We propose to acquire an integrated computer system for large data storage, high-performance computation, and state-of-the-art visualization that links to present and next generation terascale- to-petascale computers at the national supercomputing centers to support large-scale and long- time biomolecular simulations of membrane processes, bionanotechnological devices, cell mechanics, cellular energy transformation, and gene transcription. Hundred-terabyte simulation datasets will be stored on a disk array with a capacity of 204 terabytes and accessed by multiple 10-gigabit/s networks. High-performance analysis of the stored data will be enabled through two large shared memory (256 gigabytes each) servers and through graphics processing unit acceleration (NVIDIA Teslas with 4 teraFLOP/s single precision floating point arithmetic performance) equivalent to hundreds of cores per processor in real performance on envisioned applications. Through NVIDIA Quadro graphics accelerators with 4 gigabytes of memory, teraFLOP/s floating point performance, and 102 gigabyte/s memory bandwidth, the system will drive four single-user visualization front ends and a state-of-the-art 9.8 million pixel multi-user graphics projection sys- tem. The system will support ongoing experimental-computational collaborative projects among NIH investigators at the University of Illinois at Urbana-Champaign to resolve, in atomic detail, single molecule processes involving DNA helicases, lipoprotein assembly, protein synthesis in the ribosome, muscle force generation and elasticity, voltage-gated ion channels, membrane trans- port, and bioenergetics, as well as DNA single base pair detection in nanopores. The projects carry out simulations on terascale-petascale computers at national supercomputing centers that generate 10-100 terabytes of data which need to be stored, analyzed, and visualized locally. Technological advances at the centers leading to 1,000-fold data size increases must be matched by adequate local data analysis equipment. The proposed system serves this purpose. The Principal Investigator directs the NIH Resource for Macromolecular Modeling and Bioinformatics that will operate the system, is a leader in developing the needed biomolecular modeling and analysis software, and is an expert user of the technologies employed by the new system, in particular graphics processing unit acceleration.
The proposed computational microscopy system will assist in devising treatments against cancers, muscle disorders, cardiovascular disorders, in fighting drug resistance, and in discovering new drugs, e.g., new antibiotics. Experiments on DNA, lipoproteins, protein synthesis, muscle function, and nerve activity are interpreted through computer simulations that provide a tom by a tom views of the body's molecular machines. These views reveal the chemical detail needed to develop new pharmacological treatments.
|Harrison, Christopher B; Schulten, Klaus (2012) Quantum and classical dynamics simulations of ATP hydrolysis in solution. J Chem Theory Comput 8:2328-2335|