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We introduce a new model of \emph{step} Chemical Reaction Networks (step CRNs), motivated by the step-wise addition of materials in standard lab procedures. Step CRNs have ordered reactants that transform into products via reaction rules…
We propose the chemlambda artificial chemistry, whose behavior strongly suggests that real molecules which embed Interaction Nets patterns and real chemical reactions which resemble Interaction Nets graph rewrites could be a realistic path…
A method which casts the chemical source term computation into an artificial neural network (ANN)-inspired form is presented. This approach is well-suited for use on emerging supercomputing platforms that rely on graphical processing units…
Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of…
Key processes in biological and chemical systems are described by networks of chemical reactions. From molecular biology to biotechnology applications, computational models of reaction networks are used extensively to elucidate their…
The thermodynamic and dynamical conditions necessary to observe indefinite growth in homogeneous open chemical reaction networks (CRNs) satisfying mass action kinetics were presented in Srinivas et al. (2023): Unimolecular CRNs can only…
Robustness of biochemical systems has become one of the central questions in Systems Biology, although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the…
Principles of feedback control have been shown to naturally arise in biological systems and successfully applied to build synthetic circuits. In this work we consider Biochemical Reaction Networks (CRNs) as a paradigm for modelling…
The potential of synthetic biology techniques for designing complex cellular circuits able to solve complicated computations opens a whole domain of exploration, beyond experiments and theory. Such cellular circuits could be used to carry…
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…
We present a novel method for identifying a biochemical reaction network based on multiple sets of estimated reaction rates in the corresponding reaction rate equations arriving from various (possibly different) experiments. The current…
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…
Dynamical systems in biology are complex, and one often does not have comprehensive knowledge about the interactions involved. Chemical reaction network (CRN) inference aims to identify, from observing species concentrations over time, the…
We investigate the dynamics of chemical reaction networks (CRNs) with the goal of deriving an upper bound on their reaction rates. This task is challenging due to the nonlinear nature and discrete structure inherent in CRNs. To address…
The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage,…
Computer algebra methods for analyzing reaction networks often rely on the assumption of mass-action kinetics, which transform the governing ODEs into polynomial systems amenable to techniques such as Gr\"obner basis computation and related…
In this work, we design a type of controller that consists of adding a specific set of reactions to an existing mass-action chemical reaction network in order to control a target species. This set of reactions is effective for both…
The evolution of the genome has led to very sophisticated and complex regulation. Because of the abundance of non-coding RNA (ncRNA) in the cell, different species will promiscuously associate with each other, suggesting collective dynamics…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…
The promise of chemical computation lies in controlling systems incompatible with traditional electronic micro-controllers, with applications in synthetic biology and nano-scale manufacturing. Computation is typically embedded in…