Related papers: Rigorous derivation of Michaelis-Menten kinetics i…
The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be…
The prevalent scheme of a diffusion-mediated bimolecular reaction $A+B\rightarrow P$ is an adaptation of that proposed by Briggs and Haldane for enzyme action [{\em Biochem J.\/}, 19:338--339, 1925]. The purpose of this Note is to explain,…
Lattice-based stochastic simulators are commonly used to study biological reaction-diffusion processes. Some of these schemes that are based on the reaction-diffusion master equation (RDME), can simulate for extended spatial and temporal…
Systems composed of large numbers of interacting agents often admit an effective coarse-grained description in terms of a multidimensional stochastic dynamical system, driven by small-amplitude intrinsic noise. In applications to…
The kinetic theory for a fluid of hard spheres which undergo endothermic and/or exothermic reactions with mass transfer is developed. The exact balance equations for concentration, density, velocity and temperature are derived. The Enskog…
The application of the quasi-steady-state approximation to the Michaelis-Menten reaction embedded in large open chemical reaction networks is a popular model reduction technique in deterministic and stochastic simulations of biochemical…
We study the reaction kinetics of end-functionalized polymer chains dispersed in an unreactive polymer melt. Starting from an infinite hierarchy of coupled equations for many-chain correlation functions, a closed equation is derived for the…
The interactions between diffusing molecules and membrane-bound receptors drive numerous cellular processes. In this work, we develop a spatial model of molecular interactions with membrane receptors by homogenizing the cell membrane and…
The general theory of a complex system of nonlinear chemical reactions is a primary language of chemistry that includes chemical engineering and cellular biochemistry. Its significance as an analytical framework, however, has not been fully…
In this paper, we investigate generalized Carleman kinetic equation for n$\ge$2 and prove convergence towards the solution of equation with fast diffusion or porous medium type, $u_t=\Delta u^m$ ($0\le m\le2$), in its diffusive hydrodynamic…
Enzymes show two distinct transport behaviors in the presence of their substrates in solution. First, their diffusivity enhances with increasing substrate concentration. In addition, enzymes perform directional motion toward regions with…
In this paper, a class of reaction-diffusion equations for Multiple Sclerosis is presented. These models are derived by means of a diffusive limit starting from a proper kinetic description, taking account of the underlying microscopic…
The quasi-steady state assumption (QSSA) forms the basis for rigorous mathematical justification of the Michaelis-Menten formalism commonly used in modeling a broad range of intracellular phenomena. A critical supposition of QSSA-based…
Physics of self-propelled objects at the nanoscale is a rapidly developing research field where recent experiments focused on motion of individual catalytic enzymes. Contrary to the experimental advancements, theoretical understanding of…
This paper establishes existence, uniqueness, and an L^1-comparison principle for weak solutions of a PDE system modeling phase transition reaction-diffusion in congested crowd motion. We consider a general reaction term and mixed…
We study kinetics of diffusion-limited catalytically-activated $A + B \to B$ reactions taking place in three dimensional systems, in which an annihilation of diffusive $A$ particles by diffusive traps $B$ may happen only if the encounter of…
Kinetic Monte Carlo methods such as the Gillespie algorithm model chemical reactions as random walks in particle number space. The inter-reaction times are exponentially distributed under the assumption that the system is well mixed. We…
Quasi-steady state reductions for the irreversible Michaelis--Menten reaction mechanism are of interest both from a theoretical and an experimental design perspective. A number of publications have been devoted to extending the parameter…
For over 30 years, mode-coupling theory (MCT) has been the de facto theoretic description of dense fluids and the liquid-glass transition. MCT, however, is limited by its ad hoc construction and lacks a mechanism to institute corrections.…
The use of mathematical methods for the analysis of chemical reaction systems has a very long history, and involves many types of models: deterministic versus stochastic, continuous versus discrete, and homogeneous versus spatially…