Related papers: Thermodynamic validity criterion for the irreversi…
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…
The theory of irreversible thermodynamics for arbitrarily curved lipid membranes is presented here. The coupling between elastic bending and irreversible processes such as intra-membrane lipid flow, intra-membrane phase transitions, and…
Active matter describes systems whose constituents convert energy from their surroundings into directed motion, such as bacteria or catalytic colloids. We establish a thermodynamic law for dilute suspensions of interacting active particles…
The aim of this paper is to determine lost works in a molecular engine and compare results with macro (classical) heat engines. Firstly, irreversible thermodynamics are reviewed for macro and molecular cycles. Secondly, irreversible…
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…
Switch-like motifs are among the basic building blocks of biochemical networks. A common motif that can serve as an ultrasensitive switch consists of two enzymes acting antagonistically on a substrate, one making and the other removing a…
Michaelis-Menten equation is a basic equation of enzyme kinetics and gives an acceptable approximation of real chemical reaction processes. Analyzing the derivation of this equation yields the fact that its good performance of approximating…
Despite its simplicity, it seems to my best of knowledge that the possibly simplest approach towards deriving equations governing irreversible thermodynamics from gas-kinetic considerations within the framework of classical mechanics has…
Path thermodynamic formulation of non-equilibrium reactive systems is considered. It is shown through simple practical examples that this approach can lead to results that contradict well established thermodynamic properties of such…
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…
Irreversible thermodynamics of simple fluids have been connected recently to the theory of dynamical systems and some interesting assumptions have been made about the nature of the associated invariant measures. We show that the tests of…
Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
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,…
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…
A comparison is made between conventional Michaelis-Menten kinetics and two models that take into account the duration of the conformational changes that take place at the molecular level during the catalytic cycle of a monomer. The models…
The emergence of irreversibility in physical processes, despite the fundamentally reversible nature of quantum mechanics, remains an open question in physics. This thesis explores the intricate relationship between quantum mechanics and…
We consider a stochastic model of the Michaelis-Menten (MM) enzyme kinetic reactions in terms of Stochastic Differential Equations (SDEs) driven by Poisson Random Measures (PRMs). It has been argued that among various Quasi-Steady State…
In multi-criteria decision making (MCDM) problems, ratings are assigned to the alternatives on different criteria by the expert group. In this paper, we propose a thermodynamically consistent model for MCDM using the analogies for…
The approach to a substantiation of thermodynamics is offered. A conservative system of interacting elements, which is not in equilibrium, is used as a model. This system is then split into small subsystems that are accepted as being in…