The National Institute for Computational Sciences

Biophysical Modeling and Simulation

Kraken’s ability to simulate phenomena beyond the bounds of observation promises to significantly improve our understanding in multiple scientific arenas. For example, despite our knowledge of the human body, some of the most elementary biological processes remain a mystery, at least for now.

Researchers from the University of Utah are using experimental data to perform unprecedented molecular dynamics simulations on protein-mediated membrane remodeling, a process fundamental to the most basic behaviors such as movement and thinking. This phenomenon, in which proteins attach to biological membranes (liposomes, vesicles) and alter their shapes, is crucial to the exchange of neurotransmitters at nerve cell synapses.

By pairing observed X-ray crystal structures with modeled “chunks” of membrane surrounded by water, the team can observe what goes on at atomistic scales in respect to both size and time (40 to 100 nanoseconds). The resulting model will then be used for larger simulations implementing larger timescales, thus giving researchers a better view of the entire process. The relatively recent discovery of the role of proteins makes this a fundamental area of research for which the full potential is currently incalculable.