References

  1. K. Akiyama, K. Matsuzaki & H. Hayashi (2005): Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi. Nature 435(7043), pp. 824–827, doi:10.1038/nature03608.
  2. M. Aldinucci, M. Coppo, F. Damiani, M. Drocco, E. Giovannetti, E. Grassi, E. Sciacca, S. Spinella & A. Troina (2010): CWC Simulator. Dipartimento di Informatica, Università di Torino. Available at http://sourceforge.net/projects/cwcsimulator/.
  3. M. Aldinucci, M. Coppo, F. Damiani, M. Drocco, M. Torquati & A. Troina (2011): On Designing Multicore-Aware Simulators for Biological Systems. In: Proc. of Intl. Euromicro PDP 2011: Parallel Distributed and network-based Processing. IEEE Computer Society, pp. 318–325.
  4. Marco Aldinucci & Massimo Torquati (2009): FastFlow website. FastFlow. http://mc-fastflow.sourceforge.net/.
  5. S. Asimi, V. Gianinazzi-Pearson & S. Gianinazzi (1980): Influence of increasing soil phosphorus levels on interactions between vesicular-arbuscular mycorrhizae and Rhizobium in soybeans.. Canadian Journal of Botany 58(20), pp. 2200–2205, doi:10.1139/b80-253.
  6. R. Barbuti, A. Maggiolo-Schettini, P. Milazzo, P. Tiberi & A. Troina (2008): Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways. Transactions on Computational Systems Biology IX, pp. 86–113.
  7. R. Barbuti, A. Maggiolo-Schettini, P. Milazzo & A. Troina (2006): A Calculus of Looping Sequences for Modelling Microbiological Systems. Fundam. Inform. 72(1-3), pp. 21–35.
  8. Roberto Barbuti, Andrea Maggiolo-Schettini, Paolo Milazzo & Giovanni Pardini (2009): Spatial Calculus of Looping Sequences. Electr. Notes Theor. Comput. Sci. 229(1), pp. 21–39, doi:10.1016/j.entcs.2009.02.003.
  9. Roberto Barbuti, Andrea Maggiolo-Schettini, Paolo Milazzo, Giovanni Pardini & Luca Tesei (2011): Spatial P systems. Natural Computing 10(1), pp. 3–16, doi:10.1007/s11047-010-9187-z.
  10. A. Besserer, V. Puech-Pagès, P. Kiefer, V. Gomez-Roldan, A. Jauneau, S. Roy, J.C. Portais, C. Roux, G. Bécard & N. Séjalon-Delmas (2006): Strigolactones stimulate arbuscular mycorrhizal fungi by activating mitochondria. PLoS Biology 4(7), pp. 1239–1247, doi:10.1371/journal.pbio.0040226.
  11. BioBITs website. http://www.biobits.di.unipmn.it/.
  12. P. Bonfante-Fasolo (1984): Anatomy and morphology of VA mycorrhizae. VA mycorrhiza.
  13. Federico Buti, Diletta Cacciagrano, Flavio Corradini, Emanuela Merelli & Luca Tesei (2010): BioShape: a spatial shape-based scale-independent simulation environment for biological systems. Procedia CS 1(1), pp. 827–835, doi:10.1016/j.procs.2010.04.090.
  14. L. Cardelli (2004): Brane Calculi. In: Proc. of CMSB'04, LNCS 3082. Springer, pp. 257–278.
  15. Luca Cardelli & Philippa Gardner (2010): Processes in Space. In: Proc. of the 6th international conference on Computability in Europe, CiE'10. Springer-Verlag, pp. 78–87.
  16. M. Chabaud, A. Genre, B.J. Sieberer, A. Faccio, J. Fournier, M. Novero, D.G. Barker & P. Bonfante (2011): Arbuscular mycorrhizal hyphopodia and germinated spore exudates trigger Ca2+ spiking in the legume and nonlegume root epidermis. New Phytologist, doi:10.1111/j.1469-8137.2010.03464.x.
