Related papers: Information geometric bound on general chemical re…
We identify the thermodynamic conditions necessary to observe indefinite growth in homogeneous open chemical reaction networks (CRNs) satisfying mass action kinetics. We also characterize the thermodynamic efficiency of growth by…
We propose a direct optimization framework for learning reduced and sparse chemical reaction networks (CRNs) from time-series trajectory data. In contrast to widely used indirect methods-such as those based on sparse identification of…
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…
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…
Proposals for molecular communication networks as part of a future internet of bio-nano-things have become more intricate and the question of practical implementation is gaining more importance. One option is to apply detailed chemical…
The popularity of molecular computation has given rise to several models of abstraction, one of the more recent ones being Chemical Reaction Networks (CRNs). These are equivalent to other popular computational models, such as Vector…
We mathematically prove that chemical reaction networks without hidden layers can solve tasks for which spiking neural networks require hidden layers. Our proof uses the deterministic mass-action kinetics formulation of chemical reaction…
The Chemical Reaction Network (CRN) is a well-studied model that describes the interaction of molecules in well-mixed solutions. In 2014, Qian and Winfree [22] proposed the abstract surface chemical reaction network model (sCRN), which…
Genetic regulatory networks (GRNs) have been widely studied, yet there is a lack of understanding with regards to the final size and properties of these networks, mainly due to no network currently being complete. In this study, we analyzed…
This paper is concerned with programming adaptive linear neural networks (ALNNs) using chemical reaction networks (CRNs) equipped with mass-action kinetics. Through individually programming the forward propagation and the backpropagation of…
Reaction networks have become a major modelling framework in the biological sciences from epidemiology and population biology to genetics and cellular biology. In recent years, much progress has been made on stochastic reaction networks…
In order to fully exploit the potential of molecular communication (MC) for intra-body communication, practically implementable cellular receivers are an important long-term goal. A variety of receiver architectures based on chemical…
Recently, Hessian geometry - an extension of information geometry - has emerged as a framework to naturally connect the geometries appearing in the theory of chemical reaction networks (CRN) to their inherent thermodynamical and kinetic…
Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This work presents a computational methodology for searching for…
Step Chemical Reaction Networks (step CRNs) are an augmentation of the Chemical Reaction Network (CRN) model where additional species may be introduced to the system in a sequence of ``steps.'' We study step CRN systems using a weak subset…
Both natural and synthetic chemical systems not only exhibit a range of non-trivial dynamics, but also transition between qualitatively different dynamical behaviours as environmental parameters change. Such transitions are called…
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…
Graphs and hypergraphs provide powerful abstractions for modeling interactions among a set of entities of interest and have been attracting a growing interest in the literature thanks to many successful applications in several fields. In…
We show that adding new chemical species into the reactions of a chemical reaction network (CRN) in such a way that the rank of the network remains unchanged preserves its capacity for multiple nondegenerate equilibria and/or periodic…
We present a data-driven verification approach that determines whether or not a given chemical reaction network (CRN) satisfies a given property, expressed as a formula in a modal logic. Our approach consists of three phases, integrating…