A Geometrical Refinement of Shape Calculus Enabling Direct Simulation

Federico Buti, Flavio Corradini, Emanuela Merelli, Luca Tesei

2012

Abstract

The Shape Calculus is a bio-inspired timed and spatial calculus for describing 3D geometrical shapes moving in a space. Its purpose is twofold: i) modelling and formally verifying (not only) biological systems, and ii) simulating the models for validation and hypothesis testing. The original geometric primitives of the calculus are highly abstract: the associated simulator needs to attach a lot of code to the model specification in order to perform an effective simulation. In this work we propose a calculus refinement in which a detailed 3D characterization of the geometric primitives is injected into the syntax of the calculus. In this way, models written with the new syntax can be directly simulated.

References

  1. Aleksandrov, A. D. (2005). Convex polyhedra. Springer monographs in mathematics. Springer.
  2. Bartocci, E., Cacciagrano, D. R., Berardini, M. R. D., Merelli, E., and Tesei, L. (2010a). Timed operational semantics and well-formedness of shape calculus. Sci. Ann. Comp. Sci., 20:32-52.
  3. Bartocci, E., Corradini, F., Berardini, M. R. D., Merelli, E., and Tesei, L. (2010b). Shape calculus. a spatial mobile calculus for 3d shapes. Sci. Ann. Comp. Sci., 20:1-31.
  4. Belov, G. (2002). A modified algorithm for convex decomposition of 3d polyhedra. Technical Report MATH-NM-03-2002, Institut fü r Numerische Mathematik,Technische Universität, Dresden. http://www.math.tu-dresden.de/ belov/cd3/cd3.ps.
  5. Buti, F., Cacciagrano, D. R., Callisto De Donato, M., Corradini, F., Merelli, E., and Tesei, L. (2011a). Bioshape: End-user development for simulating biological systems. In Costabile, M., Dittrich, Y., Fischer, G., and Piccinno, A., editors, End-User Development, volume 6654 of Lecture Notes in Computer Science, pages 379-382. Springer Berlin / Heidelberg. 10.1007/978- 3-642-21530-8 45.
  6. Buti, F., Cacciagrano, D. R., Corradini, F., Merelli, E., and Tesei, L. (2010a). BioShape: a spatial shape-based scale-independent simulation environment for biological systems. Procedia Computer Science, 1(1):827- 835. Proc. of 7th Int. Workshop on Multiphysics Multiscale Systems, ICCS 2010.
  7. Buti, F., Cacciagrano, D. R., Corradini, F., Merelli, E., and Tesei, L. (To appear 2011b). A uniform multiscale meta-model of BioShape. Electronic Notes in Theoretical Computer Science. Proc. of Cs2Bio 2011, June 9th, Reykjavik, Iceland.
  8. Buti, F., Cacciagrano, D. R., Corradini, F., Merelli, E., Tesei, L., and Pani, M. (2010b). Bone Remodelling in BioShape. Electronic Notes in Theoretical Computer Science, 268:17-29. Proc. of CS2Bio 2010.
  9. Corradini, F. and Merelli, E. (2005). Hermes: Agent-based middleware for mobile computing. In Bernardo, M. and Bogliolo, A., editors, Formal Methods for Mobile Computing, volume 3465 of Lecture Notes in Computer Science, pages 234-270. Springer Berlin / Heidelberg.
  10. Cousot, P. and Cousot, R. (1977). Abstract interpretation: a unified lattice model for static analysis of programs by construction or approximation of fixpoints. In In Proc. of POPL'77, pages 238-252. ACM.
  11. Ericson, C. (2005). Real-time collision detection. Number v. 1 in Morgan Kaufmann Series in Interactive 3D Technology. Elsevier.
  12. Ferrari, M. (2005). Cancer nanotechnology: opportunities and challenges. Nature Reviews Cancer, 5(3):161- 171.
  13. Grupe, A., Germer, S., Usuka, J., Aud, D., Belknap, J. K., Klein, R. F., Ahluwalia, M. K., Higuchi, R., and Peltz, G. (2001). In Silico Mapping of Complex DiseaseRelated Traits in Mice. Science, 292(5523):1915- 1918.
  14. Hartman, J. and Wernecke, J. (1996). The VRML 2.0 handbook: building moving worlds on the web. Addison Wesley Longman Publishing Co., Inc., Redwood City, CA, USA.
  15. Hoffmann, C. M. (1989). Geometric and solid modeling: an introduction. Morgan Kaufmann series in computer graphics and geometric modeling. Morgan Kaufmann.
  16. Kawasaki, E. S. and Player, A. (2005). Nanotechnology, nanomedicine, and the development of new, effective therapies for cancer. Nanomedicine: Nanotechnology, Biology and Medicine, 1(2):101 - 109.
  17. Keil, J. M. (2000). Polygon decomposition. In Sack, J. and Urrutia, J., editors, Handbook of Computational Geometry, pages 491-518. Elsevier.
  18. Kitano, H. (2002). Systems biology: a brief overview. Science, 295(5560):1662-1664.
  19. Kumar, C. S. S. R. (2007). Nanomaterials for medical diagnosis and therapy. Nanotechnologies for the life sciences. Wiley-VCH.
  20. Lim, H. A. (2004). Nanotechnology in diagnostics and drug delivery. Medicinal Chemistry Research, 13(6- 7):401-413.
  21. Manos, S., Zasada, S., and Coveney, P. V. (2008). Life or Death Decision-making: The Medical Case for Largescale, On-demand Grid Computing. CTWatch Quarterly, 4(1).
  22. Mäntylä, M. (1988). An Introduction to Solid Modeling. Computer Science Press, College Park, MD.
  23. Milner, R. (1982). A Calculus of Communicating Systems. Springer-Verlag New York, Inc., Secaucus, NJ, USA.
  24. Minton, A. P. (1998). Molecular crowding: Analysis of effects of high concentrations of inert cosolutes on biochemical equilibria and rates in terms of volume exclusion. In Gary K. Ackers, M. L. J., editor, Energetics of Biological Macromolecules Part B, volume 295 of Methods in Enzymology, pages 127 - 149. Academic Press.
  25. Mirtich, B. (1998). V-clip: fast and robust polyhedral collision detection. ACM Trans. Graph., 17:177-208.
  26. Murray, J. D. and VanRyper, W. (1996). Encyclopedia of graphics file formats. O'Reilly Series. O'Reilly & Associates.
  27. Repenning, A. (2005). Inflatable icons: Diffusion-based interactive extrusion of 2d images into 3d models. Journal of Graphics, Gpu, and Game Tools, 10(1):1-15.
  28. Takahashi, K., Arjunan, S. N. V., and Tomita, M. (2005). Space in systems biology of signaling pathwaystowards intracellular molecular crowding in silico. FEBS letters, 579(8):1783-1788.
  29. Taylor, C. A., Draney, M. T., Ku, J. P., Parker, D., Steele, B. N., Wang, K., and Zarins, C. K. (1999). Biomedical paper predictive medicine: Computational techniques in therapeutic decision-making.
  30. Torchilin, V. P. (2006). Nanoparticulates as drug carriers. Imperial College Press.
  31. Van den Berg, B., Ellis, R. J., and Dobson, C. M. (1999). Effects of macromolecular crowding on protein folding and aggregation. The European Molecular Biology Organization Journal, 18(24):6927-6933.
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Paper Citation


