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Browsing by Author "Egri-Nagy, A."
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Algebraic analysis of the computation in the Belousov-Zhabotinsky reaction
Dini, P.; Nehaniv, C.L.; Egri-Nagy, A.; Schilstra, M. (Springer Nature, 2012)We analyse two very simple Petri nets inspired by the Oregonator model of the Belousov-Zhabotinsky reaction using our stochastic Petri net simulator. We then perform the Krohn-Rhodes holonomy decomposition of the automata ... -
Algebraic properties of automata associated to Petri nets and applications to computation in biological systems
Egri-Nagy, A.; Nehaniv, C.L. (2008)Biochemical and genetic regulatory networks are often modeled by Petri nets. We study the algebraic structure of the computations carried out by Petri nets from the viewpoint of algebraic automata theory. Petri nets comprise ... -
Automatic Analysis of Computation in BioChemical Reactions
Egri-Nagy, A.; Nehaniv, C.L.; Rhodes, J.L.; Schilstra, M. (2008)We propose a modeling and analysis method for biochemical reactions based on finite state automata. This is a completely different approach compared to traditional modeling of reactions by differential equations. Our method ... -
The NetBuilder project: development of a tool for constructing, simulating, evolving, and analysing complex regulatory networks
Wegner, K.; Knabe, J.; Robinson, M.; Egri-Nagy, A.; Schilstra, M. (2007) -
On straight words and minimal permutators in finite transformation semigroups.
Egri-Nagy, A.; Nehaniv, C.L. (Springer, 2011)Motivated by issues arising in computer science, we investigate the loop-free paths from the identity transformation and corresponding straight words in the Cayley graph of a finite transformation semigroup with a fixed ... -
On the skeleton of a finite transformation semigroup
Egri-Nagy, A.; Nehaniv, C.L. (2010)There are many ways to construct hierarchical decompositions of transformation semigroups. The holonomy algorithm is especially suitable for computational implementations and it is used in our software package. The structure ...