Related papers: Minimal autocatalytic networks
A model of an evolving network of interacting molecular species is shown to exhibit repeated rounds of crashes in which several species get rapidly depopulated, followed by recoveries. The network inevitably self-organizes into an…
Universal intermittent dynamics in a random catalytic reaction network, induced by smallness in the molecule number is reported. Stochastic simulations for a random catalytic reaction network subject to a flow of chemicals show that the…
Reaction networks taken with mass-action kinetics arise in many settings, from epidemiology to population biology to systems of chemical reactions. Bistable reaction networks are posited to underlie biochemical switches, which motivates the…
A general methodology is proposed to engineer a system of interacting components (particles) which is able to self-regulate their concentrations in order to produce any prescribed output in response to a particular input. The methodology is…
We address a fundamental question: under which conditions do the dynamics and thermodynamics of open chemical reaction networks (CRNs), grounded on the notion of idealized chemostats that exchange selected species, emerge from underlying…
The design and synthesis of complex and large mimicked biochemical networks de novo is an unsolved problem in synthetic biology. To address this limitation without resorting to ad hoc computations and experiments, a predictive mathematical…
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…
Within a fully microscopic setting, we derive a variational principle for the non-equilibrium steady states of chemical reaction networks, valid for time-scales over which chemical potentials can be taken to be slowly varying: at…
A challenge of molecular self-assembly is to understand how to design particles that self-assemble into a desired structure and not any of a potentially large number of undesired structures. Here we use simulation to show that a strategy of…
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…
A small-world cellular automaton network has been formulated to simulate the long-range interactions of complex networks using unconventional computing methods in this paper. Conventional cellular automata use local updating rules. The new…
One of the main goals of Artificial Life is to research the conditions for the emergence of life, not necessarily as it is, but as it could be. Artificial Chemistries are one of the most important tools for this purpose because they provide…
Biological regulatory networks depend upon chemical interactions to process information. Engineering such molecular computing systems is a major challenge for synthetic biology and related fields. The chemical reaction network (CRN) model…
Under suitable assumptions, the dynamic behaviour of a chemical reaction network is governed by an autonomous set of polynomial ordinary differential equations over continuous variables representing the concentrations of the reactant…
External flows of energy, entropy, and matter can cause sudden transitions in the stability of biological and industrial systems, fundamentally altering their dynamical function. How might we control and design these transitions in chemical…
Chemical reactions occur in energy, environmental, biological, and many other natural systems, and the inference of the reaction networks is essential to understand and design the chemical processes in engineering and life sciences. Yet,…
New checkable criteria for persistence of chemical reaction networks are proposed, which extend and complement those obtained by the authors in previous work. The new results allow the consideration of reaction rates which are time-varying,…
We show that discrete distributions on the $d$-dimensional non-negative integer lattice can be approximated arbitrarily well via the marginals of stationary distributions for various classes of stochastic chemical reaction networks. We…
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…
The concept of (auto)catalytic systems has become a cornerstone in understanding evolutionary processes in various fields. The common ground is the observation that for the production of new species/goods/ideas/elements etc. the…