The slowdown factor helps provide a realistic estimate of the delay in communication and computation time when multiple applications share the coupled system. Berman noted that many of the computational biology applications that had been discussed might be suitable for the kinds of studies of optimization and scheduling done in the group. A model problem need only be partitionable, with some communication between tasks. Real problems are needed to drive the computer science research, Berman said, and researchers' codes benefit from being developed for both performance and portability. She encouraged scientists with appropriate high-performance problems interested in implementation on networked systems to contact her group.
Proteins fold too fast to warrant the conclusion that they sample all possible states.
Their view is that in the earlier stages a protein possesses a large ensemble of structures. The researchers assume that this landscape resembles a many-dimensional funnel leading through a myriad of pathways to the native structure. The bottleneck may be seen as a large ensemble of structures representing possible folding pathways. Once a pathway is found, discrete kinetic intermediates appear as epiphenomena of the path taken until, like a liquid becoming glassy, a transition is made to the native state. Indeed, the analogy to fluid behavior near a critical point seems to be valid for proteins, and the relevant states correspond enough to put the simple simulations into direct contact with experiments like those performed by Jennings and her group.