Related papers: Minimal autocatalytic networks
An algorithm is given in this paper for the computation of dynamically equivalent weakly reversible realizations with the maximal number of reactions, for chemical reaction networks (CRNs) with mass action kinetics. The original problem…
Autonomous computations that rely on automated reaction network elucidation algorithms may pave the way to make computational catalysis on a par with experimental research in the field. Several advantages of this approach are key to…
This paper presents new results about the optimization based generation of chemical reaction networks (CRNs) of higher deficiency. Firstly, it is shown that the graph structure of the realization containing the maximal number of reactions…
Here we focus on the challenge of verifying the correctness of molecular implementations of abstract chemical reaction networks, where operation in a well-mixed "soup" of molecules is stochastic, asynchronous, concurrent, and often involves…
Self-replicating systems based on information-coding polymers are of crucial importance in biology. They also recently emerged as a paradigm in material design on nano- and micro-scales. We present a general theoretical and numerical…
Much of the theory on chemical-reaction networks (CRNs) has been developed in the ideal-solution limit, where interactions between the solutes are negligible. However, there is a large variety of phenomena in biological cells and…
Chemical reaction networks (CRNs) model systems where molecules interact according to a finite set of reactions such as $A + B \to C$, representing that if a molecule of $A$ and $B$ collide, they disappear and a molecule of $C$ is produced.…
Coupled chemical interactions in a well-mixed solution are commonly formalized as chemical reaction networks (CRNs). However, despite the widespread use of CRNs in the natural sciences, the range of computational behaviors exhibited by CRNs…
We study the dynamics of a system made up of particles of two different species undergoing irreversible quadratic autocatalytic reactions: $A + B \to 2A$. We especially focus on the reaction velocity and on the average time at which the…
A biological system consists of a variety of polymers that are synthesized from monomers, by catalysis that exists only for some long polymers. It is important to elucidate the emergence and sustenance of such autocatalytic polymerization.…
The question of existence of nonexpansive chaotic almost minimal (CAM) systems, and the existence of CAM systems on every residually finite group, were raised in a recent paper of Van Cyr, Bryna Kra and Scott Schmieding. We construct…
The research concerns the dynamics of complex autonomous Kauffman networks. The article defines and shows using simulation experiments half-chaotic networks, which exhibit features much more similar to typically modeled systems like a…
The interaction of phase-separating systems with chemical reactions is of great interest in various contexts, from biology to material science. In biology, phase separation is thought to be the driving force behind the formation of…
Which reaction networks, when taken with mass-action kinetics, have the capacity for multiple steady states? There is no complete answer to this question, but over the last 40 years various criteria have been developed that can answer this…
Analysis of large continuous-time stochastic systems is a computationally intensive task. In this work we focus on population models arising from chemical reaction networks (CRNs), which play a fundamental role in analysis and design of…
Much attention has been focused in recent years on the following algebraic problem arising from applications: which chemical reaction networks, when taken with mass-action kinetics, admit multiple positive steady states? The interest behind…
Chemical kinetics plays an important role in governing the thermal evolution in reactive flows problems. The possible interactions between chemical species increase drastically with the number of species considered in the system. Various…
We consider chemical reaction networks taken with mass action kinetics. The steady states of such a system are solutions to a system of polynomial equations. Even for small systems the task of finding the solutions is daunting. We develop…
An explanatory model for the emergence of evolvable units must display emerging structures that (1) preserve themselves in time (2) self-reproduce and (3) tolerate a certain amount of variation when reproducing. To tackle this challenge,…
Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemical knowledge. A first key step for rule learning is the…