Related papers: Conformational Nonequilibrium Enzyme Kinetics: Gen…
The driving force for active physical and biological systems is determined by both the underlying landscape and the non-equilibrium curl flux. While landscape can be quantified in the experiments by the histograms of the collecting…
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,…
Enyzme kinetics are cyclic. We study a Markov renewal process model of single-enzyme turnover in nonequilibrium steady-state (NESS) with sustained concentrations for substrates and products. We show that the forward and backward cycle times…
We introduce a reaction-path statistical mechanics formalism based on the principle of large deviations to quantify the kinetics of single-molecule enzymatic reaction processes under the Michaelis-Menten mechanism, which exemplifies an…
The century-long Michaelis-Menten rate law and its modifications in the modeling of biochemical rate processes stand on the assumption that the concentration of the complex of interacting molecules, at each moment, rapidly approaches an…
In biochemical systems the Michaelis-Menten (MM) scheme is one of the best-known models of the enzyme- catalyzed kinetics. In the academic literature the MM approximation has been thoroughly studied in the context of differential equation…
Reactions with enzymes are critical in biochemistry, where the enzymes act as catalysis in the process. One of the most used mechanisms for modeling enzyme-catalyzed reactions is the Michaelis-Menten (MM) kinetic. In the ODE level, i.e.…
The hyperbolic dependence of catalytic rate on substrate concentration is a classical result in enzyme kinetics, quantified by the celebrated Michaelis-Menten equation. The ubiquity of this relation in diverse chemical and biological…
Recent fluorescence spectroscopy measurements of the turnover time distribution of single-enzyme turnover kinetics of $\beta$-galactosidase provide evidence of Michaelis-Menten kinetics at low substrate concentration. However, at high…
The Michaelis-Menten mechanism is probably the best known model for an enzyme-catalyzed reaction. For spatially homogeneous concentrations, QSS reductions are well known, but this is not the case when chemical species are allowed to…
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…
Chemical reaction network theory is a powerful framework to describe and analyze chemical systems. While much about the concentration profile in an equilibrium state can be determined in terms of the graph structure, the overall reaction's…
Enzyme kinetics are cyclic. A more realistic reversible three-step mechanism of the Michaelis-Menten kinetics is investigated in detail, and three kinds of waiting cycle times $T$, $T_{+}$, $T_{-}$ are defined. It is shown that the mean…
Michaelis--Menten analysis is often conducted by nonlinear least squares under a constant-variance assumption, even though enzyme-kinetic data frequently display concentration-dependent heteroscedasticity and often include repeated or…
In this paper we derive several quasi steady-state approximations (QSSAs) to the stochastic reaction network describing the Michaelis-Menten enzyme kinetics. We show how the different assumptions about chemical species abundance and…
The method developed by Michaelis and Menten was foundational in the development of our understanding of biochemical reaction kinetics. Extended models of metabolism encapsulated by reaction rate theory, stochastic reaction models, and…
We develop an general formalism of single enzyme kinetics in two dimension where substrates diffuse stochastically on a square lattice in presence of disorder. The dynamics of the model could be decoupled effectively to two stochastic…
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…
We study the ensemble velocity of non-processive motor proteins, described with multiple chemical states. In particular, we discuss the velocity as a function of ATP concentration. Even a simple model which neglects the strain-dependence of…
There is a vast amount of literature concerning the appropriateness of various perturbation parameters for the standard quasi-steady state approximation in the Michaelis-Menten reaction mechanism, and also concerning the relevance of these…