  17. M. Coppo, F. Damiani, M. Drocco, E. Grassi, M. Guether & A. Troina (2011): Modelling Ammonium Transporters in Arbuscular Mycorrhiza Symbiosis. Transactions on Computational Systems Biology XIII, pp. 85–109.
  18. Mario Coppo, Ferruccio Damiani, Maurizio Drocco, Elena Grassi, Eva Sciacca, Salvatore Spinella & Angelo Troina (2010): Hybrid Calculus of Wrapped Compartments. In: 4th International Meeting on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC'10) 40. EPTCS, pp. 102–120, doi:10.4204/EPTCS.40.8.
  19. Mario Coppo, Ferruccio Damiani, Maurizio Drocco, Elena Grassi & Angelo Troina (2010): Stochastic Calculus of Wrapped Compartments. In: 8th Workshop on Quantitative Aspects of Programming Languages (QAPL'10) 28. EPTCS, pp. 82–98, doi:10.4204/EPTCS.28.6.
  20. V. Danos & C. Laneve (2004): Formal molecular biology. Theor. Comput. Sci. 325(1), pp. 69–110, doi:10.1016/j.tcs.2004.03.065.
  21. P. Degano, D. Prandi, C. Priami & P. Quaglia (2006): Beta-binders for Biological Quantitative Experiments. Electr. Notes Theor. Comput. Sci. 164(3), pp. 101–117, doi:10.1016/j.entcs.2006.07.014.
  22. A. Genre & P. Bonfante (2007): Check-in procedures for plant cell entry by biotrophic microbes. Molecular Plant-Microbe Interactions 20(9), pp. 1023–1030, doi:10.1094/MPMI-20-9-1023.
  23. A. Genre, M. Chabaud, T. Timmers, P. Bonfante & D.G. Barker (2005): Arbuscular mycorrhizal fungi elicit a novel intracellular apparatus in Medicago truncatula root epidermal cells before infection. The Plant Cell Online 17(12), pp. 3489, doi:10.1105/tpc.105.035410.
  24. D. Gillespie (1977): Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, pp. 2340–2361, doi:10.1021/j100540a008.
  25. M.J. Harrison (2005): Signaling in the arbuscular mycorrhizal symbiosis. Annu. Rev. Microbiol. 59, pp. 19–42, doi:10.1146/annurev.micro.58.030603.123749.
  26. C.M. Hepper (1983): The effect of nitrate and phosphate on the vesicular-arbuscular mycorrhizal infection of lettuce. New Phytologist 93(3), pp. 389–399, doi:10.1111/j.1469-8137.1983.tb03439.x.
  27. H. Javot, R.V. Penmetsa, N. Terzaghi, D.R. Cook & M.J. Harrison (2007): A Medicago truncatula phosphate transporter indispensable for the arbuscular mycorrhizal symbiosis. Proceedings of the National Academy of Sciences 104(5), pp. 1720, doi:10.1073/pnas.0608136104.
  28. B. Kholodenko (2006): Cell-signalling dynamics in time and space. Nature Reviews Molecular Cell Biology 7, pp. 165–176, doi:10.1038/nrm1838.
  29. S. Kosuta, M. Chabaud, G. Lougnon, C. Gough, J. Dénarié, D.G. Barker & G. Bécard (2003): A Diffusible Factor from Arbuscular Mycorrhizal Fungi Induces Symbiosis-Specific MtENOD11 Expression in Roots ofMedicago truncatula. Plant Physiology 131(3), pp. 952, doi:10.1104/pp.011882.
  30. S. Kosuta, S. Hazledine, J. Sun, H. Miwa, R.J. Morris, J.A. Downie & G.E.D. Oldroyd (2008): Differential and chaotic calcium signatures in the symbiosis signaling pathway of legumes. Proceedings of the National Academy of Sciences 105(28), pp. 9823, doi:10.1073/pnas.0803499105.
