Highlights of our Work

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Since Leuwenhook, microscopic images of living matter have been produced with radiation, from light to X-rays. With the advent of ever more reliable computational methodologies, molecular dynamics has reached the status of a trusted research instrument. This instrument is particularly powerful for imaging nanoscale, i.e., 10-100 nanometer size, systems. This month our group brought three computers on-line that can serve to image nanoscale systems, three 48-processor rack-mount Xeon clusters (pictured) running our MD program NAMD. One such cluster, a nanoscale system of 300,000 atoms imaged over a nanosecond at the most advanced simulation conditions possible today, requires four days of computing. The Clustermatic software from Los Alamos National Laboratory makes each cluster of 48 processors appear to biomedical researchers as a single machine and allows interactive simulations to temporarily displace long-running NAMD jobs. The clusters have been used already for a study of balance and hearing in the human inner ear. These senses are intrinsically mechanical, relying on hair cells to convert vibration to ion channel modulation. Ankyrin, a protein formed by repeats of a 33-amino-acid domain, is thought to act as a molecular spring in mechanotransduction channels. Explaining the mechanism of ankyrin elasticity requires large simulations of 340,000 atoms that apply repeatedly stretching forces to the protein and monitor its response, revealing a mechanical behavior ideally suited for its biological function. The clusters are presently also used to design artificial nanopores for sequencing of DNA.