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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…
Classical Petri nets provide a canonical model of concurrency, with unfolding semantics linking nets, occurrence nets, and event structures. No comparable framework exists for quantum concurrency: existing ''quantum Petri nets'' lack…
We present a computational procedure to characterize the signs of sensitivities of steady states to parameter perturbations in chemical reaction networks.
The exploration of pathways and alternative pathways that have a specific function is of interest in numerous chemical contexts. A framework for specifying and searching for pathways has previously been developed, but a focus on which of…
Process mining is concerned with deriving formal models capable of reproducing the behaviour of a given organisational process by analysing observed executions collected in an event log. The elements of an event log are finite sequences…
Petri Net is a formalism to describe changes between 2 or more states across discrete time and has been used to model many systems. We present PNet - a pure Python library for Petri Net modeling and simulation in Python programming…
We propose a new method for computing the language intersection of two Time Petri nets (TPN); that is the sequence of labels in timed traces common to the execution of two TPN. Our approach is based on a new product construction between…
Electric circuits manipulate electric charge and magnetic flux via a small set of discrete components to implement useful functionality over continuous time-varying signals represented by currents and voltages. Much of the same…
This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…
Classical Petri nets provide a canonical model of concurrency, with unfolding semantics linking nets, occurrence nets, and event structures. No comparable framework exists for quantum concurrency: existing ''quantum Petri nets'' lack…
The calculation of reactive properties is a challenging task in chemical reaction discovery. Machine learning (ML) methods play an important role in accelerating electronic structure predictions of activation energies and reaction…
The concept of (auto)catalytic systems has become a cornerstone in understanding evolutionary processes in various fields. The common ground is the observation that for the production of new species/goods/ideas/elements etc. the…
Chemical kinetics plays an important role in governing the thermal evolution in reactive flows problems. The possible interactions between chemical species increase drastically with the number of species considered in the system. Various…
A chemical reaction network (CRN) is composed of reactions that can be seen as interactions among entities called species, which exist within the system. Endowed with kinetics, CRN has a corresponding set of ordinary differential equations…
To what extent do the characteristic features of a chemical reaction network reflect its purpose and function? In general, one argues that correlations between specific features and specific functions are key to understanding a complex…
In many scientific fields, there is an interest in understanding the way in which complex chemical networks evolve. The chemical networks which researchers focus upon, have become increasingly complex and this has motivated the development…
Reversible computation is an unconventional form of computing where any executed sequence of operations can be executed in reverse at any point during computation. It has recently been attracting increasing attention in various research…
Thermodynamic aspects of chemical reactions have a long history in the Physical Chemistry literature. In particular, biochemical cycles - the building-blocks of biochemical systems - require a source of energy to function. However, although…
We consider stochastic models of chemical reaction networks with time dependent input rates and several types of molecules. We prove that, in despite of strong time dependence of input rates, there is a kind of homeostasis phenomenon: far…
In this paper, we propose a novel technique, referred to as the Lyapunov Function PDEs technique, to diagnose persistence of chemical reaction networks with mass-action kinetics. The technique allows that every network is attached to a…