Related papers: Switching rates of multi-step reactions
Near a bifurcation point a system experiences critical slowing down. This leads to scaling behavior of fluctuations. We find that a periodically driven system may display three scaling regimes and scaling crossovers near a saddle-node…
We consider the reaction zone that grows between separated regions of diffusing species $A$ and $B$ that react according to $mA+nB\to 0$, within the framework of the mean-fieldlike reaction-diffusion equations. For distances from the centre…
We present a computer-assisted approach to locating approximate coarse optimal switching policies between stationary states of chemically reacting systems described by microscopic/stochastic evolution rules. The ``coarse time-stepper"…
Nuclear reaction rates determine the abundances of isotopes in stellar burning processes. A multitude of reactions determine the reaction flow pattern which is described in terms of reaction network simulations. The reaction rates are…
We suggest an iterative approach to computing K-step maximum likelihood estimates (MLE) of the parametric components in semiparametric models based on their profile likelihoods. The higher order convergence rate of K-step MLE mainly depends…
We consider a general class of autocatalytic reactions, that has been shown to display stochastically switching behaviour (Discreteness Induced Transitions) in some parameter regimes. This behaviour was shown to occur when either the…
Systems switching between different dynamical phases is an ubiquitous phenomenon. The general understanding of such a process is limited. To this end, we present a general expression that captures fluctuations of a system exhibiting a…
A simple stochastic model of a self regulating gene that displays bistable switching is analyzed. While on, a gene transcribes mRNA at a constant rate. Transcription factors can bind to the DNA and affect the gene's transcription rate.…
We investigate a family of multiple-stable processes that may exhibit either long-range or short-range dependence, depending on the parameters. There are two parameters for the processes, the memory parameter $\beta\in(0,1)$ and the…
We propose a method for calculating the reaction rates and transition amplitudes of generic process taking place in a many body system in equilibrium. The relationship of the scattering and decay amplitudes as calculated in Thermo Field…
This study address the computational determination of catalytic reaction rates by moving beyond traditional Transition State Theory (TST), addressing its limitations in complex systems. The Hill relation framework, integrated with Adaptive…
This work is devoted to quantifying how periodic perturbation can change the rate of metastable transition in stochastic mechanical systems with weak noises. A closed-form explicit expression for approximating the rate change is provided,…
A sampling procedure to compute exactly the rate of activated processes arising in systems at equilibrium or nonequilibrium steady state is presented. The procedure is a generalization of the method in [A. Warmflash, P. Bhimalapuram, and A.…
Transitions in the qualitative behavior of chemical reaction dynamics with a decrease in molecule number have attracted much attention. Here, a method based on a Markov process with a tridiagonal transition matrix is applied to the analysis…
The means to obtain the rate constants of a chemical reaction is a fundamental open problem in both science and the industry. Traditional techniques for finding rate constants require either chemical modifications of the reactants or…
The ab initio calculation of exact quantum reaction rate constants comes at a high cost due to the required dynamics of reactants on multidimensional potential energy surfaces. In turn, this impedes the rapid design of the kinetics for…
We introduce a machine learning approach for extracting fine-grained representations of protein evolution from molecular dynamics datasets. Metastable switching linear dynamical systems extend standard switching models with a…
A complete derivation, from first principles, of the reaction-rate formula for a generic reaction taking place in an out of equilibrium quantum-field system is given. It is shown that the formula involves no finite-volume correction. Each…
Based on our experience in kinetic modeling of coupled multiple metabolic pathways we propose a generic rate equation for the dynamical modeling of metabolic kinetics. Its symmetric form makes the kinetic parameters (or functions) easy to…
Rate processes are simple and analytically tractable models for many dynamical systems which switch stochastically between a discrete set of quasi stationary states but they may also approximate continuous processes by coarse grained,…