相关论文: Computing Threshold Circuits with Bimolecular Void…

Chemical reaction networks, or CRNs, are known to stably compute semilinear Boolean-valued predicates and functions, provided that all reactions are irreversible. However, this property does not hold for wet-lab implementations, as all…

The Turing completeness of continuous chemical reaction networks (CRNs) states that any computable real function can be computed by a continuous CRN on a finite set of molecular species, possibly restricted to elementary reactions, i.e.…

Well-mixed chemical reaction networks (CRNs) contain many distinct chemical species with copy numbers that fluctuate in correlated ways. While those correlations are typically monitored via Monte Carlo sampling of stochastic trajectories,…

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…

Similarly to gear systems in vehicles, most chemical reaction networks (CRNs) involved in energy transduction have at their disposal multiple transduction pathways, each characterized by distinct efficiencies. We conceptualize these…

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…

One of the puzzles left open by energetic analyses of irreversible stochastic processes is that boundary conditions that prevent the performance of work or the dissipation of heat make no contribution to an entropy-production budget; yet we…

In most natural sciences there is currently the insight that it is necessary to bridge gaps between different processes which can be observed on different scales. This is especially true in the field of chemical reactions where the…

Bistability plays a central role in the gene regulatory networks (GRNs) controlling many essential biological functions, including cellular differentiation and cell cycle control. However, establishing the network topologies that can…

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…

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…

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…

A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as…

The stochastic kinetics of BRN are described by a chemical master equation (CME) and the underlying laws of mass action. The CME must be usually solved numerically by generating enough traces of random reaction events. The resulting…

Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad protein-protein interactions and post-translational…

We propose a Kron-based model-order reduction method for mass-action kinetics chemical reaction networks (CRN) with constant inflow and proportional outflow. The reduced-order models preserve the CRN structure and we establish that the…

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…

We classify the functions $f:\mathbb{N}^2 \rightarrow \mathbb{N}$ which are stably computable by output-oblivious Stochastic Chemical Reaction Networks (CRNs), i.e., systems of reactions in which output species are never reactants. While it…

Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemical knowledge. A first key step for rule learning is the…

Model reduction of fast-slow chemical reaction networks based on the quasi-steady state approximation fails when the fast subsystem has first integrals. We call these first integrals approximate conservation laws. In order to define fast…