Related papers: Pathway Realisability in Chemical Networks
Here we focus on the challenge of verifying the correctness of molecular implementations of abstract chemical reaction networks, where operation in a well-mixed "soup" of molecules is stochastic, asynchronous, concurrent, and often involves…
Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This work presents a computational methodology for searching for…
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…
For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These…
Sampled structure sequences obtained, for instance, from real-time reactivity explorations or first-principles molecular dynamics simulations contain valuable information about chemical reactivity. Eventually, such sequences allow for the…
We present an elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level. Networks are modelled mathematically as directed multi-hypergraphs, with vertices corresponding to molecules and…
The search for pathways that optimize the formation of a particular target molecule in a reaction network is a key problem in many settings, including reactor systems. Chemical reaction networks are mathematically well represented as…
Chemical reaction networks (CRNs) model the behavior of molecules in a well-mixed system. The emerging field of molecular programming uses CRNs not only as a descriptive tool, but as a programming language for chemical computation.…
In this paper we introduce a new network reachability problem where the goal is to find the most reliable path between two nodes in a network, represented as a directed acyclic graph. Individual edges within this network may fail according…
Modular verification is a technique used to face the state explosion problem often encountered in the verification of properties of complex systems such as concurrent interactive systems. The modular approach is based on the observation…
Neural networks have demonstrated a wide range of successes, but their ``black box" nature raises concerns about transparency and reliability. Previous research on ReLU networks has sought to unwrap these networks into linear models based…
In this paper we investigate the reachability and observability properties of a network system, running a Laplacian based average consensus algorithm, when the communication graph is a path or a cycle. More in detail, we provide necessary…
We introduce a novel technique for checking reachability in Petri nets that relies on a recently introduced compositional algebra of nets. We prove that the technique is correct, and discuss our implementation. We report promising…
We define the idea of {\it real path quantum theory}, a realist generalisation of quantum theory in which it is postulated that the configuration space path actually followed by a closed quantum system is probabilistically chosen. This is…
Programmable photonic integrated circuits (PPICs) are an emerging technology recently proposed as an alternative to custom-designed application-specific integrated photonics. Light routing is one of the most important functions that need to…
Answering realistic questions about biological systems and pathways similar to the ones used by text books to test understanding of students about biological systems is one of our long term research goals. Often these questions require…
Detectability describes the property of a system whose current and the subsequent states can be uniquely determined after a finite number of observations. In this paper, we developed a novel approach to verifying strong detectability and…
We investigate Petri nets with data, an extension of plain Petri nets where tokens carry values from an infinite data domain, and executability of transitions is conditioned by equalities between data values. We provide a decision procedure…
In a previous paper we introduced immediate observation Petri nets, a subclass of Petri nets with application domains in distributed protocols (population protocols) and theoretical chemistry (chemical reaction networks). IO nets enjoy many…
A fundamental problem in the study of complex networks is to provide quantitative measures of correlation and information flow between different parts of a system. To this end, several notions of communicability have been introduced and…