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Code Glossary
An Interaction is when a particle interacts with a surface such as a planar surface (modelling a membrane) or cylindrical surface (modelling a microtubule or strand of DNA). A reaction between two particles is NOT an interaction but a reaction.
A (sub)space that a particle can live on such as the membrane, microtuble or also the three dimensional space.
A generalized surface in the simulation system, such as a plane (two dimensional surface) or rod (one dimensional surface) modeling a membrane or microtuble.
A shell is a thing (can be a sphere or cylinder) that is drawn about one or more particles and defines an volume where no other particles can come. We usually refer to this as the 'protective domain'.
The number of particles that are contained in the shell (1 for a single, 2 for a pair, many for a multi)
An independent diffusion process that takes place inside a Shell. Diffusion in multiple dimensions can be a single coordinate but can also be broken up into independent diffusion processes. The diffusion of a particle in a cylindrical Shell can for example be broken up in diffusion parallel to the 'flat side' and the radial direction (two independent coordinates). The diffusion and reaction between two particles is also broken up into two coordinates, an inter particle diffusion coordinate (iv) and the diffusion of the center of mass.
The volume or area within a shell where the center of mass of a particle can come. This also defines the domains used for the Green's functions. In the simple cases where shell was spherical and the particle could reach everywhere, this was the 'mobility_radius'.