Related papers: Compiling Elementary Mathematical Functions into F…
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…
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…
Information processing relying on biochemical interactions in the cellular environment is essential for biological organisms. The implementation of molecular computational systems holds significant interest and potential in the fields of…
The class of functions from the integers to the integers computable in polynomial time has been characterized recently using discrete ordinary differential equations (ODE), also known as finite differences. In the framework of ordinary…
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…
Mathematical modelling has traditionally relied on detailed system knowledge to construct mechanistic models. However, the advent of large-scale data collection and advances in machine learning have led to an increasing use of data-driven…
Chemical reaction networks (CRNs) are fundamental computational models used to study the behavior of chemical reactions in well-mixed solutions. They have been used extensively to model a broad range of biological systems, and are primarily…
Artificial neural networks (NNs) can be implemented using chemical reaction networks (CRNs), where the concentrations of species act as inputs and outputs. In such biochemical computing, noise-robust computing is crucial due to the…
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,…
We establish a generalized work theorem for stochastic chemical reaction networks (CRNs). By using a compensated Poisson jump process, we identify a martingale structure in a generalized entropy defined relative to an auxiliary backward…
Marcello, in 1997, formally proved that chemical kinetics can make a universal computer i.e they can replicate any digital circuit. Recently, Soloveichik et al. showed that chemical kinetics can perform fast and reliable Turing Universal…
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…
MC networks are envisioned to enable synthetic information exchange between nanoscale biological entities. For many algorithm proposals in the MC research field, the question of implementation at nanoscales and in biological environments…
Molecular computation based on chemical reaction networks (CRNs) has emerged as a promising paradigm for designing programmable biochemical systems. However, the implementation of complex computations still requires excessively large and…
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 $m \geq 1$.…
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…
For polynomial ODE models, we introduce and discuss the concepts of exact and approximate conservation laws, which are the first integrals of the full and truncated sets of ODEs. For fast-slow systems, truncated ODEs describe the fast…
The study of Chemical Reaction Networks (CRN's) is a very active field. Earlier well-known results \cite{Feinberg:def_01:87, Anderson:product_dist:10} identify a topological quantity called deficiency, for any CRN, which, when exactly equal…
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,…
Reconstruction of biochemical reaction networks is a central topic in systems biology which raises crucial theoretical challenges in system identification. Nonlinear Ordinary Differential Equations (ODEs) that involve polynomial and…