This proposal seeks funding for a new high performance, parallel computer for computational biology and chemistry, specifically to study the structure and function of biological macromolecules. Washington State University has built considerable strengths in the studies of biological macromolecules, of which both the Nuclear Magnetic Resonance (NMR) Center and the new X-Ray Crystallographic facilities are important components. However, the key feature missing is the lack of computing power. Computers provide the crucial link since they are needed both for processing the large data sets obtained from NMR and crystallographic structure determination experiments as well as for theoretical studies such as molecular dynamics simulations and electronic structure calculations that provide the connection between structure and function and that also provide new directions for experiments. Modern research in structural biology requires fast computers, with ever increasing needs because of rapid advances in experimental methods that require analysis of larger and larger data sets and because of the increasing importance of computer simulations in understanding structure function relationships. In addition to daily computational needs, each of the five principal investigators has projects that require massive computing capabilities. These projects include studies of myosin, enzymesubstrate complexes, electron transfer complexes, protein-nucleic acid complexes, and the role of water in protein function. Currently, computing for structural biology at WSU is being carried on workstations owned by individual investigators. Many of these workstations are more than 5 years old, which means that they are at the limit of hardware reliability and are orders of magnitude behind current workstations in speed. For instance, computer simulations currently being carried out take weeks of computer time on our fastest workstations (IBM RS/6000 350). The only university facilities are an IBM 3090-300 and a VAX cluster (slower than many personal computers), which are heavily overused and expensive. Moreover, our most commonly used commercial software is not available for these computers. Although new inexpensive workstations (5 to 7 times faster than our RS/6000) may be used for many simple problems, researchers at WSU are facing more and more problems that require very fast computation, huge amounts of memory and/or huge amounts of disk space beyond the reach of individual investigators, even those that use computers as a major research tool. These needs can be met in part by Supercomputing Centers, but these centers are becoming overloaded so a middle level between that route and workstations is a vital need not currently met on this campus. Parallel processing computers such as the one proposed here are an ideal solution for academic research. They can have speeds equivalent to vector supercomputers such as Cray computers, but at a fraction of the cost. These computers have multiple processors of the same type that are found in the fastest workstations, but the combination of these processors into a single chassis provides several important advantages over multiple independent workstations. First, computation speed can increase almost linearly with the number of processors by distributing the computational "load" across several processors. Second, expensive resources such as memory and software can be shared by multiple users. Third, operations and maintenance of a single machine are much less, leading to a great saving in personnel time. Fourth, different processors may be dedicated to different types of usage at different times, allowing efficient usage of the processors. Finally, the modular nature allows investigators to increase the efficiency of the machine by simply adding additional processors if money becomes available. The proposed computer will replace our outdated workstations in fulfilling routine computational needs, but more importantly, will allow investigators at WSU to pursue the new avenues not possible on those workstations. Moreover, it will have an impact on not only the researchers currently directly involved in structural biology, but will provide a means of introducing state-of-the-art computational methods in structural biology and chemistry to researchers across the campus. The computer will be accessible by any networked personal computer or workstation, and staff are already in place who would provide consultation. With the addition of new faculty and the growing interest of existing faculty in structure-function studies, it is crucial that a new computer be obtained.
