User Projects

User project are those that use Mithral products to create other applications. Some are research projects that you may be able to get involved with.

If you have a project that should be on this list then let us know.

Projects that have used Cosm or the CS-SDK

Folding@Home - Protein folding.
Pande Group, Chemistry Department, Stanford University

Proteins are the basis of how biology gets things done. For this reason, we've sequenced the human genome -- the blueprint for all of the proteins in biology -- but how can we understand what these proteins do and how they work? One important step is to study how proteins self-assemble, or "fold." This is an extremely computationally intensive task, since proteins fold no slower than a 10 microseconds (10^-6 seconds), but we can only routinely simulate nanoseconds (10^-9 seconds).
We've developed a new way to simulate protein folding which can break the microsecond barrier by dividing the work between multiple processors in a new way -- with a near linear speed up in the number of processors. Thus, with 1000 processors, we can break the microsecond barrier and unlock the mystery of how proteins fold.
More about Cosm and Folding@home

Genome@Home - Genome sequence mining.
Pande Group, Chemistry Department, Stanford University

Genome@home studies real genomes and proteins directly, by designing new sequences for existing 3-D protein structures, which come from real genomes. The protein structure files that are sent out as work contain the Cartesian atomic coordinates of a protein. This data was obtained experimentally through X-ray crystallography or NMR techniques. Note that this was not done by us; thousands of scientists have spent decades compiling this data, which is generously made freely available to the public. By designing new sequences that could form these specific protein structures, we're setting the stage to attack a number of significant contemporary issues in structural biology, genetics, and medicine.

EON - Long time scale atomistic simulations.
Henkelman research group, Department of Chemistry and Biochemistry, University of Texas at Austin

A common problem in theoretical chemistry, condensed matter physics and materials science is the calculation of the time evolution of an atomic scale system where, for example, chemical reactions and/or diffusion occur. Generally the events of interest are quite rare (many orders of magnitude slower than the vibrational movements of the atoms), and therefore direct simulations, tracking every movement of the atoms, would take thousands of years of computer calculations on the fastest present day computer before a single event of interest can be expected to occur, hence the name EON, which is an immeasurable period of time.


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