  31. J. Krivine, R. Milner & A. Troina (2008): Stochastic Bigraphs. Electron. Notes Theor. Comput. Sci. 218, pp. 73–96, doi:10.1016/j.entcs.2008.10.006.
  32. J.A. López-Ráez, T. Charnikhova, V. Gómez-Roldán, R. Matusova, W. Kohlen, R. De Vos, F. Verstappen, V. Puech-Pages, G. Bécard & P. Mulder (2008): Tomato strigolactones are derived from carotenoids and their biosynthesis is promoted by phosphate starvation. New Phytologist 178(4), pp. 863–874, doi:10.1111/j.1469-8137.2008.02406.x.
  33. R. Matusova, K. Rani, F.W.A. Verstappen, M.C.R. Franssen, M.H. Beale & H.J. Bouwmeester (2005): The strigolactone germination stimulants of the plant-parasitic Striga and Orobanche spp. are derived from the carotenoid pathway. Plant Physiology 139(2), pp. 920, doi:10.1104/pp.105.061382.
  34. Sara Montagna & Mirko Viroli (2010): A Framework for Modelling and Simulating Networks of Cells. Electr. Notes Theor. Comput. Sci. 268, pp. 115–129, doi:10.1016/j.entcs.2010.12.009.
  35. B. Mosse (1973): Advances in the study of vesicular-arbuscular mycorrhiza. Annual Review of Phytopathology 11(1), pp. 171–196, doi:10.1146/annurev.py.11.090173.001131.
  36. G. Nagahashi & D.D. Douds Jr (2000): Partial separation of root exudate components and their effects upon the growth of germinated spores of AM fungi. Mycological Research 104(12), pp. 1453–1464, doi:10.1017/S0953756200002860.
  37. John Von Neumann (1966): Theory of Self-Reproducing Automata. University of Illinois Press, Champaign, IL, USA.
  38. G.E.D. Oldroyd & J.A. Downie (2008): Coordinating nodule morphogenesis with rhizobial infection in legumes. Annu. Rev. Plant Biol. 59, pp. 519–546, doi:10.1146/annurev.arplant.59.032607.092839.
  39. Nicolas Oury & Gordon Plotkin (2011): Multi-Level Modelling via Stochastic Multi-Level Multiset Rewriting. Draft submitted to MSCS.
  40. C. Priami, A. Regev, E. Y. Shapiro & W. Silverman (2001): Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Inf. Process. Lett. 80(1), pp. 25–31, doi:10.1016/S0020-0190(01)00214-9.
  41. G. Paun (2002): Membrane computing. An introduction. Springer.
  42. A. Regev, E. M. Panina, W. Silverman, L. Cardelli & E. Y. Shapiro (2004): BioAmbients: an abstraction for biological compartments. Theor. Comput. Sci. 325(1), pp. 141–167, doi:10.1016/j.tcs.2004.03.061.
  43. A. Regev & E. Shapiro (2002): Cells as computation. Nature 419, pp. 343, doi:10.1007/3-540-36481-1_1.
  44. C. Sbrana & M. Giovannetti (2005): Chemotropism in the arbuscular mycorrhizal fungus Glomus mosseae. Mycorrhiza 15(7), pp. 539–545, doi:10.1007/s00572-005-0362-5.
  45. E Sciacca, S Spinella, A Genre & C Calcagno (2011): Analysis of Calcium Spiking in Plant Root Epidermis through CWC Modeling. In: CS2BIO11, pp. 1–12.
  46. R. Toth & R.M. Miller (1984): Dynamics of arbuscule development and degeneration in a Zea mays mycorrhiza. American journal of botany 71(4), pp. 449–460, doi:10.2307/2443320.
  47. K. Yoneyama, Y. Takeuchi & T. Yokota (2001): Production of clover broomrape seed germination stimulants by red clover root requires nitrate but is inhibited by phosphate and ammonium. Physiologia Plantarum 112(1), pp. 25–30, doi:10.1034/j.1399-3054.2001.1120104.x.

Comments and questions to: eptcs@eptcs.org
For website issues: webmaster@eptcs.org