Related papers: A Generic Rate Equation for modeling Enzymatic Rea…
Steady states are frequently used to investigate the long-term behaviors of (bio)-chemical systems. Recently, there has been a growing interest in network-based approaches due to their efficiency in deriving parametrizations of positive…
The kinetics of chemical reactions are determined by the law of mass action, which has been successfully applied to homogeneous, dilute mixtures. At non-dilute conditions, interactions among the components can give rise to coexisting…
Finding representative reaction pathways is necessary for understanding mechanisms of molecular processes, but is considered to be extremely challenging. We propose a new method to construct reaction paths based on mean first-passage times.…
A complete formulation is given of an exact kinetic theory for lattice gases. This kinetic theory makes possible the calculation of corrections to the usual Boltzmann / Chapman-Enskog analysis of lattice gases due to the buildup of…
We propose a unified, human-readable, machine-processable novel syntax/notation designed to comprehensively describe reactions, molecules and excitation states. Our notation resolves inconsistencies in existing data representations and…
We propose a novel approach to the estimation of multiple Graphical Models to analyse temporal patterns of association among a set of metabolites over different groups of patients. Our motivating application is the Southall And Brent…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
In this paper, we propose a globally hyperbolic regularization to the general Grad's moment system in multi-dimensional spaces. Systems with moments up to an arbitrary order are studied. The characteristic speeds of the regularized moment…
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…
A geometrical model which captures the main ingredients governing atom-diatom collinear chemical reactions is proposed. This model is neither near-integrable nor hyperbolic, yet it is amenable to analysis using a combination of the recently…
Chemical reactions are the fundamental building blocks of drug design and organic chemistry research. In recent years, there has been a growing need for a large-scale deep-learning framework that can efficiently capture the basic rules of…
Protein synthesis is one of the most fundamental biological processes, which consumes a significant amount of cellular resources. Despite existence of multiple mathematical models of translation, varying in the level of mechanistical…
We present some qualitative aspects concerning the solution to the mathematical model describing the dynamical behavior of the reversible chemical reaction SO2(g)+1/2O2(g)<=>SO3(g) carried out in a catalytic reactor used in the process of…
In this paper we discuss the question of how to decide when a general chemical reaction system is incapable of admitting multiple equilibria, regardless of parameter values such as reaction rate constants, and regardless of the type of…
Classical theories of chemical kinetics assume independent reactions in dilute solutions, whose rates are determined by mean concentrations. In condensed matter, strong interactions alter chemical activities and create inhomogeneities that…
For a detailed understanding of chemical processes in nature and industry, we need accurate models of chemical reactions in complex environments. While Eyring transition state theory is commonly used for modeling chemical reactions, it is…
Enzyme kinetics has historically been described by deterministic models, with the Michaelis-Menten (MM) equation serving as a paradigm. However, recent experimental and theoretical advances have made it clear that stochastic fluctuations,…
A new tool for modeling electrochemical kinetics is presented. An extension of the Stochastic Simulation Algorithm framework to electrochemical systems is proposed. The physical justifications and constraints for the derivation of a…
More than a century has passed since van't Hoff and Arrhenius formulated their celebrated rate theories, but there are still elusive aspects in the temperature-dependent phase transition kinetics of molecular systems. Here I present a…
Kinetic equations play a major rule in modeling large systems of interacting particles. Recently the legacy of classical kinetic theory found novel applications in socio-economic and life sciences, where processes characterized by large…