Related papers: Autocatalysis in Reaction Networks
Autocatalysis underlies the ability of chemical and biochemical systems to replicate. Recently, Blokhuis et al. gave a stoechiometric definition of autocatalysis for reaction networks, stating the existence of a combination of reactions…
For reaction networks arising in systems biology, the capacity for two or more steady states, that is, multistationarity, is an important property that underlies biochemical switches. Another property receiving much attention recently is…
Reaction networks, or equivalently Petri nets, are a general framework for describing processes in which entities of various kinds interact and turn into other entities. In chemistry, where the reactions are assigned "rate constants", any…
For the networks that are linear conjugate to complex balanced systems, the delayed version may include two classes of networks: one class is still linear conjugate to the delayed complex balanced network, the other is not. In this paper,…
A family of results, referred to as inheritance results, tell us which enlargements of a chemical reaction network (CRN) preserve its capacity for nontrivial behaviours such as multistationarity and oscillation. In this paper, the following…
In this and a companion paper we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first…
Open chemical reaction systems involve matter-exchange with the surroundings. As a result, species can accumulate inside a system during the course of the reaction. We study the role of network topology in governing the concentration…
This essay aims to propose construction theory, a new domain of theoretical research on machine construction, and use it to shed light on a fundamental relationship between living and computational systems. Specifically, we argue that…
We define a subclass of Chemical Reaction Networks called Post-Translational Modification systems. Important biological examples of such systems include MAPK cascades and two-component systems which are well-studied experimentally as well…
Given a dynamical system with polynomial right-hand side, can it be generated by a reaction network that possesses certain properties? This question is important because some network properties may guarantee specific dynamical properties,…
I analyse a model of an evolving network represented as a directed graph; each node corresponds to one molecular species and the links to catalytic interactions between species. Over short timescales the graph remains fixed while relative…
We study a model for the evolution of chemical species under a combination of population dynamics on a short time scale and a selection mechanism on a longer time scale. Least fit nodes are replaced by new nodes whose links are attached to…
Bistability plays a central role in the gene regulatory networks (GRNs) controlling many essential biological functions, including cellular differentiation and cell cycle control. However, establishing the network topologies that can…
While interdependent systems have usually been associated with increased fragility, we show that strengthening the interdependence between dynamical processes on different networks can make them more robust. By coupling the dynamics of…
The concept of the limiting step is extended to the asymptotology of multiscale reaction networks. Complete theory for linear networks with well separated reaction rate constants is developed. We present algorithms for explicit…
The resilience of a Boolean query is the minimum number of tuples that need to be deleted from the input tables in order to make the query false. A solution to this problem immediately translates into a solution for the more widely known…
Chemical reaction networks taken with mass-action kinetics are dynamical systems that arise in chemical engineering and systems biology. In general, determining whether a chemical reaction network admits multiple steady states is difficult,…
Many complex networks display remarkable resilience under external perturbations, internal failures and environmental changes, yet they can swiftly deteriorate into dysfunction upon the removal of a few keystone nodes. Discovering theories…
We establish a new relationship between monotonicity and contractivity and use this connection to describe a new general class of weakly contractive reaction networks. The new class is characterized by the stoichiometry matrix of the…
Catalytically active macromolecules are envisioned as key building blocks in development of artificial nanomotors. However, theory and experiments report conflicting findings regarding their dynamics. The lack of consensus is mostly caused…