<bibliography>
 <citation type="article" key="akiyama2005plant">
  <author>K. Akiyama</author>
  <author>K. Matsuzaki</author>
  <author>H. Hayashi</author>
  <year>2005</year>
  <title>Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi</title>
  <journal>Nature</journal>
  <volume>435</volume>
  <number>7043</number>
  <pages>824&#8211;827</pages>
  <doi>10.1038/nature03608</doi>
 </citation>
 <citation type="manual" key="HCWC_SIM">
  <author>M. Aldinucci</author>
  <author>M. Coppo</author>
  <author>F. Damiani</author>
  <author>M. Drocco</author>
  <author>E. Giovannetti</author>
  <author>E. Grassi</author>
  <author>E. Sciacca</author>
  <author>S. Spinella</author>
  <author>A. Troina</author>
  <year>2010</year>
  <title>CWC Simulator</title>
  <organization>Dipartimento di Informatica, Universit&#224; di Torino</organization>
  <url>http://sourceforge.net/projects/cwcsimulator/</url>
 </citation>
 <citation type="inproceedings" key="ACDDTT_PDP11">
  <author>M. Aldinucci</author>
  <author>M. Coppo</author>
  <author>F. Damiani</author>
  <author>M. Drocco</author>
  <author>M. Torquati</author>
  <author>A. Troina</author>
  <year>2011</year>
  <title>On Designing Multicore-Aware Simulators for Biological Systems</title>
  <booktitle>Proc. of Intl. Euromicro PDP 2011: Parallel Distributed and network-based Processing</booktitle>
  <publisher>IEEE Computer Society</publisher>
  <pages>318&#8211;325</pages>
 </citation>
 <citation type="manual" key="fastflow:web">
  <author>Marco Aldinucci</author>
  <author>Massimo Torquati</author>
  <year>2009</year>
  <title>FastFlow website</title>
  <organization>FastFlow</organization>
  <note>http://mc-fastflow.sourceforge.net/</note>
 </citation>
 <citation type="article" key="asimi1980influence">
  <author>S. Asimi</author>
  <author>V. Gianinazzi-Pearson</author>
  <author>S. Gianinazzi</author>
  <year>1980</year>
  <title>Influence of increasing soil phosphorus levels on interactions between vesicular-arbuscular mycorrhizae and Rhizobium in soybeans.</title>
  <journal>Canadian Journal of Botany</journal>
  <volume>58</volume>
  <number>20</number>
  <pages>2200&#8211;2205</pages>
  <doi>10.1139/b80-253</doi>
 </citation>
 <citation type="article" key="BMMTT08">
  <author>R. Barbuti</author>
  <author>A. Maggiolo-Schettini</author>
  <author>P. Milazzo</author>
  <author>P. Tiberi</author>
  <author>A. Troina</author>
  <year>2008</year>
  <title>Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways</title>
  <journal>Transactions on Computational Systems Biology</journal>
  <volume>IX</volume>
  <pages>86&#8211;113</pages>
 </citation>
 <citation type="article" key="BMMT06">
  <author>R. Barbuti</author>
  <author>A. Maggiolo-Schettini</author>
  <author>P. Milazzo</author>
  <author>A. Troina</author>
  <year>2006</year>
  <title>A Calculus of Looping Sequences for Modelling Microbiological Systems</title>
  <journal>Fundam. Inform.</journal>
  <volume>72</volume>
  <number>1-3</number>
  <pages>21&#8211;35</pages>
 </citation>
 <citation type="article" key="BMMP09">
  <author>Roberto Barbuti</author>
  <author>Andrea Maggiolo-Schettini</author>
  <author>Paolo Milazzo</author>
  <author>Giovanni Pardini</author>
  <year>2009</year>
