Related papers: Input-to-state stability-based chemical reaction n…
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…
Molecular computation in chemical reaction networks (CRNs) now constitutes a foundational framework for designing programmable biological systems. However, prevailing design methodologies primarily treat parallelism of chemical reactions as…
In the field of molecular computation based on chemical reaction networks (CRNs), leveraging parallelism to enable coupled mass-action systems (MASs) to retain predefined computational functionality has been a research focus. MASs…
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…
Embedding computation in biochemical environments incompatible with traditional electronics is expected to have wide-ranging impact in synthetic biology, medicine, nanofabrication and other fields. Natural biochemical systems are typically…
Chemical Reaction Networks (CRNs) provide a useful abstraction of molecular interaction networks in which molecular structures as well as mass conservation principles are abstracted away to focus on the main dynamical properties of the…
A chemical reaction network (CRN) is composed of reactions that can be seen as interactions among entities called species, which exist within the system. Endowed with kinetics, CRN has a corresponding set of ordinary differential equations…
We study the composability of discrete chemical reaction networks (CRNs) that stably compute (i.e., with probability 0 of error) integer-valued functions $f:\mathbb{N}^d\to\mathbb{N}$. We consider output-oblivious CRNs in which the output…
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…
We propose a unified framework that allows for the full mechanistic reconstruction of chemical reaction networks (CRNs) from concentration data. The framework utilizes an integral formulation of the differential equations governing the…
We present a differentiable formulation of abstract chemical reaction networks (CRNs) that can be trained to solve a variety of computational tasks. Chemical reaction networks are one of the most fundamental computational substrates used by…
We consider how to generate chemical reaction networks (CRNs) from functional specifications. We propose a two-stage approach that combines synthesis by satisfiability modulo theories and Markov chain Monte Carlo based optimisation. First,…
We initiate the study of rate-constant-independent computation of Boolean predicates and numerical functions in the continuous model of chemical reaction networks (CRNs), which model the amount of a chemical species as a nonnegative,…
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…
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.…
Chemical reaction networks (CRNs) are directed graphs with reactant or product complexes as vertices, and reactions as arcs. A CRN is weakly reversible if each of its connected components is strongly connected. Weakly reversible networks…
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…
We study the model of continuous chemical reaction networks (CRNs), consisting of reactions such as $A+B \to C+D$ that can transform some continuous, nonnegative real-valued quantity (called a *concentration*) of chemical species $A$ and…
Motivation: A Chemical Reaction Network (CRN) is a set of chemical reactions, which can be very complex and difficult to analyze. Indeed, dynamical properties of CRNs can be described by a set of non-linear differential equations that…
Chemical reaction networks (CRNs) model the behavior of chemical reactions in well-mixed solutions and they can be designed to perform computations. In this tutorial we give an overview of various computational models for CRNs. Moreover, we…