Abstract: In our collaborative work with biophysicists, the goal for the computer scientists has always been clear: improve the performance of biophysical simulations. The particular code that we have studied and improved over the years is Molecular Dynamics (MD) simulation, a code that simulates the 3D structure of proteins over time, providing biophysicists with clues to explain how proteins accomplish their functions. The typical execution time of a single simulation is 30 days, thus any improvement in performance can have a significant impact.

During this collaboration, we have developed the concept of the "performance pipeline," which describes all of the components necessary to achieve high performance. In this talk, I'll describe the pipeline, along with results of our work at several stages in the pipeline, including parallel computation, better use of memory hierarchies, new algorithms, better programming languages (along with their associated compilers), specialized hardware, and software techniques to overcome hardware bottlenecks. The talk will begin with a brief overview of our work, and then focus on two significant parts algorithms that explore temporal (rather than spatial) simplification, and faster methods of finding square roots (an essential component of all 3D calculations).

Short Bio: Lars Nyland is an Associate Professor in the Mathematical and Computer Sciences Department at the Colorado School of Mines in Golden, Colorado. His research interests include high performance computing, 3D range imaging and computer graphics. Prior to his current appointment, he was a Research Associate Professor at the University of North Carolina at Chapel Hill, where he spent 12 years on the research track. During his time in Chapel Hill, he invented the Deltasphere-3000 scene digitizer, now sold by 3rdTech, in Chapel Hill, NC. He received his Ph.D. and M.A. from Duke University in 1991 and 1983 respectively, and his B.S. (with highest honors) from Pratt Institute in 1981. Outside of work, he enjoys wood-turning, ultimate frisbee, winter sports and family life.