  <title>Spatial Calculus of Looping Sequences</title>
  <journal>Electr. Notes Theor. Comput. Sci.</journal>
  <volume>229</volume>
  <number>1</number>
  <pages>21&#8211;39</pages>
  <doi>10.1016/j.entcs.2009.02.003</doi>
 </citation>
 <citation type="article" key="BMMPT11">
  <author>Roberto Barbuti</author>
  <author>Andrea Maggiolo-Schettini</author>
  <author>Paolo Milazzo</author>
  <author>Giovanni Pardini</author>
  <author>Luca Tesei</author>
  <year>2011</year>
  <title>Spatial P systems</title>
  <journal>Natural Computing</journal>
  <volume>10</volume>
  <number>1</number>
  <pages>3&#8211;16</pages>
  <doi>10.1007/s11047-010-9187-z</doi>
 </citation>
 <citation type="article" key="besserer2006strigolactones">
  <author>A. Besserer</author>
  <author>V. Puech-Pag&#232;s</author>
  <author>P. Kiefer</author>
  <author>V. Gomez-Roldan</author>
  <author>A. Jauneau</author>
  <author>S. Roy</author>
  <author>J.C. Portais</author>
  <author>C. Roux</author>
  <author>G. B&#233;card</author>
  <author>N. S&#233;jalon-Delmas</author>
  <year>2006</year>
  <title>Strigolactones stimulate arbuscular mycorrhizal fungi by activating mitochondria</title>
  <journal>PLoS Biology</journal>
  <volume>4</volume>
  <number>7</number>
  <pages>1239&#8211;1247</pages>
  <doi>10.1371/journal.pbio.0040226</doi>
 </citation>
 <citation type="misc" key="BioBITs:web">
  <title>BioBITs website</title>
  <note>http://www.biobits.di.unipmn.it/</note>
 </citation>
 <citation type="article" key="bonfante1984anatomy">
  <author>P. Bonfante-Fasolo</author>
  <year>1984</year>
  <title>Anatomy and morphology of VA mycorrhizae</title>
  <journal>VA mycorrhiza</journal>
 </citation>
 <citation type="article" key="BCCMT10">
  <author>Federico Buti</author>
  <author>Diletta Cacciagrano</author>
  <author>Flavio Corradini</author>
  <author>Emanuela Merelli</author>
  <author>Luca Tesei</author>
  <year>2010</year>
  <title>BioShape: a spatial shape-based scale-independent simulation environment for biological systems</title>
  <journal>Procedia CS</journal>
  <volume>1</volume>
  <number>1</number>
  <pages>827&#8211;835</pages>
  <doi>10.1016/j.procs.2010.04.090</doi>
 </citation>
 <citation type="inproceedings" key="Car04">
  <author>L. Cardelli</author>
  <year>2004</year>
  <title>Brane Calculi</title>
  <booktitle>Proc. of CMSB'04</booktitle>
  <series>LNCS</series>
  <volume>3082</volume>
  <publisher>Springer</publisher>
  <pages>257&#8211;278</pages>
 </citation>
 <citation type="inproceedings" key="CG10">
  <author>Luca Cardelli</author>
  <author>Philippa Gardner</author>
  <year>2010</year>
  <title>Processes in Space</title>
  <booktitle>Proc. of the 6th international conference on Computability in Europe</booktitle>
  <series>CiE'10</series>
  <publisher>Springer-Verlag</publisher>
  <pages>78&#8211;87</pages>
 </citation>
 <citation type="article" key="chabaud2011arbuscular">
  <author>M. Chabaud</author>
  <author>A. Genre</author>
  <author>B.J. Sieberer</author>
  <author>A. Faccio</author>
  <author>J. Fournier</author>
  <author>M. Novero</author>
  <author>D.G. Barker</author>
  <author>P. Bonfante</author>
  <year>2011</year>
  <title>Arbuscular mycorrhizal hyphopodia and germinated spore exudates trigger Ca2+ spiking in the legume and nonlegume root epidermis</title>
