相关论文: Rigorous derivation of Michaelis-Menten kinetics i…

Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have…

Molecular agitation more rapid than thermal Brownian motion is reported for cellular environments, motor proteins, synthetic molecular motors, enzymes, and common chemical reactions, yet that chemical activity couples to molecular motion…

Density dependent families of Markov chains, such as the stochastic models of mass-action chemical kinetics, converge for large values of the indexing parameter $N$ to deterministic systems of differential equations (Kurtz, 1970). Moreover…

We develop a new fast-diffusion approximation for the kinetics of deposition of extended objects on a linear substrate, accompanied by diffusional relaxation. This new approximation plays the role of the mean-field theory for such processes…

The purpose of this work is the study of \textit{chemotaxis} and how to model it through the equations of Keller-Segel. \textit{Chemotaxis} is a natural process which induces the organisms to direct their movement according to certain…

The step motions considered are those in which crystallization is controlled by a single diffusion process, either the substance diffusion for growth from solution or the flow of latent heat from the step for growth from melt. Quasi-static…

Multisite covalent modification of proteins is omnipresent in eukaryotic cells. A well-known example is the mitogen-activated protein kinase (MAPK) cascade, where in each layer of the cascade a protein is phosphorylated at two sites. It has…

Conditional human motion synthesis (HMS) aims to generate human motion sequences that conform to specific conditions. Text and audio represent the two predominant modalities employed as HMS control conditions. While existing research has…

The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian Dynamics (BD) or…

Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These…

We derive diffusive macroscopic equations for the particle and energy density of a system whose time evolution is described by a kinetic equation for the one particle position and velocity function f(r,v,t) that consists of a part that…

We provide a detailed multiscale analysis of a system of particles interacting through a dynamical network of links. Starting from a microscopic model, via the mean field limit, we formally derive coupled kinetic equations for the particle…

Altering chemical reactivity and material structure in confined optical environments is on the rise, and yet, a conclusive understanding of the microscopic mechanisms remains elusive. This originates mostly from the fact that accurately…

The stochastic dynamics of biochemical reaction networks can be accurately described by discrete-state Markov processes where each chemical reaction corresponds to a state transition of the process. Due to the largeness problem of the state…

Reaction-diffusion models have been used over decades to study biological systems. In this context, evolution equations for probability distribution functions and the associated stochastic differential equations have nowadays become…

We show that the force generated by active enzyme molecules are strong enough to influence the dynamics of their surroundings under artificial crowded environments. We measured the behavior of polymer microparticles in a…

A discretization scheme is introduced for a set of convection-diffusion equations with a non-linear reaction term, where the convection velocity is constant for each reactant. This constancy allows a transformation to new spatial variables,…

A novel formulation of fluid dynamics as a kinetic theory with tailored, on-demand constructed particles removes any restrictions on Mach number and temperature as compared to its predecessors, the lattice Boltzmann methods and their…

In this paper we prove that the well-known quasi-steady state approximations, commonly used in enzyme kinetics, which can be interpreted as the reduced system of a differential system depending on a perturbative parameter, according to…

We study the effect of restart, and retry, on the mean completion time of a generic process. The need to do so arises in various branches of the sciences and we show that it can naturally be addressed by taking advantage of the classical…