Following is an in-depth exploration of supercomputers.
Tremendously more powerful than typical business or home computers, supercomputersâ€™ calculations can happen at speeds of nanoseconds. They can figure out difficult problems or analyze incredibly complex and large amounts of data in amazingly short time periods. Following are examples of their use in biotechnology.
Through supercomputing and wireless mobile health technologies, more than 8,000 practicing oncologists and nurses are now connected to the data. The new infrastructure has the capability to analyze 5,000 patients a day. This is the promise of genomics and pharmacogenomics starting to come to life in a meaningful way.
But what is even more important in the story is the fact that this critical genomics data [via the Human Genome Project] clearly is making patientsâ€™ lives better. Because these health care teams now have precise information about patients early in their treatment cycle, in the past year the number of cases where these doctors have made incorrect recommendations has dropped from 32% to virtually zero.
This is an example of real personalized, patient-centered care. This is value in both outcomes and cost savings. This is a big advance, not just in medical treatment, but in the way medical care is delivered.
New York Genome Center, a consortium of academic, medical and industry officials, will use Watson [The IBM supercomputer that beat human contestants on â€œJeopardy!â€�] to sequence the DNA of cancer tumors at much faster rates than would be possible if done by a human being. The DNA information would then be combined with clinical information and fed to Watson to help determine the best way to treat a particular patient.
What makes Watson unique is that it isn't programed like most computers. Instead of relying on the information that's put into it, Watson learns by "reading" vast amounts of information and combining it with the results of previous work to find answers to problemsâ€¦..
Dr. Robert Darnell, New York Genome's president, CEO and scientific director, says that to completely analyze one person's brain tumor, doctors would have to sequence 800 billion base pairs of DNA, adding that it took him a year to sequence 140 pairs by himself. In comparison, Watson can sequence 75 million base pairs in one second.
And Darnell says that once doctors know a tumor's genetic makeup, they can use Watson's computing abilities to determine the best treatment for a patient based on the tumor's mutations. For instance, if a child's leukemia shows genetic traits similar to melanoma, a melanoma drug might be successful in shrinking that child's tumor, he says.
"This is the proverbial needle in the haystack and the haystack is enormous," Kelly [the director of IBM research] says. "Watson can do in seconds what would take people years. And we can get it down to a really personal level."
Proteins are made of long strands of amino acids folded into complex three-dimensional shapes. Their function is driven by their form. When a protein misfolds, there can be serious consequences, including disorders like cystic fibrosis and Alzheimer's disease [as well as Huntingtonâ€™s and many other degenerative and neurodegenerative disorders].
Finding out how proteins fold â€” and how folding can go wrong â€” could be the first step in curing these diseasesâ€¦..Blue Gene isn't the only supercomputer to work on this problem, which requires massive amounts of power to simulate mere microseconds of folding time. Using simulations, researchers have uncovered the folding strategies of several proteins, including one found in the lining of the mammalian gutâ€¦..
Think you have a pretty good idea of how your blood flows? Think again. The total length of all of the veins, arteries and capillaries in the human body is between 60,000 and 100,000 miles. To map blood flow through this complex system in real time, Brown University professor of applied mathematics George Karniadakis works with multiple laboratories and multiple computer clustersâ€¦..
Karniadakas and his team describe the flow of blood through the brain of a typical person compared with blood flow in the brain of a person with hydrocephalus, a condition in which cranial fluid builds up inside the skull. The results could help researchers better understand strokes, traumatic brain injury and other vascular brain diseases, the authors writeâ€¦..
Potential pandemics like the H1N1 swine flu require a fast response on two fronts: First, researchers have to figure out how the virus is spreading. Second, they have to find drugs to stop it.
Supercomputers can help with both. During the recent H1N1 outbreak, researchers at Virginia Polytechnic Institute and State University in Blacksburg, Va., used an advanced model of disease spread called EpiSimdemics to predict the transmission of the fluâ€¦â€¦
Meanwhile, researchers at the University of Illinois at Urbana-Champagne and the University of Utah were using supercomputers to peer into the virus itself. Using the Ranger supercomputer at the TACC in Austin, Texas, the scientists unraveled the structure of swine flu.
They figured out how drugs would bind to the virus and simulated the mutations that might lead to drug resistance. The results showed that the virus was not yet resistant, but would be soon, according to a report by the TeraGrid computing resources center. Such simulations can help doctors prescribe drugs that won't promote resistance.
If scientists can control cellular functions such as movement and development, they can cripple cells and pathogens that are causing disease in the bodyâ€¦..
The results, published in Nature Communications, stand apart from previous research because of the computational power applied to the problemâ€¦..
Phenylalanine pairs capable of forming a molecular switch are also present in many other signaling proteins, including receptors in human cells, making it an attractive target for drug design and biotechnology applicationsâ€¦â€¦
â€œWith Titan [the USâ€™s largest supercomputer] we will begin to see how the signal propagates across chemoreceptors,â€� Zhulin said. â€œWe think this will start to explain how signals are amplified by these remarkable molecular machines [the workings of biological molecules in nature].â€�â€¦..