We present a novel and simple method to numerically calculate Fisher information matrices for stochastic chemical kinetics models. The linear noise approximation is used to derive model equations and a likelihood function that leads to an efficient computational algorithm. Our approach reduces the problem of calculating the Fisher information matrix to solving a set of ordinary differential equ...

A theoretical analysis of the initial rates of product appearance in both compartments of a specifically designed diffusion cell separated by an asymmetrical enzyme membrane is presented. Variable substrate concentrations and different substrate diffusional limitations were considered. Our analysis shows that, under specific conditions, not only a product accumulation occurs in the compartment ...

This paper is aimed at understanding what happens to the propensity functions (rates) of bimolecular chemical reactions when the volume occupied by the reactant molecules is not negligible compared to the containing volume of the system. For simplicity our analysis focuses on a one-dimensional gas of N hard-rod molecules, each of length l. Assuming these molecules are distributed randomly and u...

We study the origin of evolution. Evolution is based on replication, mutation, and selection. But how does evolution begin? When do chemical kinetics turn into evolutionary dynamics? We propose "prelife" and "prevolution" as the logical precursors of life and evolution. Prelife generates sequences of variable length. Prelife is a generative chemistry that proliferates information and produces d...

The initial kinetics of Cr(III) oxidation on mineral surfaces is poorly understood, yet a significant portion of the oxidation process occurs during the first seconds of reaction. In this study, the initial rates of Cr(III) oxidation on hydrous manganese oxide (HMO) were measured at three different pH values (pH 2.5, 3, and 3.5), using a quick X-ray absorption fine structure spectroscopy (Q-XAF...

We study the fast irreversible bimolecular reaction in a two-dimensional chaotic flow. The reactants are initially segregated and together fill the whole domain. Simulations show that the reactant concentration decays exponentially with rate lambda and then crosses over to the algebraic law of chemical kinetics in the final stage of the reaction. We estimate the crossover time from the reaction...

Spontaneous self-assemblies of biomolecules can generate geometrical patterns. Our findings provide an insight into the mechanism of self-assembled ring pattern generation by human serum albumin (HSA). The self-assembly is a process guided by kinetic and thermodynamic parameters. The generated protein ring patterns display a behavior which is geometrically related to a n-simplex model and is ex...