• Corpus ID: 7974779

Shape Calculus. A Spatial Mobile Calculus for 3D Shapes

@article{Bartocci2010ShapeCA,
  title={Shape Calculus. A Spatial Mobile Calculus for 3D Shapes},
  author={Ezio Bartocci and Fl{\'a}vio Corradini and Maria Rita Di Berardini and Emanuela Merelli and Luca Tesei},
  journal={Sci. Ann. Comput. Sci.},
  year={2010},
  volume={20},
  pages={1-31}
}
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 speci ed with a timed CCS-like process algebra using a notion of channel to naturally model binding sites on the surface of shapes. The calculus embeds collision detection and response, binding of compatible 3D processes and split of composed 3D 
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References

SHOWING 1-10 OF 34 REFERENCES
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
A Shape Calculus for Biological Processes
TLDR
It is discussed how the features of the calculus can be used to model biological processes, for instance biochemical reactions, in order to describe 3D shapes moving in a space.
A Spatial Extension to the π Calculus
TLDR
The operational semantics of SpacePi defines the interplay between movement, communication, and time-triggered events in the modeling of molecular biological processes like diffusion, active transportation in cell signaling, and spatial structures.
A spatial model and simulator for metabolic pathways
TLDR
A model for describing a portion of cytoplasm with components involved in metabolic pathways, each enzyme, metabolite and complex is represented by an autonomous software agent, according to MichaelisMenten kinetics.
Bone Remodelling in BioShape
Brane Calculi
TLDR
This work introduces a family of process calculi with dynamic nested membranes that are tightly coupled to membranes, and can perform interactions on both sides of a membrane.
Bone Remodelling: A Complex Automata-Based Model Running in BioShape
TLDR
This work exploits the Complex Automata paradigm and the BioShape 3D spatial simulator for describing the bone remodelling process in terms of a 2-scale aggregation of uniform Cellular Automata coupled by a well-established composition pattern and proposes a model suitable for handling different scales in a uniform way.
Beta Binders for Biological Interactions
TLDR
Binders and operators are added to wrap a process just as membranes enclose some living matter and hence to mimick biological interfaces to describe the dynamics of those interfaces.
...
...