in Harvard Style

Buti F., Corradini F., Merelli E. and Tesei L. (2012). A Geometrical Refinement of Shape Calculus Enabling Direct Simulation . In Proceedings of the 2nd International Conference on Simulation and Modeling Methodologies, Technologies and Applications - Volume 1: SIMULTECH, ISBN 978-989-8565-20-4, pages 218-227. DOI: 10.5220/0004060802180227


in Bibtex Style

@conference{simultech12,
author={Federico Buti and Flavio Corradini and Emanuela Merelli and Luca Tesei},
title={A Geometrical Refinement of Shape Calculus Enabling Direct Simulation},
booktitle={Proceedings of the 2nd International Conference on Simulation and Modeling Methodologies, Technologies and Applications - Volume 1: SIMULTECH,},
year={2012},
pages={218-227},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004060802180227},
isbn={978-989-8565-20-4},
}


in EndNote Style

TY - CONF
JO - Proceedings of the 2nd International Conference on Simulation and Modeling Methodologies, Technologies and Applications - Volume 1: SIMULTECH,
TI - A Geometrical Refinement of Shape Calculus Enabling Direct Simulation
SN - 978-989-8565-20-4
AU - Buti F.
AU - Corradini F.
AU - Merelli E.
AU - Tesei L.
PY - 2012
SP - 218
EP - 227
DO - 10.5220/0004060802180227