Related papers: Siphons in chemical reaction networks

Stochastic chemical reaction networks (CRNs) are complex systems which combine the features of concurrent transformation of multiple variables in each elementary reaction event, and nonlinear relations between states and their rates of…

We consider stochastic models of chemical reaction networks with time dependent input rates and several types of molecules. We prove that, in despite of strong time dependence of input rates, there is a kind of homeostasis phenomenon: far…

An inverse problem framework for constructing reaction systems with prescribed properties is presented. Kinetic transformations are defined and analysed as a part of the framework, allowing an arbitrary polynomial ordinary differential…

We study synchronization processes in networks of slightly non identical chaotic systems, for which a complete invariant synchronization manifold does not rigorously exist. We show and quantify how a slightly dispersed distribution in…

In this paper we introduce a new representation for the multistationarity region of a reaction network, using polynomial superlevel sets. The advantages of using this polynomial superlevel set representation over the already existing…

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…

We introduce a unifying and generalizing framework for complex and detailed balanced steady states in chemical reaction network theory. To this end, we generalize the graph commonly used to represent a reaction network. Specifically, we…

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…

Autocatalytic Sets are reaction networks theorised as networks at the basis of life. Their main feature is the ability of spontaneously emerging and self-reproducing. The Reflexively and Food-generated theory provides a formal definition of…

Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…

The dominant paradigm in origin of life research is that of an RNA world. However, despite experimental progress towards the spontaneous formation of RNA, the RNA world hypothesis still has its problems. Here, we introduce a novel…

Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…

Chemical reactions that couple to systems that phase separate have been implicated in diverse contexts from biology to materials science. However, how a particular set of chemical reactions (chemical reaction network, CRN) would affect the…

The homological scaffold leverages persistent homology to construct a topologically sound summary of a weighted network. However, its crucial dependency on the choice of representative cycles hinders the ability to trace back global…

We show that very simple molecular systems, modeled as chemical reaction networks, can have behaviors that exhibit dramatic phase transitions at certain population thresholds. Moreover, the magnitudes of these thresholds can thwart attempts…

We establish that mass conserving single terminal-linkage networks of chemical reactions admit positive steady states regardless of network deficiency and the choice of reaction rate constants. This result holds for closed systems without…

Chemical algorithms are statistical algorithms described and represented as chemical reaction networks. They are particularly attractive for traffic shaping and general control of network dynamics; they are analytically tractable, they…

In all but special circumstances, measurements of time-dependent processes reflect internal structures and correlations only indirectly. Building predictive models of such hidden information sources requires discovering, in some way, the…

Chemical reaction networks (CRNs) are prototypical complex systems because reactions are nonlinear and connected in intricate ways, and they are also essential to understand living systems. Here, I discuss how recent developments in…

Superbubbles are acyclic induced subgraphs of a digraph with single entrance and exit that naturally arise in the context of genome assembly and the analysis of genome alignments in computational biology. These structures can be computed in…