  <journal>New Phytologist</journal>
  <doi>10.1111/j.1469-8137.2010.03464.x</doi>
 </citation>
 <citation type="article" key="CDDGGT_TCSB11">
  <author>M. Coppo</author>
  <author>F. Damiani</author>
  <author>M. Drocco</author>
  <author>E. Grassi</author>
  <author>M. Guether</author>
  <author>A. Troina</author>
  <year>2011</year>
  <title>Modelling Ammonium Transporters in Arbuscular Mycorrhiza Symbiosis</title>
  <journal>Transactions on Computational Systems Biology</journal>
  <volume>XIII</volume>
  <pages>85&#8211;109</pages>
 </citation>
 <citation type="inproceedings" key="MECBIC10">
  <author>Mario Coppo</author>
  <author>Ferruccio Damiani</author>
  <author>Maurizio Drocco</author>
  <author>Elena Grassi</author>
  <author>Eva Sciacca</author>
  <author>Salvatore Spinella</author>
  <author>Angelo Troina</author>
  <year>2010</year>
  <title>Hybrid Calculus of Wrapped Compartments</title>
  <booktitle>4th International Meeting on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC'10)</booktitle>
  <volume>40</volume>
  <publisher>EPTCS</publisher>
  <pages>102&#8211;120</pages>
  <doi>10.4204/EPTCS.40.8</doi>
 </citation>
 <citation type="inproceedings" key="preQAPL2010">
  <author>Mario Coppo</author>
  <author>Ferruccio Damiani</author>
  <author>Maurizio Drocco</author>
  <author>Elena Grassi</author>
  <author>Angelo Troina</author>
  <year>2010</year>
  <title>Stochastic Calculus of Wrapped Compartments</title>
  <booktitle>8th Workshop on Quantitative Aspects of Programming Languages (QAPL'10)</booktitle>
  <volume>28</volume>
  <publisher>EPTCS</publisher>
  <pages>82&#8211;98</pages>
  <doi>10.4204/EPTCS.28.6</doi>
 </citation>
 <citation type="article" key="DL04">
  <author>V. Danos</author>
  <author>C. Laneve</author>
  <year>2004</year>
  <title>Formal molecular biology</title>
  <journal>Theor. Comput. Sci.</journal>
  <volume>325</volume>
  <number>1</number>
  <pages>69&#8211;110</pages>
  <doi>10.1016/j.tcs.2004.03.065</doi>
 </citation>
 <citation type="article" key="DPPQ06">
  <author>P. Degano</author>
  <author>D. Prandi</author>
  <author>C. Priami</author>
  <author>P. Quaglia</author>
  <year>2006</year>
  <title>Beta-binders for Biological Quantitative Experiments</title>
  <journal>Electr. Notes Theor. Comput. Sci.</journal>
  <volume>164</volume>
  <number>3</number>
  <pages>101&#8211;117</pages>
  <doi>10.1016/j.entcs.2006.07.014</doi>
 </citation>
 <citation type="article" key="genre2007check">
  <author>A. Genre</author>
  <author>P. Bonfante</author>
  <year>2007</year>
  <title>Check-in procedures for plant cell entry by biotrophic microbes</title>
  <journal>Molecular Plant-Microbe Interactions</journal>
  <volume>20</volume>
  <number>9</number>
  <pages>1023&#8211;1030</pages>
  <doi>10.1094/MPMI-20-9-1023</doi>
 </citation>
 <citation type="article" key="genre2005arbuscular">
  <author>A. Genre</author>
  <author>M. Chabaud</author>
  <author>T. Timmers</author>
  <author>P. Bonfante</author>
  <author>D.G. Barker</author>
  <year>2005</year>
  <title>Arbuscular mycorrhizal fungi elicit a novel intracellular apparatus in Medicago truncatula root epidermal cells before infection</title>
  <journal>The Plant Cell Online</journal>
  <volume>17</volume>
