Related papers: Robust Biomolecular Finite Automata
While the field of first-principles explorations into chemical reaction space has been continuously growing, the development of strategies for analyzing resulting chemical reaction networks (CRNs) is lagging behind. A CRN consists of…
History-deterministic automata are those in which nondeterministic choices can be correctly resolved stepwise: there is a strategy to select a continuation of a run given the next input letter so that if the overall input word admits some…
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…
A process algebra is proposed, whose semantics maps a term to a nondeterministic finite automaton (NFA, for short). We prove a representability theorem: for each NFA $N$, there exists a process algebraic term $p$ such that its semantics is…
Weighted finite automata (WFA) can expressively model functions defined over strings but are inherently linear models. Given the recent successes of nonlinear models in machine learning, it is natural to wonder whether ex-tending WFA to the…
In a previous work, we introduced an input/output variant of stochastic automata (IOSA) that, once the model is closed (i.e., all synchronizations are resolved), the resulting automaton is fully stochastic, that is, it does not contain…
Cataloging the complex behaviors of dynamical systems can be challenging, even when they are well-described by a simple mechanistic model. If such a system is of limited analytical tractability, brute force simulation is often the only…
We show that some natural output conventions for error-free computation in chemical reaction networks (CRN) lead to a common level of computational expressivity. Our main results are that the standard consensus-based output convention have…
1-way quantum finite automata are deterministic and reversible in nature, which greatly reduces its accepting property. In fact the set of languages accepted by 1-way quantum finite automata is a proper subset of regular languages. In this…
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…
We propose a fully autonomous, thermodynamically consistent set of chemical reactions that implements a spiking neuron. This chemical neuron is able to learn input patterns in a Hebbian fashion. The system is scalable to arbitrarily many…
We propose an automaton model which is a combination of symbolic and register automata, i.e., we enrich symbolic automata with memory. We call such automata Register Match Automata (RMA). RMA extend the expressive power of symbolic…
Living systems operate out of equilibrium, continuously consuming energy to sustain organised, functional states. Their emergent behaviour usually relies on a set of interconnected chemical reaction networks (CRNs) driven by external fluxes…
A general methodology is proposed to engineer a system of interacting components (particles) which is able to self-regulate their concentrations in order to produce any prescribed output in response to a particular input. The methodology is…
Here we propose an extension of the (deterministic and the nondeterministic) finite automaton with translucent letters (DFAwtl and NFAwtl), which lies between these automata and their non-returning variants (that is, the nr-DFAwtl and the…
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,…
We present the open-source tool finsm.io, a tool for creating, simulating and exporting deterministic and non-deterministic finite state automata (DFA/NFA). We first describe the conceptual background on which the tool is based, followed by…
Recent research in both the experimental and mathematical communities has focused on biochemical interaction systems that satisfy an "absolute concentration robustness" (ACR) property. The ACR property was first discovered experimentally…
Proposals for molecular communication networks as part of a future internet of bio-nano-things have become more intricate and the question of practical implementation is gaining more importance. One option is to apply detailed chemical…
We observe that the classical Cartesian product construction for the intersection of (languages of) nondeterministic finite automata (NFA) is non-optimal in the worst case, if the automata have many transitions. For a fixed alphabet, the…