Erik Lindahl, Stockholm Bioinformatics Center
Thermodynamical properties of biological molecules
through loosely coupled or distributed simulations:
protein folding and insertion in biomembranes
High performance computing applications have increased tremendously
the last decade or two, and it is now quite possible to simulate many
processes that were completely impossible only a few years ago. Yet,
many of the most important practical problems occur on scales of length
and time that are several orders of magnitude beyond this, particularly
in biochemistry/biology.
I will present some of the approaches we have
used to overcome these limitations, and which have enabled us not only
to simulate and model events that previously were considered
"impossible",
but also doing it with standard hardware instead of supercomputers. This
will be illustrated with examples from our recent work on folding of
small
globular proteins in water as well as understanding the entire
process of
how amino acids are inserted into bilayers to form membrane proteins,
but
many of the underlying modeling ideas are universally applicable.