Related papers: Reachability in Restricted Chemical Reaction Netwo…
Temporal networks are a class of time-varying networks, which change their topology according to a given time-ordered sequence of static networks (known as subsystems). This paper investigates the reachability and controllability of…
Chemical reaction networks (CRNs) are a standard formalism used in chemistry and biology to reason about the dynamics of molecular interaction networks. In their interpretation by ordinary differential equations, CRNs provide a…
We use real-world contact sequences, time-ordered lists of contacts from one person to another, to study how fast information or disease can spread across network of contacts. Specifically we measure the reachability time -- the average…
Inferring chemical reaction networks (CRN) from concentration time series is a challenge encouragedby the growing availability of quantitative temporal data at the cellular level. This motivates thedesign of algorithms to infer the…
Regular model checking is a well-established technique for the verification of regular transition systems (RTS): transition systems whose initial configurations and transition relation can be effectively encoded as regular languages. In…
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…
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…
A control system consists of a plant component and a controller which periodically computes a control input for the plant. We consider systems where the controller is implemented by a feedforward neural network with ReLU activations. The…
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…
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…
Stochastic evolution of Chemical Reactions Networks (CRNs) over time is usually analysed through solving the Chemical Master Equation (CME) or performing extensive simulations. Analysing stochasticity is often needed, particularly when some…
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…
Chemical reaction networks (CRNs) provide a convenient language for modelling a broad variety of biological systems. These models are commonly studied with respect to the time series they generate in deterministic or stochastic simulations.…
Unordered data Petri nets (UDPN) are an extension of classical Petri nets with tokens that carry data from an infinite domain and where transitions may check equality and disequality of tokens. UDPN are well-structured, so the coverability…
Many reaction networks arising in applications are multistationary, that is, they have the capacity for more than one steady state; while some networks exhibit absolute concentration robustness (ACR), which means that some species…
Informally, a chemical reaction network is "atomic" if each reaction may be interpreted as the rearrangement of indivisible units of matter. There are several reasonable definitions formalizing this idea. We investigate the computational…
We investigate a class of stochastic chemical reaction networks with $n{\ge}1$ chemical species $S_1$, \ldots, $S_n$, and whose complexes are only of the form $k_iS_i$, $i{=}1$,\ldots, $n$, where $(k_i)$ are integers. The time evolution of…
A frequent problem in settings where a unique resource must be shared among users is how to resolve the contention that arises when all of them must use it, but the resource allows only for one user each time. The application of efficient…
Neural networks achieve outstanding accuracy in classification and regression tasks. However, understanding their behavior still remains an open challenge that requires questions to be addressed on the robustness, explainability and…
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…