Related papers: Beyond Michaelis-Menten: Allosteric Rate Control o…
The equilibration of enzyme and complex concentrations in deterministic Michaelis-Menten reaction networks underlies the hyperbolic dependence between the input (substrates) and output (products). This relationship was first obtained by…
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…
In this paper, we investigate how stochastic reaction processes are affected by external perturbations. We describe an extension of the deterministic metabolic control analysis (MCA) to the stochastic regime. We introduce stochastic…
Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…
In a conformational nonequilibrium steady state (cNESS), enzyme turnover is modulated by the underlying conformational dynamics. Based on a discrete kinetic network model, we use the integrated probability flux balance method to derive the…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
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…
Many chemical reactions in biological cells occur at very low concentrations of constituent molecules. Thus, transcriptional gene-regulation is often controlled by poorly expressed transcription-factors, such as E.coli lac repressor with…
We introduce a model of the Relentless Congestion Control proposed by Matt Mathis. Relentless Congestion Control (RCC) is a modification of the AIMD (Additive Increase Multiplicative Decrease) congestion control which consists in decreasing…
The Michaelis-Menten enzymatic reaction is sufficient to perceive many subtleties of network modeling, including the concentration and time scales separations, the formal equivalence between bulk phase and single-molecule approaches, or the…
Chaos control techniques have been applied to a wide variety of experimental systems, including magneto-elastic ribbons, lasers, chemical reactions, arrhythmic cardiac tissue, and spontaneously bursting neuronal networks. An underlying…
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 develop a theory of enzyme catalysis within biological cells where the substrate concentration [S](t) is time dependent, in contrast to the Michaelis-Menten theory that assumes a steady state. We find that the time varying concentration…
A controller for a Discrete Event System must achieve its goals despite that its environment being capable of resolving race conditions between controlled and uncontrolled events.Assuming that the controller loses all races is sometimes…
Reaction Coordinates (RCs) are indicators of hidden, low-dimensional mechanisms that govern the long-term behavior of high-dimensional stochastic processes. We present a novel and general variational characterization of optimal RCs and…
Predictive Feedback Control is an easy-to-implement method to stabilize unknown unstable periodic orbits in chaotic dynamical systems. Predictive Feedback Control is severely limited because asymptotic convergence speed decreases with…
The Mackey--Glass equation, which was proposed to illustrate nonlinear phenomena in physiological control systems, is a classical example of a simple looking time delay system with very complicated behavior. Here we use a novel approach for…
Enzyme kinetics has historically been described by deterministic models, with the Michaelis-Menten (MM) equation serving as a paradigm. However, recent experimental and theoretical advances have made it clear that stochastic fluctuations,…
Balancing a bicycle is typical for the balance control humans perform as a part of a whole range of behaviors (walking, running, skating, skiing, etc.). This paper presents a general model of balance control and applies it to the balancing…
One major objective of controlling classical chaotic dynamical systems is exploiting the system's extreme sensitivity to initial conditions in order to arrive at a predetermined target state. In a recent letter [Phys.~Rev.~Lett. 130, 020201…