Related papers: Single Molecule Michaelis-Menten Equation beyond Q…
Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an…
We present a model of an ATP-fueled molecular machine which push a polymer through a pore channel. The machine acts between two levels (working-waiting), and the working one remains active for a fixed time giving a constant force. The…
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 consider reaction networks that admit a singular perturbation reduction in a certain parameter range. The focus of this paper is on deriving "small parameters" (briefly for small perturbation parameters), to gauge the accuracy of the…
A protein undergoes conformational dynamics with multiple time scales, which results in fluctuating enzyme activities. Recent studies in single molecule enzymology have observe this "age-old" dynamic disorder phenomenon directly. However,…
We recall the perturbation expansion for Michaelis-Menten kinetics, beyond the standard quasi-steady-state approximation (sQSSA). Against this background, we are able to appropriately apply the alternative approach to the study of…
The estimation of the kinetic parameters requires the careful design of experiments under a constrained set of conditions. Many estimates reported in the literature incorporate protocols that leverage simplified mathematical models known as…
Biochemical processes typically involve huge numbers of individual reversible steps, each with its own dynamical rate constants. For example, kinetic proofreading processes rely upon numerous sequential reactions in order to guarantee the…
We present a simple and robust technique to extract kinetic rate models and thermodynamic quantities from single molecule time traces. SMACKS (Single Molecule Analysis of Complex Kinetic Sequences) is a maximum likelihood approach that…
Single-molecule biophysics has transformed our understanding of the fundamental molecular processes involved in living biological systems, but also of the fascinating physics of life. Far more exotic than a collection of exemplars of soft…
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…
The limit of small entropy production is reached in relaxing systems long after preparation, and in stationary driven systems in the limit of small driving power. Surprisingly, for extended systems this limit is not in general the…
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…
We have proposed the neck linker swing model to investigate the mechanism of mechanochemical coupling of kinesin. The Michaelis-Menten-like curve for velocity vs ATP concentration at different loads has been obtained, which is in agreement…
In this work we study the diffusion mechanisms in lithium disilicate melt using molecular dynamics simulation, which has an edge over other simulation methods because it can track down actual atomic rearrangements in materials once a…
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…
Complex biochemical pathways or regulatory enzyme kinetics can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. This discipline provides a set of tools for quantifying and understanding the…
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…
Single molecule fluorescence tracking provides information at nm-scale and ms-temporal resolution about the dynamics and interaction of individual molecules in a biological environment. While the dynamic behavior of isolated molecules can…
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…