MOLECULAR PATHWAYS AS CONCURRENT SYSTEMS
We realized that molecules,
which are structures, could be represented by their potential behavior: the
process in which they may participate.
For example, according to this approach, an enzyme is the enzymatic reaction
it may catalyze [example].
In fact, biochemical processes and concurrent communication systems share many
features. In both cases, multiple entities exist concurrently, interact and
modify each other. Based on this analogy, the Pi-calculus,
originally developed for the specification of computational processes, could
also be used to model biochemical ones.
We employ 5 major principles in
modeling biochemical processes as concurrent systems:
Pathways, molecules and molecular domains as
computational processes [example]
Complementary molecular determinants
correspond as communication channels [example]
Molecular interaction and modification as
communication and change of channel names [example]
The integrity of molecules, complexes and compartment
as channels with restricted scope [example]
The formation of complexes and translocation
of molecule as extrusion of restricted channels [example]
Based on this strong
correspondence between the calculus and biochemical networks,
we can incrementally represent detailed information on biochemical systems in a
structured, biologically faithful fashion. The resulting representations can be
used in simulation, analysis and verification.
Step-by-step detailed explanations are
available in our papers and in
the BioSPI course.
Additional illustrative examples can be found
in our presentations and posters.
Molecular
identity, complexes, and localization are treated better within the ambient calculus
[slides]