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Chemical Reaction Networks (CRNs) are a well-established model of distributed computing characterized by quantities of molecular species that can transform or change through applications of reactions. A fundamental problem in CRNs is the…
Chemical reaction networks (CRNs) model the behavior of molecules in a well-mixed system. The emerging field of molecular programming uses CRNs not only as a descriptive tool, but as a programming language for chemical computation.…
We analyze the computational complexity of basic reconfiguration problems for the recently introduced surface Chemical Reaction Networks (sCRNs), where ordered pairs of adjacent species nondeterministically transform into a different…
Across many disciplines, chemical reaction networks (CRNs) are an established population model defined as a system of coupled nonlinear ordinary differential equations. In many applications, for example, in systems biology and epidemiology,…
In a previous paper we introduced immediate observation Petri nets, a subclass of Petri nets with application domains in distributed protocols (population protocols) and theoretical chemistry (chemical reaction networks). IO nets enjoy many…
Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming advances in synthetic biology,…
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,…
Random graph models have been instrumental in characterizing complex networks, but chemical reaction networks (CRNs) are better represented as hypergraphs. Traditional models of random CRNs often reduce CRNs to bipartite graphs,…
Reachability queries ask whether there exists a path from the source vertex to the target vertex on a graph. Recently, several powerful reachability queries, such as Label-Constrained Reachability (LCR) queries and Regular Path Queries…
Formal methods have enabled breakthroughs in many fields, such as in hardware verification, machine learning and biological systems. The key object of interest in systems biology, synthetic biology, and molecular programming is chemical…
This paper studies the (discrete) \emph{chemical reaction network (CRN)} computational model that emerged in the last two decades as an abstraction for molecular programming. The correctness of CRN protocols is typically established under…
In this essay, we investigate some relations between Chemical Reaction Networks (CRN) and Mathematical Epidemiology (ME) and report on several pleasant surprises which we had simply by putting these two topics together. Firstly, we propose…
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,…
Reconfigurable broadcast networks (RBN) are a model of distributed computation in which agents can broadcast messages to other agents using some underlying communication topology which can change arbitrarily over the course of executions.…
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…
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…
Inspired by Anderson et al. [J. R. Soc. Interface, 2014] we study the long-term behavior of discrete chemical reaction networks (CRNs). In particular, using techniques from both Petri net theory and CRN theory, we provide a powerful…
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 almost-sure reachability problem in a distributed system obtained as the asynchronous composition of N copies (called processes) of the same automaton (called protocol), that can communicate via a shared register with finite…
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…