A Molecular Elevator, Science, vol.303, issue.5665, pp.1845-1849, 2004. ,
DOI : 10.1126/science.1094791
Molecular devices and machines - Concepts and perspectives for the nano world, 2008. ,
BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains, Bioinformatics, vol.20, issue.17, p.3289, 2004. ,
DOI : 10.1093/bioinformatics/bth378
Efficient formulation of the stochastic simulation algorithm for chemically reacting systems, The Journal of Chemical Physics, vol.121, issue.9, pp.4059-4067, 2004. ,
DOI : 10.1063/1.1778376
Brane Calculi, Danos and Schächter [15], pp.257-278 ,
DOI : 10.1016/S0020-0190(01)00214-9
Transition metal complexes as molecular machine prototypes, Chem. Soc. Rev., vol.289, issue.19, pp.358-366, 2006. ,
DOI : 10.1039/B604484K
The Bio-PEPA Tool Suite, 2009 Sixth International Conference on the Quantitative Evaluation of Systems, pp.309-310, 2009. ,
DOI : 10.1109/QEST.2009.27
Modelizations and simulations of nano devices in nanok calculus, LNCS, vol.4695, pp.168-183, 2007. ,
URL : https://hal.archives-ouvertes.fr/inria-00241554
<mml:math altimg="si2.gif" display="inline" overflow="scroll" xmlns:xocs="http://www.elsevier.com/xml/xocs/dtd" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.elsevier.com/xml/ja/dtd" xmlns:ja="http://www.elsevier.com/xml/ja/dtd" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:tb="http://www.elsevier.com/xml/common/table/dtd" xmlns:sb="http://www.elsevier.com/xml/common/struct-bib/dtd" xmlns:ce="http://www.elsevier.com/xml/common/dtd" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:cals="http://www.elsevier.com/xml/common/cals/dtd"><mml:mstyle mathvariant="monospace"><mml:mi>nano</mml:mi></mml:mstyle><mml:mi>??</mml:mi></mml:math>: A calculus for the modeling and simulation of nano devices, Theoretical Computer Science, vol.408, issue.1, pp.17-30, 2008. ,
DOI : 10.1016/j.tcs.2008.07.006
Rule-Based Modelling, Symmetries, Refinements, FMSB, pp.103-122, 2008. ,
DOI : 10.1007/978-3-540-68413-8_8
URL : https://hal.archives-ouvertes.fr/inria-00528339
Abstracting the Differential Semantics of Rule-Based Models: Exact and Automated Model Reduction, 2010 25th Annual IEEE Symposium on Logic in Computer Science, pp.362-381, 2010. ,
DOI : 10.1109/LICS.2010.44
URL : https://hal.archives-ouvertes.fr/hal-00520112
Abstract Interpretation of Cellular Signalling Networks, VMCAI, pp.83-97, 2008. ,
DOI : 10.1007/978-3-540-78163-9_11
URL : https://hal.archives-ouvertes.fr/inria-00528352
Formal molecular biology, Theoretical Computer Science, vol.325, issue.1, pp.69-110, 2004. ,
DOI : 10.1016/j.tcs.2004.03.065
URL : https://hal.archives-ouvertes.fr/hal-00164591
The kappa-lattice: Decidability boundaries for qualitative analysis in biological languages, Degano and Gorrieri [16], pp.158-172 ,
Formal Cell Biology in Biocham, Formal Cell Biology in Biocham. In SFM Lecture Notes in Computer Science, vol.5016, pp.54-80, 2008. ,
DOI : 10.1007/978-3-540-68894-5_3
Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels, The Journal of Physical Chemistry A, vol.104, issue.9, pp.1876-1889, 2000. ,
DOI : 10.1021/jp993732q
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, vol.19, issue.4, pp.524-531, 2003. ,
DOI : 10.1093/bioinformatics/btg015
Towards Synthetic Molecular Muscles: Contraction and Stretching of a Linear Rotaxane Dimer, Angewandte Chemie, vol.8, issue.18, pp.3284-3287, 2000. ,
DOI : 10.1002/1521-3773(20000915)39:18<3284::AID-ANIE3284>3.0.CO;2-7
Dynamic compartments in the imperative pi-calculus, pp.235-250 ,
URL : https://hal.archives-ouvertes.fr/inria-00422970
The Attributed Pi Calculus, Lecture Notes in Computer Science, vol.5307, pp.83-102, 2008. ,
DOI : 10.1007/978-3-540-88562-7_10
URL : https://hal.archives-ouvertes.fr/inria-00308970
Biochemical Reaction Rules with Constraints, Lecture Notes in Computer Science, vol.411, issue.2, pp.338-357, 2011. ,
DOI : 10.1007/978-3-540-71316-6_28
URL : https://hal.archives-ouvertes.fr/inria-00544387
On the Relationship between ??-Calculus and Finite Place/Transition Petri Nets, Lecture Notes in Computer Science, vol.46, issue.2, pp.463-480, 2009. ,
DOI : 10.1007/3-540-60218-6_4
Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus, CMSB, pp.184-199, 2007. ,
DOI : 10.1007/978-3-540-75140-3_13
Beta Binders for Biological Interactions, Danos and Schächter [15], pp.20-33 ,
DOI : 10.1016/S0020-0190(01)00214-9
BioAmbients: an abstraction for biological compartments, Theoretical Computer Science, vol.325, issue.1, pp.141-167, 2004. ,
DOI : 10.1016/j.tcs.2004.03.061
Efficient modeling, simulation and coarse-graining of biological complexity with NFsim, Nature Methods, vol.104, issue.2, p.177183, 2011. ,
DOI : 10.1038/nmeth.1546
Complex Functional Rates in Rule-Based Languages for Biochemistry, Biochemistry. Transactions on Computational Systems Biology ,
DOI : 10.1007/978-3-642-35524-0_6
URL : https://hal.archives-ouvertes.fr/hal-00825138