  <number>12</number>
  <pages>3489</pages>
  <doi>10.1105/tpc.105.035410</doi>
 </citation>
 <citation type="article" key="G77">
  <author>D. Gillespie</author>
  <year>1977</year>
  <title>Exact stochastic simulation of coupled chemical reactions</title>
  <journal>J. Phys. Chem.</journal>
  <volume>81</volume>
  <pages>2340&#8211;2361</pages>
  <doi>10.1021/j100540a008</doi>
 </citation>
 <citation type="article" key="harrison2005signaling">
  <author>M.J. Harrison</author>
  <year>2005</year>
  <title>Signaling in the arbuscular mycorrhizal symbiosis</title>
  <journal>Annu. Rev. Microbiol.</journal>
  <volume>59</volume>
  <pages>19&#8211;42</pages>
  <doi>10.1146/annurev.micro.58.030603.123749</doi>
 </citation>
 <citation type="article" key="hepper1983effect">
  <author>C.M. Hepper</author>
  <year>1983</year>
  <title>The effect of nitrate and phosphate on the vesicular-arbuscular mycorrhizal infection of lettuce</title>
  <journal>New Phytologist</journal>
  <volume>93</volume>
  <number>3</number>
  <pages>389&#8211;399</pages>
  <doi>10.1111/j.1469-8137.1983.tb03439.x</doi>
 </citation>
 <citation type="article" key="javot2007medicago">
  <author>H. Javot</author>
  <author>R.V. Penmetsa</author>
  <author>N. Terzaghi</author>
  <author>D.R. Cook</author>
  <author>M.J. Harrison</author>
  <year>2007</year>
  <title>A Medicago truncatula phosphate transporter indispensable for the arbuscular mycorrhizal symbiosis</title>
  <journal>Proceedings of the National Academy of Sciences</journal>
  <volume>104</volume>
  <number>5</number>
  <pages>1720</pages>
  <doi>10.1073/pnas.0608136104</doi>
 </citation>
 <citation type="article" key="K06">
  <author>B. Kholodenko</author>
  <year>2006</year>
  <title>Cell-signalling dynamics in time and space</title>
  <journal>Nature Reviews Molecular Cell Biology</journal>
  <volume>7</volume>
  <pages>165&#8211;176</pages>
  <doi>10.1038/nrm1838</doi>
 </citation>
 <citation type="article" key="kosuta2003diffusible">
  <author>S. Kosuta</author>
  <author>M. Chabaud</author>
  <author>G. Lougnon</author>
  <author>C. Gough</author>
  <author>J. D&#233;nari&#233;</author>
  <author>D.G. Barker</author>
  <author>G. B&#233;card</author>
  <year>2003</year>
  <title>A Diffusible Factor from Arbuscular Mycorrhizal Fungi Induces Symbiosis-Specific MtENOD11 Expression in Roots ofMedicago truncatula</title>
  <journal>Plant Physiology</journal>
  <volume>131</volume>
  <number>3</number>
  <pages>952</pages>
  <doi>10.1104/pp.011882</doi>
 </citation>
 <citation type="article" key="kosuta2008differential">
  <author>S. Kosuta</author>
  <author>S. Hazledine</author>
  <author>J. Sun</author>
  <author>H. Miwa</author>
  <author>R.J. Morris</author>
  <author>J.A. Downie</author>
  <author>G.E.D. Oldroyd</author>
  <year>2008</year>
  <title>Differential and chaotic calcium signatures in the symbiosis signaling pathway of legumes</title>
  <journal>Proceedings of the National Academy of Sciences</journal>
  <volume>105</volume>
  <number>28</number>
  <pages>9823</pages>
  <doi>10.1073/pnas.0803499105</doi>
 </citation>
 <citation type="article" key="KMT08">
  <author>J. Krivine</author>
  <author>R. Milner</author>
  <author>A. Troina</author>
  <year>2008</year>
