Related papers: Log-Linear Reaction Quotient Dynamics
Dynamic properties of chemical reactions and appropriate relationships for open chemical equilibrium are discussed in approach of the chemical dynamics. New way to calculate composition of chemical systems in open equilibrium, based on the…
Systems biology uses large networks of biochemical reactions to model the functioning of biological cells from the molecular to the cellular scale. The dynamics of dissipative reaction networks with many well separated time scales can be…
Living systems are maintained out-of-equilibrium by external driving forces. At stationarity, they exhibit emergent selection phenomena that break equilibrium symmetries and originate from the expansion of the accessible chemical space due…
Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems…
Reaction systems are discrete dynamical systems inspired by bio-chemical processes, whose dynamical behaviour is expressed by set-theoretic operations on finite sets. Reaction systems thus provide a description of bio-chemical phenomena…
Driven chemical reactions can control the macroscopic properties of droplets, like their size. Such active droplets are critical in structuring the interior of biological cells. Cells also need to control where and when droplets appear, so…
Very often, models in biology, chemistry, physics, and engineering are systems of polynomial or power-law ordinary differential equations, arising from a reaction network. Such dynamical systems can be generated by many different reaction…
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…
Chemical affinities are responsible for driving active matter systems out of equilibrium. At the nano-scale, molecular machines interact with the surrounding environment and are subjected to external forces. The mechano-chemical coupling…
We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
The general theory of a complex system of nonlinear chemical reactions is a primary language of chemistry that includes chemical engineering and cellular biochemistry. Its significance as an analytical framework, however, has not been fully…
We derive the equations of motion describing the feedback control of quantum systems in the regime of "good control", in which the control is sufficient to keep the system close to the desired state. One can view this regime as the quantum…
A self-consistent quadratic theory is presented to account for nonlinear contributions in quantum dynamics. Evolution equations are shown to depend on higher-order gradients of the Hamiltonian, which are incorporated via their equations 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…
Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…
We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where…
Many mathematical models for biological phenomena, such as the spread of diseases, are based on reaction-diffusion equations for densities of interacting cell populations. We present a consistent derivation of reaction-diffusion equations…
Current formulations of nonequilibrium thermodynamics of open chemical reaction networks only consider chemostats as free-energy sources sustaining nonequilibrium behaviours. Here, we extend the theory to include incoherent light as a…
The unique fluctuation-dissipation theorem for equilibrium stands in contrast with the wide variety of nonequilibrium linear response formulae. Their most traditional approach is "analytic", which, in the absence of detailed balance,…