Abstract
We develop a process calculus – the nano κ Calculus – for modeling, analyzing and predicting the properties of molecular devices. The nano κ Calculus is equipped with a simple stochastic model, that we use to model and simulate the behaviour of a molecular shuttle, a basic nano device currently used for building more complex systems.
This is a preview of subscription content, log in via an institution to check access.
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Ashton, P.R., Ballardini, R., Balzani, V., Credi, A., Baxter, I., Fyfe, M.C.T., Gandolfi, M.T., Gómez-López, M., Martínez-Díaz, M.-V., Piersanti, A., Spencer, N., Stoddart, J.F., Venturi, M., White, A.J.P., Williams, D.J.: Acid-base controllable molecular shuttles. Journal of Am. Chem. Soc. 120, 11932–11942 (1998)
Badjic, J.D., Balzani, V., Credi, A., Silvi, S., Stoddart, J.F.: A molecular elevator. Science 303, 1845–1849 (2004)
Balzani, V., Credi, A., Venturi, M.: Molecular devices and machines – concepts and perspectives for the nano world. Wiley-VCH, Weinheim (2007)
Cardelli, L.: On process rate semantics (2007)
Cardelli, L., Phillips, A.: Spim homepage At (2006), research.microsoft.com/~aphillip/spim/
Champin, B., Mobian, P., Sauvage, J.-P.: Transition metal complexes as molecular machine prototypes. Chemical Society Reviews 36(2), 358–366 (2006)
Danos, V., Laneve, C.: Formal molecular biology. Theoretical Computer Science 325(1), 69–110 (2004)
Garaudée, S., Silvi, S., Venturi, M., Credi, A., Flood, A.H., Stoddart, J.F.: Shuttling dynamics in an acid-base-switchable [2] rotaxane. Chem. Phys. Chem. 6, 2145 (2005)
Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340–2361 (1977)
Gilmore, S., Hillston, J.: The pepa workbench: a tool to support a process algebra-based approach to performance modelling. In: Proc. of the 7th int. conference on Computer performance evaluation: modelling techniques and tools, Secaucus, NJ, USA, pp. 353–368. Springer, New York (1994)
Hermanns, H.: Interactive Markov Chains. LNCS, vol. 2428. Springer, Heidelberg (2002)
Huang, T.-J., Brough, B., Ho, C.-M., Liu, Y., Flood, A.H., Bonvallet, P.A., Tseng, H.-R., Stoddart, J.F., Baller, M., Magonov, S.: A nanomechanical device based on linear molecular motors. Applied Physics Letters 85(22), 5391–5393 (2004)
Jimenez, M.C., Dietrich-Buchecker, C., Sauvage, J.-P.: Towards synthetic molecular muscles: Contraction and stretching of a linear rotaxane dimer. Angew. Chem. Int. Ed. 39(18), 3284–3287 (2000)
Laneve, C., Tarissan, F.: A simple calculus of protein and cells. In: Proceeding of MeCBIC 2006. ENTCS, vol. 1677 (2007)
Martínez-Díaz, M.-V., Spencer, N., Stoddart, J.F.: The self-assembly of a switchable [2]rotaxane. Angew. Chem. Int. Ed. Engl. 36, 1904–1907 (1997)
Milner, R.: Communicating and mobile systems: the π-calculus. Cambridge University Press, Cambridge (1999)
Plotkin, G.D.: A Structural Approach to Operational Semantics. Technical Report DAIMI FN-19, University of Aarhus (1981)
Priami, C.: Stochastic pi-calculus. Computer Journal 38(7), 578–589 (1995)
Priami, C., Regev, A., Shapiro, E., Silverman, W.: Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters 80, 25–31 (2001)
Sauvage, J.-P., Dietrich-Bucheker, C.O. (eds.): Molecular catenanes, rotaxanes and knots. Wiley-VCH, Weinheim (1999)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Credi, A., Garavelli, M., Laneve, C., Pradalier, S., Silvi, S., Zavattaro, G. (2007). Modelization and Simulation of Nano Devices in nano κ Calculus. In: Calder, M., Gilmore, S. (eds) Computational Methods in Systems Biology. CMSB 2007. Lecture Notes in Computer Science(), vol 4695. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-75140-3_12
Download citation
DOI: https://doi.org/10.1007/978-3-540-75140-3_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-75139-7
Online ISBN: 978-3-540-75140-3
eBook Packages: Computer ScienceComputer Science (R0)