systems of reacting particles in states which largely deviate from typical behavior. The rare event statistics is obtained from the master equation which describes the dynamics of the probability…
Intermolecular hydrogen transfer free radical reactions are common in the combustion process and in a number of organic chemistry reactions. Therefore, evaluating the pressure and temperature-dependent rate constants of them is of great…
An explicit rate switch scheme monitors the load at each link and gives feedback to the sources. We define the overload factor as the ratio of the input rate to the available capacity. In this paper, we present four overload based ABR…