  <title>Stochastic Bigraphs</title>
  <journal>Electron. Notes Theor. Comput. Sci.</journal>
  <volume>218</volume>
  <pages>73&#8211;96</pages>
  <doi>10.1016/j.entcs.2008.10.006</doi>
 </citation>
 <citation type="article" key="lopez2008tomato">
  <author>J.A. L&#243;pez-R&#225;ez</author>
  <author>T. Charnikhova</author>
  <author>V. G&#243;mez-Rold&#225;n</author>
  <author>R. Matusova</author>
  <author>W. Kohlen</author>
  <author>R. De Vos</author>
  <author>F. Verstappen</author>
  <author>V. Puech-Pages</author>
  <author>G. B&#233;card</author>
  <author>P. Mulder</author>
  <year>2008</year>
  <title>Tomato strigolactones are derived from carotenoids and their biosynthesis is promoted by phosphate starvation</title>
  <journal>New Phytologist</journal>
  <volume>178</volume>
  <number>4</number>
  <pages>863&#8211;874</pages>
  <doi>10.1111/j.1469-8137.2008.02406.x</doi>
 </citation>
 <citation type="article" key="matusova2005strigolactone">
  <author>R. Matusova</author>
  <author>K. Rani</author>
  <author>F.W.A. Verstappen</author>
  <author>M.C.R. Franssen</author>
  <author>M.H. Beale</author>
  <author>H.J. Bouwmeester</author>
  <year>2005</year>
  <title>The strigolactone germination stimulants of the plant-parasitic Striga and Orobanche spp. are derived from the carotenoid pathway</title>
  <journal>Plant Physiology</journal>
  <volume>139</volume>
  <number>2</number>
  <pages>920</pages>
  <doi>10.1104/pp.105.061382</doi>
 </citation>
 <citation type="article" key="MV10">
  <author>Sara Montagna</author>
  <author>Mirko Viroli</author>
  <year>2010</year>
  <title>A Framework for Modelling and Simulating Networks of Cells</title>
  <journal>Electr. Notes Theor. Comput. Sci.</journal>
  <volume>268</volume>
  <pages>115&#8211;129</pages>
  <doi>10.1016/j.entcs.2010.12.009</doi>
 </citation>
 <citation type="article" key="mosse1973advances">
  <author>B. Mosse</author>
  <year>1973</year>
  <title>Advances in the study of vesicular-arbuscular mycorrhiza</title>
  <journal>Annual Review of Phytopathology</journal>
  <volume>11</volume>
  <number>1</number>
  <pages>171&#8211;196</pages>
  <doi>10.1146/annurev.py.11.090173.001131</doi>
 </citation>
 <citation type="article" key="nagahashi2000partial">
  <author>G. Nagahashi</author>
  <author>D.D. Douds Jr</author>
  <year>2000</year>
  <title>Partial separation of root exudate components and their effects upon the growth of germinated spores of AM fungi</title>
  <journal>Mycological Research</journal>
  <volume>104</volume>
  <number>12</number>
  <pages>1453&#8211;1464</pages>
  <doi>10.1017/S0953756200002860</doi>
 </citation>
 <citation type="book" key="vN66">
  <author>John Von Neumann</author>
  <year>1966</year>
  <title>Theory of Self-Reproducing Automata</title>
  <publisher>University of Illinois Press</publisher>
  <address>Champaign, IL, USA</address>
 </citation>
 <citation type="article" key="oldroyd2008coordinating">
  <author>G.E.D. Oldroyd</author>
  <author>J.A. Downie</author>
  <year>2008</year>
  <title>Coordinating nodule morphogenesis with rhizobial infection in legumes</title>
  <journal>Annu. Rev. Plant Biol.</journal>
  <volume>59</volume>
  <pages>519&#8211;546</pages>
  <doi>10.1146/annurev.arplant.59.032607.092839</doi>
 </citation>
