Related papers: Minimal autocatalytic networks
We describe a large class of chemical reaction networks, those endowed with a subtle structural property called concordance. We show that the class of concordant networks coincides precisely with the class of networks which, when taken with…
This paper (parts I and II) provides an expository introduction to monotone and near-monotone dynamical systems associated to biochemical networks, those whose graphs are consistent or near-consistent. Many conclusions can be drawn from…
Various hypotheses exist about the paths used for communication between the nodes of complex networks. Most studies simply suppose that communication goes via shortest paths, while others have more explicit assumptions about how routing…
A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as…
Some results are presented on how oscillation is inherited by chemical reaction networks (CRNs) when they are built in natural ways from smaller oscillatory networks. The main results describe four important ways in which a CRN can be…
Chemically fueled supramolecular systems can exhibit complex, time-dependent behaviors reminiscent of living matter when maintained far from equilibrium by continuous energy or fuel consumption. Here, we introduce a minimal…
A self-organising model is proposed to explain the criticality in cortical networks deduced from recent observations of neuronal avalanches. Prevailing understanding of self-organised criticality (SOC) dictates that conservation of energy…
Neural systems process information in a dynamical regime between silence and chaotic dynamics. This has lead to the criticality hypothesis which suggests that neural systems reach such a state by self-organizing towards the critical point…
We develop a formal model of the emergence of self-constructing objects (e.g. heteropolymers with autocatalytic capability) in an open system, which don't contain such objects initially. The objects are constructed from subunits (e.g.…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
The apparent difficulty of designing simple autocatalysts that grow exponentially in the absence of enzymes, external drives or ingenious internal mechanisms severely constrains scenarios for the emergence of evolution by natural selection…
This paper (parts I and II) provides an expository introduction to monotone and near-monotone dynamical systems associated to biochemical networks, those whose graphs are consistent or near-consistent. Many conclusions can be drawn from…
We consider the problem of learning data-driven replicas for stiff systems of ordinary differential equations arising in chemical kinetics that can be evaluated with high computational efficiency. We first focus on training emulators for…
We show that if a chemical reaction network (CRN) admits nondegenerate (resp., linearly stable) oscillation, and we add new reversible reactions involving new species to this CRN, then the new CRN so created also admits nondegenerate…
In Nature, the primary goal of any network is to survive. This is less obvious for engineering networks (electric power, gas, water, transportation systems etc.) that are expected to operate under normal conditions most of time. As a…
We consider stochastic descriptions of chemical reaction networks in which there are both fast and slow reactions, and for which the time scales are widely separated. We develop a computational algorithm that produces the generator of the…
We investigate the properties of large random conservative chemical reaction networks composed of elementary reactions endowed with either mass-action or saturating kinetics, assigning kinetic parameters in a thermodynamically-consistent…
Various functions of a network of excitable units can be enhanced if the network is in the `critical regime', where excitations are, on average, neither damped nor amplified. An important question is how can such networks self-organize to…
Among all characteristics exhibited by natural and man-made networks the small-world phenomenon is surely the most relevant and popular. But despite its significance, a reliable and comparable quantification of the question `how small is a…
Living systems operate out of equilibrium, continuously consuming energy to sustain organised, functional states. Their emergent behaviour usually relies on a set of interconnected chemical reaction networks (CRNs) driven by external fluxes…