Related papers: Nets with Mana: A Framework for Chemical Reaction …
This paper presents new results about the optimization based generation of chemical reaction networks (CRNs) of higher deficiency. Firstly, it is shown that the graph structure of the realization containing the maximal number of reactions…
Energy functions for pure and heterogenous systems are one of the backbones for molecular simulation of condensed phase systems. With the advent of machine learned potential energy surfaces (ML-PESs) a new era has started. Statistical…
In this article we contribute to the moment analysis of branching processes in catalytic media. The many-to-few lemma based on the spine technique is used to derive a system of (discrete space) partial differential equations for the number…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…
Quantum hydrodynamics is the emergent classical dynamics governing transport of conserved quantities in generic strongly-interacting quantum systems. Recent matrix product operator methods have made simulations of quantum hydrodynamics in…
Chemical reaction network theory is a field of applied mathematics concerned with modeling chemical systems, and can be used in other contexts such as in systems biology to study cellular signaling pathways or epidemiology to study the…
Autocatalytic chemical reaction networks can collectively replicate or maintain their constituents despite degradation reactions only above a certain threshold, which we refer to as the decay threshold. When the chemical network has a…
Petri Nets (PN) are widely used for modeling concurrent and distributed systems, but face challenges in modeling adaptive systems. To address this, we have formalized "rewritable" PT nets (RwPT) using Maude, a declarative language with…
In the late 1970s, C.A. Petri introduced partially ordered event occurrences (runs), then called \emph{processes}, as the appropriate model to describe the individual evolutions of distributed systems. Here, we present a unified framework…
Reversing Petri nets (RPNs) have recently been proposed as a net-basedapproach to model causal and out-of-causal order reversibility. They are based on the notion of individual tokens that can be connected together via bonds. In this paper…
An inverse problem framework for constructing reaction systems with prescribed properties is presented. Kinetic transformations are defined and analysed as a part of the framework, allowing an arbitrary polynomial ordinary differential…
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…
Developing accurate models for chemical reactors is often challenging due to the complexity of reaction kinetics and process dynamics. Traditional approaches require retraining models for each new system, limiting generalizability and…
We classify all additive invariants of open Petri nets: these are $\mathbb{N}$-valued invariants which are additive with respect to sequential and parallel composition of open Petri nets. In particular, we prove two classification theorems:…
In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses…
The analysis of biological networks has benefited from the richness of Boolean networks (BNs) and the associated theory. These results have been further fortified in recent years by the emergence of Most Permissive (MP) semantics, combining…
We investigate bisimulation equivalence on Petri nets under durational semantics. Our motivation was to verify the conjecture that in durational setting, the bisimulation equivalence checking problem becomes more tractable than in ordinary…
This article characterizes certain small multistationary chemical reaction networks. We consider the set of fully open networks, those for which all chemical species participate in inflow and outflow, containing one non-flow (reversible or…
Reversible computations constitute an unconventional form of computing where any sequence of performed operations can be undone by executing in reverse order at any point during a computation. It has been attracting increasing attention as…