Petri nets: an introduction
Deterministic tree pushdown automata and monadic tree rewriting systems
Journal of Computer and System Sciences
Hyperedge replacement graph grammars
Handbook of graph grammars and computing by graph transformation
Information and Computation - Special issue on EXPRESS 1997
Well-structured transition systems everywhere!
Theoretical Computer Science
Decidable Approximations of Term Rewriting Systems
RTA '96 Proceedings of the 7th International Conference on Rewriting Techniques and Applications
Bottom-Up Tree Pushdown Automata and Rewrite Systems
RTA '91 Proceedings of the 4th International Conference on Rewriting Techniques and Applications
Theoretical Computer Science - Special issue: Computational systems biology
Computation: finite and infinite machines
Computation: finite and infinite machines
When ambients cannot be opened
Theoretical Computer Science - Foundations of software science and computation structures
On Reachability and Spatial Reachability in Fragments of BioAmbients
Electronic Notes in Theoretical Computer Science (ENTCS)
Applying the Graph Minor Theorem to the Verification of Graph Transformation Systems
CAV '08 Proceedings of the 20th international conference on Computer Aided Verification
Reachability Analysis in BioAmbients
Electronic Notes in Theoretical Computer Science (ENTCS)
The pathalyzer: a tool for analysis of signal transduction pathways
RECOMB'05 Proceedings of the 2005 joint annual satellite conference on Systems biology and regulatory genomics
Modelization and simulation of nano devices in nanok calculus
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Formal cell biology in biocham
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Petri nets for systems and synthetic biology
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Abstract interpretation of cellular signalling networks
VMCAI'08 Proceedings of the 9th international conference on Verification, model checking, and abstract interpretation
Reachability analysis in boxed ambients
ICTCS'05 Proceedings of the 9th Italian conference on Theoretical Computer Science
Deciding reachability in mobile ambients
ESOP'05 Proceedings of the 14th European conference on Programming Languages and Systems
Graph theory for rule-based modeling of biochemical networks
Transactions on Computational Systems Biology VII
Programming in Biomolecular Computation
Electronic Notes in Theoretical Computer Science (ENTCS)
Hunting distributed malware with the κ-calculus
FCT'11 Proceedings of the 18th international conference on Fundamentals of computation theory
Computational biology: a programming perspective
Formal modeling
Reachability problems in BioAmbients
Theoretical Computer Science
Complex functional rates in rule-based languages for biochemistry
Transactions on Computational Systems Biology XIV
Complex Functional Rates in the Modeling of Nano Devices (Extended Abstract)
Electronic Notes in Theoretical Computer Science (ENTCS)
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The κ -calculus is a formalism for modelling molecular biology where molecules are terms with internal state and sites, bonds are represented by shared names labelling sites, and reactions are represented by rewriting rules. Depending on the shape of the rewriting rules, a lattice of dialects of κ can be obtained. We analyze the expressive power of some of these dialects by focusing on the thin boundary between decidability and undecidability for problems like reachability and coverability.