(Audio
and slides from talks)
January
19, 2007-- 4:00 p.m. at the Fields Institute Dr.
John Parkinson, Hospital for Sick Children
Spatio-Temporal
Simulations of Cellular Processes
High throughput
genomic technologies are leading to the generation of
vast amounts of data detailing cellular components,
their expression,
interactions and dynamics. Due to the inherent complexity,
understanding
the relationships of these components within higher
order biological
processes is non-intuitive and requires the application
of mathematical
and computational modelling tools. To date, a variety
of such tools have
been proposed that attempt to simulate the behavior
of the molecular
components. In general, these tools tend to rely on
the use of ordinary
and partial differential equations which typically neglect
the spatial
organization of molecules by treating the system as
a homogenous mixture
of components. However there is increasing evidence
which suggests that
spatial factors such as molecular crowding and protein
co-localization
can significantly influence pathway function and efficiency.
In this
talk I will introduce Cell++, a spatio-temporal modelling
platform that
performs three-dimensional simulations of biochemical
pathways.
Combining a cellular automata engine with Brownian dynamics,
Cell++ is
capable of simulating the bulk properties of large quantities
of small
molecules (e.g. glucose and ATP), while simultaneously
allowing larger
molecules such as enzymes to be treated as more complex
entities. We are
beginning to apply Cell++ within a variety of biological
contexts and
will present some initial findings from studies of metabolic
pathways,
signal transduction pathways, lipid raft mediated signalling
and calcium
wave propagation.
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