Related papers: Nets with Mana: A Framework for Chemical Reaction …
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…
The ability to reason beyond established knowledge allows Organic Chemists to solve synthetic problems and to invent novel transformations. Here, we propose a model which mimics chemical reasoning and formalises reaction prediction as…
The Bond Graph approach and the Chemical Reaction Network approach to modelling biomolecular systems developed independently. This paper brings together the two approaches by providing a bond graph interpretation of the chemical reaction…
A compositional Petri net-based semantics is given to a simple language allowing pointer manipulation and parallelism. The model is then applied to give a notion of validity to the judgements made by concurrent separation logic that…
The reachability semantics for Petri nets can be studied using open Petri nets. For us an "open" Petri net is one with certain places designated as inputs and outputs via a cospan of sets. We can compose open Petri nets by gluing the…
Motor enzymes catalyze chemical reactions, like the hydrolysis of ATP, and in the process they also perform work. Recent studies indicate that motor enzymes perform work with specific intermediate steps in their catalyzed reactions,…
Recent work by the authors equips Petri occurrence nets (PN) with probability distributions which fully replace nondeterminism. To avoid the so-called confusion problem, the construction imposes additional causal dependencies which restrict…
The dynamics of a chemical reaction network (CRN) is often modelled under the assumption of mass action kinetics by a system of ordinary differential equations (ODEs) with polynomial right-hand sides that describe the time evolution of…
Continuous-time Markov chains are frequently used as stochastic models for chemical reaction networks, especially in the growing field of systems biology. A fundamental problem for these Stochastic Chemical Reaction Networks (SCRNs) is to…
Finding representative reaction pathways is necessary for understanding mechanisms of molecular processes, but is considered to be extremely challenging. We propose a new method to construct reaction paths based on mean first-passage times.…
We propose a framework for reasoning about unbounded dynamic networks of infinite-state processes. We propose Constrained Petri Nets (CPN) as generic models for these networks. They can be seen as Petri nets where tokens (representing…
A cell has the ability to convert an environmental change into the expression of genetic information through a chain of intracellular signal transduction reactions. Here, we aimed to develop a method for quantifying this signal…
At the microscopic scale, open chemical reaction networks are described by stochastic reactions that follow mass-action kinetics and are coupled to chemostats. We show that closed chemical reaction networks -- with specific stoichiometries…
Chemical reaction networks describe interactions between biochemical species. Once an underlying reaction network is given for a biochemical system, the system dynamics can be modelled with various mathematical frameworks such as continuous…
Supply chains involve geographically distributed manufacturing and assembly sites that must be coordinated under strict timing and resource constraints. While many existing approaches rely on Colored Petri Nets to model material flows, this…
Reaction networks are mainly used to model the time-evolution of molecules of interacting chemical species. Stochastic models are typically used when the counts of the molecules are low, whereas deterministic models are used when the counts…
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…
For two molecules to react they first have to meet. Yet, reaction times are rarely on par with the first-passage times that govern such molecular encounters. A prime reason for this discrepancy is stochastic transitions between reactive and…
The analysis of the structure of chemical reaction networks is crucial for a better understanding of chemical processes. Such networks are well described as hypergraphs. However, due to the available methods, analyses regarding network…
We discuss a method to describe the qualitative dynamics of chemical reaction networks in terms of symbolic dynamics. The method, that can be applied to mass-action reaction networks with separated timescales, uses solutions of the partial…