July 16, 2009

New algorithms solve computer delays

U.S. scientists say they have rewritten algorithms to resolve delays of days or even years faced by researchers designing and simulating molecules.

The time delay problem is caused by the amount of time a computer needs to run complex quantum mathematical equations, or algorithms, used during the development of more effective drugs, catalysts for fuel cells and other molecular-based materials and applications.

Stanford University Professor Todd Martinez and graduate student Ivan Ufimtsev say the algorithms they've written will run on a computer's graphical processing unit rather than the central processing unit of traditional desktop computers.

The researchers said their revamped algorithms calculated the structures of test molecules up to 650 times faster through a graphical processing unit than a molecular design program running on a computer's central processing unit.

The redesigned quantum chemistry algorithms puts molecular design in reach as well as simulations of biologically and pharmaceutically important systems such as small proteins with unprecedented accuracy and speed, Martinez said.

The research was published in the March online issue of the Journal of Chemical Theory and Computation.