Related papers: Non-normality and non-monotonic dynamics in comple…
For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive…
The eigenspectrum of a non-normal matrix, which does not commute with its Hermitian conjugate, is a central issue of non-Hermitian physics that has been extensively studied in the past few years. There is, however, another characteristic of…
For dynamical systems arising from chemical reaction networks, persistence is the property that each species concentration remains positively bounded away from zero, as long as species concentrations were all positive in the beginning. We…
We study the response of chemical reaction networks driven far from equilibrium to logarithmic perturbations of reaction rates. The response of the mean number of a chemical species is observed to be quantitively limited by number…
Analyzing nonlinear conformational relaxation dynamics in elastic networks corresponding to two classical motor proteins, we find that they respond by well-defined internal mechanical motions to various initial deformations and that these…
Nonreciprocal interactions that violate Newton's law 'actio=reactio' are ubiquitous in nature and are currently intensively investigated in active matter, chemical reaction networks, population dynamics, and many other fields. An…
Mechanisms of pattern formation---of which the Turing instability is an archetype---constitute an important class of dynamical processes occurring in biological, ecological and chemical systems. Recently, it has been shown that the Turing…
A reflection of our ultimate understanding of a complex system is our ability to control its behavior. Typically, control has multiple prerequisites: It requires an accurate map of the network that governs the interactions between the…
In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated…
Characterizing the emergence of chaotic dynamics of complex networks is an essential task in nonlinear science with potential important applications in many fields such as neural control engineering, microgrid technologies, and ecological…
Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the…
Entropy is a fundamental concept in equilibrium statistical mechanics, yet its origin in the non-equilibrium dynamics of isolated quantum systems is not fully understood. A strong consensus is emerging around the idea that the stationary…
Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. Microbial communities are…
Mass action systems capture chemical reaction networks in homogeneous and dilute solutions. We suggest a notion of generalized mass action systems that admits arbitrary nonnegative power-law rate functions and serves as a more realistic…
We derive the nonequilibrium conductance matrix for open stationary Chemical Reaction Networks (CRNs) described by a deterministic mass action kinetic equation. As an illustration, we determine the nonequilibrium conductance matrix of a CRN…
In various chemical systems enthalpy-entropy compensation (EEC) is a well-known rule of behavior, although the physical roots of it are still not completely understood. It has been frequently questioned whether EEC is a truly physical…
The quantitative convergence to equilibrium for reaction-diffusion systems arising from complex balanced chemical reaction networks with mass action kinetics is studied by using the so-called entropy method. In the first part of the paper,…
Networked dynamical systems are common throughout science in engineering; e.g., biological networks, reaction networks, power systems, and the like. For many such systems, nonlinearity drives populations of identical (or near-identical)…
Zero-one biochemical reaction networks play key roles in cell signalling such as signalling pathways regulated by protein phosphorylation. Multistability of reaction networks is a crucial dynamics feature enabling decision-making in cells.…
Previous studies have inferred robust stability of reaction networks by utilizing linear programs or iterative algorithms. Such algorithms become tedious or computationally infeasible for large networks. In addition, they operate like…