Related papers: A Generic Rate Equation for modeling Enzymatic Rea…

Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal…

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…

It is shown that the kinetics of time-reversible chemical reactions having the same equilibrium constant but different initial conditions are closely related to one another by a directly measurable symmetry relation analogous to chemical…

Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to…

The paper has two goals: It presents basic ideas, notions, and methods for reduction of reaction kinetics models: quasi-steady-state, quasi-equilibrium, slow invariant manifolds, and limiting steps. It describes briefly the current state of…

We propose a new kinetic BGK-type model for a mixture of four monatomic gases, undergoing a bimolecular and reversible chemical reaction. The elastic and reactive interactions are described separately by distinct relaxation terms and the…

We propose a general stochastic formalism for describing the evolution of chemical reactions involving a finite number of molecules. This approach is consistent with the statistical analysis based on the Chemical Master Equation, and…

Known graphical conditions for the generic or global convergence to equilibria of the dynamical system arising from a reaction network are shown to be invariant under the so-called successive removal of intermediates, a systematic procedure…

We propose a new and general formalism for elementary chemical reactions where quantum electronic variables are used as reaction coordinates. This formalism is in principle applicable to all kinds of chemical reactions ionic or covalent.…

This paper considers master equations for Markovian kinetic schemes that possess the detailed balance property. Chemical kinetics, as a prime example, often yields large-scale, highly stiff equations. Based on chemical intuitions, Sumiya et…

We consider a multi component mixture of inert gas in the kinetic regime by assuming that the total number of particles of each species remains constant. In this article we shall illustrate our model for the case of two species. To account…

The identification of trajectories that contribute to the reaction rate is the crucial dynamical ingredient in any classical chemical reactivity calculation. This problem often requires a full scale numerical simulation of the dynamics, in…

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…

All biological processes are controlled by complex systems of enzymatic chemical reactions. Although the majority of enzymatic networks have very elaborate structures, there are many experimental observations indicating that some turnover…

The ability to reason beyond established knowledge allows Organic Chemists to solve synthetic problems and to invent novel transformations. Here, we propose a model which mimics chemical reasoning and formalises reaction prediction as…

Scaling analysis exploiting timescale separation has been one of the most important techniques in the quantitative analysis of nonlinear dynamical systems in mathematical and theoretical biology. In the case of enzyme catalyzed reactions,…

Predicting enzyme kinetic parameters quantifies how efficiently an enzyme catalyzes a specific substrate under defined biochemical conditions. Canonical parameters such as the turnover number ($k_\text{cat}$), Michaelis constant…

We complete the existing literature on the kinetic theory of systems with long-range interactions. Starting from the BBGKY hierarchy, or using projection operator technics or a quasilinear theory, a general kinetic equation can be derived…

We investigate numerically a recent BGK-type model for a multi-component mixture of monatomic gases, undergoing a reversible bimolecular chemical reaction. The model replaces each collisional term of the Boltzmann equation with a relaxation…

Engineering molecular systems that exhibit complex behavior requires the design of kinetic barriers. For example, an effective catalytic pathway must have a large barrier when the catalyst is absent. While programming such energy barriers…