Related papers: Structure and input-to-state stability for composa…
The use of mathematical models has helped to shed light on countless phenomena in chemistry and biology. Often, though, one finds that systems of interest in these fields are dauntingly complex. In this paper, we attempt to synthesize and…
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…
Input-to-state stability (ISS) unifies global asymptotic stability with respect to variations of initial conditions with robustness with respect to external disturbances. First, we present Lyapunov characterizations for input-to-state…
Robustness is an observable property for which a chemical reaction network (CRN) can maintain its functionalities despite the influence of different perturbations. In general, to verify whether a network is robust, it is necessary to…
We introduce the notion of corresponding a chemical reaction network to a split network translation, and use this novel process to extend the scope of existing network-based theory for characterizing the steady state set of mass-action…
This paper establishes a theoretical framework to describe the transition from consensus to stable clustering in multi-agent systems with nonlinear, cooperative interactions. We first establish a sharp threshold for consensus. For a broad…
We explore the range of probabilistic behaviours that can be engineered with Chemical Reaction Networks (CRNs). We show that at steady state CRNs are able to "program" any distribution with finite support in $\mathbb{N}^m$, with $m \geq 1$.…
We provide a short supplement to the paper "MAPK networks and their capacity for multistationarity due to toric steady states" by P\'erez Mill\'an and Turjanski. We show that the capacity for toric steady states in the three networks…
Identifying and explaining the structure of complex networks at different scales has become an important problem across disciplines. At the mesoscale, modular architecture has attracted most of the attention. At the macroscale, other…
We classify the functions $f:\mathbb{N}^2 \rightarrow \mathbb{N}$ which are stably computable by output-oblivious Stochastic Chemical Reaction Networks (CRNs), i.e., systems of reactions in which output species are never reactants. While it…
We study the notion of structured realizability for linear systems defined over graphs. A stabilizable and detectable realization is structured if the state-space matrices inherit the sparsity pattern of the adjacency matrix of the…
We study the set of output stable configurations of chemical reaction deciders (CRDs). It turns out that CRDs with only bimolecular reactions (which are almost equivalent to population protocols) have a special structure that allows for an…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
Chemical reaction networks (CRNs) are foundational models for describing complex biochemical processes. We study noncompetitive CRNs, a class of networks whose static states are rate-independent, and that can implement ReLU neural networks.…
Developing a mathematical understanding of autocatalysis in reaction networks has both theoretical and practical implications. We review definitions of autocatalytic networks and prove some properties for minimal autocatalytic subnetworks…
Here we address the challenge of profiling causal properties and tracking the transformation of chemical compounds from an algorithmic perspective. We explore the potential of applying a computational interventional calculus based on the…
Many reaction networks arising in applications are multistationary, that is, they have the capacity for more than one steady state; while some networks exhibit absolute concentration robustness (ACR), which means that some species…
The analysis of cyber-physical systems (CPS) is challenging due to the large state space and the continuous changes occurring in their constituent parts. Design practices favor modularity to help reducing this complexity. In a previous…
This paper deals with strong structural controllability of structured networks. A structured network is a family of structured systems (called node systems) that are interconnected by means of a structured interconnection law. The node…
Chemical reaction networks (CRN) comprise an important class of models to understand biological functions such as cellular information processing, the robustness and control of metabolic pathways, circadian rhythms, and many more. However,…