Theoretical Computer Science - Special issue: Computational systems biology
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
Rule-Based Modelling, Symmetries, Refinements
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
nanoK: A calculus for the modeling and simulation of nano devices
Theoretical Computer Science
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
On the Relationship between η-Calculus and Finite Place/Transition Petri Nets
CONCUR 2009 Proceedings of the 20th International Conference on Concurrency Theory
The κ-Lattice: Decidability Boundaries for Qualitative Analysis in Biological Languages
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Dynamic Compartments in the Imperative Π-Calculus
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
QEST '09 Proceedings of the 2009 Sixth International Conference on the Quantitative Evaluation of Systems
Modelization and simulation of nano devices in nanok calculus
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Efficient, correct simulation of biological processes in the stochastic pi-calculus
CMSB'07 Proceedings of the 2007 international conference on Computational methods in 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
Abstract interpretation of cellular signalling networks
VMCAI'08 Proceedings of the 9th international conference on Verification, model checking, and abstract interpretation
Abstracting the Differential Semantics of Rule-Based Models: Exact and Automated Model Reduction
LICS '10 Proceedings of the 2010 25th Annual IEEE Symposium on Logic in Computer Science
Biochemical reaction rules with constraints
ESOP'11/ETAPS'11 Proceedings of the 20th European conference on Programming languages and systems: part of the joint European conferences on theory and practice of software
Beta binders for biological interactions
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
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We give an overview of recent work on the rule-based modeling of nano devices. In particular, our experience in the modeling of a nanoscale elevator suggested us to enhance rule-based modeling with complex functional rates that can be used to express rates that depend on the current state of the entire complexes in which the reacting molecules reside.