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Supercomputing Science

Using Supercomputers To Find a Bacterial "Off" Switch 30

Posted by samzenpus
from the bug-crunching dept.
Nerval's Lobster writes "The comparatively recent addition of supercomputing to the toolbox of biomedical research may already have paid off in a big way: Researchers have used a bio-specialized supercomputer to identify a molecular 'switch' that might be used to turn off bad behavior by pathogens. They're now trying to figure out what to do with that discovery by running even bigger tests on the world's second-most-powerful supercomputer. The 'switch' is a pair of amino acids called Phe396 that helps control the ability of the E. coli bacteria to move under its own power. Phe396 sits on a chemoreceptor that extends through the cell wall, so it can pass information about changes in the local environment to proteins on the inside of the cell. Its role was discovered by a team of researchers from the University of Tennessee and the ORNL Joint Institute for Computational Sciences using a specialized supercomputer called Anton, which was built specifically to simulate biomolecular interactions among proteins and other molecules to give researchers a better way to study details of how molecules interact. 'For decades proteins have been viewed as static molecules, and almost everything we know about them comes from static images, such as those produced with X-ray crystallography,' according to Igor Zhulin, a researcher at ORNL and professor of microbiology at UT, in whose lab the discovery was made. 'But signaling is a dynamic process, which is difficult to fully understand using only snapshots.'"
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Using Supercomputers To Find a Bacterial "Off" Switch

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  • by rmstar (114746) on Thursday December 19, 2013 @07:35AM (#45734669)

    They are searching for an enzime that reigns in bad bacterial behavior. Would that be a naughtyase?

  • by TheRealHocusLocus (2319802) on Thursday December 19, 2013 @07:58AM (#45734733)

    Proteins are not just building blocks, they are Rubik Cubes of the organic world, and this learning process of real-time signalling has reached the [inverse] stage as when we realized that with transistor amplification in a complementary balanced pair a bistable multivibrator [wikipedia.org] was possible. The bit 'state' storage when joined with the plumbing of NAND gates is the basis for the computer.

    With Life we have been reverse engineering, poking things with sharp sticks to see where and how they break, in medicine retarding or advancing chemical mechanisms to bring a patient's complex system back to natural equilibrium (health).

    Even simple computer models can be capable of astonishing behavior [youtube.com], and it is already possible to construct systems in which parallel (but inherently different to our own) evolution may occur. The challenge is to be able to model the mechanics of life on all practical scales simultaneously to the point where we could join software gametes in a virtual crucible and grow a model embryo. Or at least an e.coli.

    Note to scientists: please do not turn off e.coli. It's important to me.

    "There is a theory which states that if ever anybody discovers exactly what the Universe is for and why it is here, it will instantly disappear and be replaced by something even more bizarre and inexplicable. There is another theory which states that this has already happened." ~Douglas Adams

    • by wbr1 (2538558)
      I was doing electronic research and purchased a bistable multivibrator from Adam and Eve once. It was not what I expected.
    • by Anonymous Coward
      We realized that with tubes you know. It didn't take transistors to come up with flip flops. It can be done with relays.
  • by Anonymous Coward on Thursday December 19, 2013 @08:45AM (#45734935)
    The future won't be Dad commuting to the Moon office in giant 1960s rockets while smoking a pipe, or the Human Species (every single one of us!) bravely heading to the stars in some sort of sci-fi vehicle (ignoring all the realities we know about space)... No, the future is far more radical than that: it's the complete understanding of how matter organizes itself into life. And how we can control it.
    • The fermi principle says that while that is the ambition of every evolving civilization in the universe, there is only a short window between when they discover the technology for radio transmission and they discover the orgasmatron, ending all progress. This is the future folks future, folks.

    • The future won't be Dad commuting to the Moon office in giant 1960s rockets while smoking a pipe, or the Human Species (every single one of us!) bravely heading to the stars in some sort of sci-fi vehicle (ignoring all the realities we know about space)... No, the future is far more radical than that: it's the complete understanding of how matter organizes itself into life. And how we can control it.

      The anthropic principle says that if your prediction is possible then it's overwhelmingly more likely that some past civilization in the vastness of time and space got their first and you yourself are the product of their research. It also says that if a civilization persists forever it must achieve a ubiquitous computational power in devices that can simulate a greater number of neural firing events that it's creator. At that singularity, where simulated life and actual life can not be distinguished by t

      • I neglected to mention the corollary. Since were just a simulation, what's your purpose. Well presumably you exist to be window dressing in a sophisticated version of Grand Theft Auto or the Sims. However, if our creators are at all like ourselves then they are vain and one of these sims is an avatar for them. Which ones? well duh... it's the famous people folks!

        your simulated life is therefore meaningless unless you reduce your degrees of separation from famous people. Your highest purpose in life i

  • We need to know how to control a pair of amino acids called Phe396 in politicians so we can slip it into their martinis to stop their bad behavior.

  • What could POSSIBLY go wrong?

  • This might be a good BOINC project, just saying.

Premature optimization is the root of all evil. -- D.E. Knuth

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