 <citation type="unpublished" key="OP11">
  <author>Nicolas Oury</author>
  <author>Gordon Plotkin</author>
  <year>2011</year>
  <title>Multi-Level Modelling via Stochastic Multi-Level Multiset Rewriting</title>
  <note>Draft submitted to MSCS</note>
 </citation>
 <citation type="article" key="PRSS01">
  <author>C. Priami</author>
  <author>A. Regev</author>
  <author>E. Y. Shapiro</author>
  <author>W. Silverman</author>
  <year>2001</year>
  <title>Application of a stochastic name-passing calculus to representation and simulation of molecular processes</title>
  <journal>Inf. Process. Lett.</journal>
  <volume>80</volume>
  <number>1</number>
  <pages>25&#8211;31</pages>
  <doi>10.1016/S0020-0190(01)00214-9</doi>
 </citation>
 <citation type="book" key="P02">
  <author>G. Paun</author>
  <year>2002</year>
  <title>Membrane computing. An introduction</title>
  <publisher>Springer</publisher>
 </citation>
 <citation type="article" key="RPSCS04">
  <author>A. Regev</author>
  <author>E. M. Panina</author>
  <author>W. Silverman</author>
  <author>L. Cardelli</author>
  <author>E. Y. Shapiro</author>
  <year>2004</year>
  <title>BioAmbients: an abstraction for biological compartments</title>
  <journal>Theor. Comput. Sci.</journal>
  <volume>325</volume>
  <number>1</number>
  <pages>141&#8211;167</pages>
  <doi>10.1016/j.tcs.2004.03.061</doi>
 </citation>
 <citation type="article" key="RS02">
  <author>A. Regev</author>
  <author>E. Shapiro</author>
  <year>2002</year>
  <title>Cells as computation</title>
  <journal>Nature</journal>
  <volume>419</volume>
  <pages>343</pages>
  <doi>10.1007/3-540-36481-1_1</doi>
 </citation>
 <citation type="article" key="sbrana2005chemotropism">
  <author>C. Sbrana</author>
  <author>M. Giovannetti</author>
  <year>2005</year>
  <title>Chemotropism in the arbuscular mycorrhizal fungus Glomus mosseae</title>
  <journal>Mycorrhiza</journal>
  <volume>15</volume>
  <number>7</number>
  <pages>539&#8211;545</pages>
  <doi>10.1007/s00572-005-0362-5</doi>
 </citation>
 <citation type="inproceedings" key="calcium_CS2BIO11">
  <author>E Sciacca</author>
  <author>S Spinella</author>
  <author>A Genre</author>
  <author>C Calcagno</author>
  <year>2011</year>
  <title>Analysis of Calcium Spiking in Plant Root Epidermis through CWC Modeling</title>
  <booktitle>CS2BIO11</booktitle>
  <pages>1&#8211;12</pages>
 </citation>
 <citation type="article" key="toth1984dynamics">
  <author>R. Toth</author>
  <author>R.M. Miller</author>
  <year>1984</year>
  <title>Dynamics of arbuscule development and degeneration in a Zea mays mycorrhiza</title>
  <journal>American journal of botany</journal>
  <volume>71</volume>
  <number>4</number>
  <pages>449&#8211;460</pages>
  <doi>10.2307/2443320</doi>
 </citation>
 <citation type="article" key="yoneyama2001production">
  <author>K. Yoneyama</author>
  <author>Y. Takeuchi</author>
  <author>T. Yokota</author>
  <year>2001</year>
  <title>Production of clover broomrape seed germination stimulants by red clover root requires nitrate but is inhibited by phosphate and ammonium</title>
  <journal>Physiologia Plantarum</journal>
  <volume>112</volume>
  <number>1</number>
  <pages>25&#8211;30</pages>
  <doi>10.1034/j.1399-3054.2001.1120104.x</doi>
 </citation>
</bibliography>
