Shape Calculus A spatial calculus for 3D colliding shapes

We present a bio-inspired calculus for describing 3D shapes moving in a space. A shape forms a 3D process when combined with a behaviour. Behaviours are specified with a timed CCS-like process algebra using a notion of channel that models naturally binding sites on the surface of shapes. Processes can represent molecules or other mobile objects. The calculus embeds collision detection and response, binding of compatible 3D processes and splitting of previously established bonds.

[1]  Jane Hillston,et al.  Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks , 2007, FBTC@CONCUR.

[2]  Christer Ericson,et al.  Real-Time Collision Detection , 2004 .

[3]  Roberto Barbuti,et al.  Spatial Calculus of Looping Sequences , 2009, FBTC@ICALP.

[4]  Daniel T. Gillespie,et al.  Simulation Methods in Systems Biology , 2008, SFM.

[5]  Robin Milner,et al.  Communication and concurrency , 1989, PHI Series in computer science.

[6]  Luca Cardelli,et al.  Brane Calculi , 2004, CMSB.

[7]  Luca Cardelli,et al.  BioAmbients: an abstraction for biological compartments , 2004, Theor. Comput. Sci..

[8]  Masaru Tomita,et al.  Space in systems biology of signaling pathways – towards intracellular molecular crowding in silico , 2005, FEBS letters.

[9]  Luca Cardelli,et al.  Processes in Space , 2010, CiE.

[10]  Ezio Bartocci,et al.  A Shape Calculus for Biological Processes , 2009, ICTCS.

[11]  Wang Yi,et al.  Real-Time Behaviour of Asynchronous Agents , 1990, CONCUR.

[12]  Emanuela Merelli,et al.  A Spatial Simulator for Metabolic Pathways , 2008 .

[13]  Mathias John,et al.  A Spatial Extension to the pi Calculus , 2008, Electron. Notes Theor. Comput. Sci..

[14]  James Hetherington,et al.  Computational challenges of systems biology , 2004, Computer.

[15]  Alberto Policriti,et al.  Stochastic Concurrent Constraint Programming and Differential Equations , 2007, QAPL.

[16]  Emanuela Merelli,et al.  A spatial model and simulator for metabolic pathways , 2008 .

[17]  Corrado Priami,et al.  Beta Binders for Biological Interactions , 2004, CMSB.