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Supercomputer Performs Simulation of Virus 230

Posted by ScuttleMonkey
from the tomatoes-can-sleep-better-at-night dept.
moller writes to tell us Red Herring is reporting that researchers from the University of California at Irvine and the University of Illinois at Urbana-Champaign have announced that they created a computer simulation of a virus. From the article: "Using one of the world's fastest computers at the U.S. National Center for Supercomputing Applications, located at the University of Illinois at Urbana-Champaign, the researchers ran a computer program devised to reverse engineer the dynamics of all atoms making up the virus particle and a tiny drop of water containing it." Nature also has an interesting write up on the research surrounding this project.
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Supercomputer Performs Simulation of Virus

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  • by macklin01 (760841) on Tuesday March 14, 2006 @05:38PM (#14919352) Homepage

    This is just fascinating, and precisely why we do high performance scientific computing. This quote piqued my interest in particular:

    The model also shows that the virus coat collapses without its genetic material. This suggests that, when reproducing, the virus builds its coat around the genetic material rather than inserting the genetic material into a complete coat. "We saw something that is truly revolutionary," Schulten says.

    So, by doing this simulation of a tiny span of time, the team was able to get new insight into the process of viral replication that would be extremely difficult to come by with experimental techniques. It also is fascinating, since we often think of viruses as little static particles that float around until they interact with a cell, and yet the simulation showed the surface pulsing. Very cool! -- Paul

    • This strikes me as very useful bio-medically, as there are a lot of things in that field that take a long time to test, or things that can't be tested physically, for ethical reasons.
      • This is an important benchmark, aswell. So if we're capable of modelling a simple virus today with a supercomputer - in 10-20 years we'll be capable of modelling that virus on our home computer and by that time supercomputers will be able to modell simple one cell organisms probably.
      • by Anonymous Coward on Tuesday March 14, 2006 @06:07PM (#14919640)
        I realize that the /. crowd is going to fellate any researcher who uses high-performance computing to draw pretty pictures, but from the Nature summary this sounds like a classic scientific case of showboating.

        The researchers were using a technique called molecular dynamics, which attempts to model the movements of atoms in a 3D structure by integrating over Newton's equations. Force, however, is calculated using a coarse, empirical function of atom positions and their chemical properties. This model is weak, and it fails to produce physically-reasonable results on a whole variety of smaller problems, so it's an exaggeration to suggest that this simulation produced anything of physical or experimental relevance. And drawing strong physical conlusions from it? That's just crazy.

        Before I get flamed by the MD crowd, I'll say that I am NOT suggesting that MD is useless. It's just that, it has a very short track record on problems of this size, and even in much smaller systems (i.e. fewer atoms), it's success rate is questionable. We can't even predict the dynamics of a single protein with this stuff -- it's absurd to suggest that it will work on an entire virus.

        In short: don't be fooled. This experiment got into Nature because of its hubris and glamour, not necessarily because of its science.

        P.S. I work in this field, so I'm posting anonymously.
        • Very good points. I'd definitely like to read the paper in greater detail. The physical assumptions will make or break a simulation, and it's always good to know the limitations of any observed results. I'll be very interested to see if future work confirms these observations...

          I definitely appreciate reading your point of view, so thanks for your post. -- Paul

        • by Chris Burke (6130) on Tuesday March 14, 2006 @06:27PM (#14919821) Homepage
          I realize that the /. crowd is going to fellate any researcher who uses high-performance computing to draw pretty pictures, but from the Nature summary this sounds like a classic scientific case of showboating.


          Now that's just unfair. I'd be talking 2nd base at best.
        • by AFairlyNormalPerson (721898) on Tuesday March 14, 2006 @06:28PM (#14919835) Journal
          "Force, however, is calculated using a coarse, empirical function of atom positions and their chemical properties."

          You give them too much credit... force field people compute *some* of the forces and ignore most of them. Long-range electrostatics are often omitted entirely (and people wonder why their RNA strands fall apart once it flops around a bit - I mean jebus, people!).

          People do these simulations to "gain atomic level insight" into the problem; however, it's very rare to hear anyone say anything "insightful" about the chemistry AND do it in a believable way.

          More "fascinating" simulations involve including a small region which is treated "quantum mechanically" and thus allow for bond formation/breaking; however, the QM models are so crude themselves that they need to be parameterized to get the "correct" answer. That's right - you heard it. It's the big secret. In order to get the more "trustable" simulations to produce something in the ballpark of remotely representing reality, you have to know "the answer" before you do the simulation and then teach the model to reproduce that "answer"... then you can write a paper and show that you're model "get's the answer" - and that's about the limit of "insight" that's often gained from these sort of simulations.
          • by protovirus (173869) on Tuesday March 14, 2006 @07:07PM (#14920155)
            [you have to know "the answer" before you do the simulation and then teach the model to reproduce that "answer"]

            Wait a minute... isn't that completely backwards for QM... shouldn't a QM simulation know the answer even before you ask the question? :)
          • by Decaff (42676) on Tuesday March 14, 2006 @09:46PM (#14921138)
            In order to get the more "trustable" simulations to produce something in the ballpark of remotely representing reality, you have to know "the answer" before you do the simulation and then teach the model to reproduce that "answer"... then you can write a paper and show that you're model "get's the answer" - and that's about the limit of "insight" that's often gained from these sort of simulations.

            You are, of course, absolutely right. Things haven't changed since I started to do this kind a long time (20 years) ago. However, you can gain some sort of insights, as you can find out which interactions (even thought they are simplified) can matter in the real world. By trying to simulate the real world, you can find out more about it, even if you aren't able to make many predictions.
        • We can't even predict the dynamics of a single protein with this stuff

          Uh, this is a troll. The AC has no idea WTF he's talking about. Either that, or he's an empiricist who can't stand to see computational science steal his thunder. Plenty of proteins have been modeled using QM/MM and had the results validated by empirical studies.

          • Plenty of proteins have been modeled using QM/MM and had the results validated by empirical studies.

            Sorry, but as far as I know there has not been a single successful simulation of protein folding. Simulation the general behaviour of a complete protein is not the same as completely understanding the interactions and structure.
            • by Salis (52373) <howard.salis@gma ... minus physicist> on Tuesday March 14, 2006 @08:07PM (#14920608) Journal
              http://www.stanford.edu/group/pandegroup/ [stanford.edu]

              They've folded proteins whose kinetics are 1st order (ie. small enough proteins).

              The folding problem is the one of the hardest ones. So don't get all blustery about it not being a solved problem. Cancer hasn't been cured yet either.
              • by Decaff (42676) on Tuesday March 14, 2006 @08:29PM (#14920742)
                The folding problem is the one of the hardest ones.

                I agree.

                So don't get all blustery about it not being a solved problem. Cancer hasn't been cured yet either.

                My point was that if you can't deal with the folding of even a moderately complex single protein, then to say you have modelled an entire virus to any significant extent is to mislead.
        • I don't see anything in the article saying that this is the completed product. In fact, the second paragraph states
          The simulation pushes today's computing power to the limit. But it is only a first step. In future researchers hope that bigger, longer simulations will reveal details about how viruses invade cells and cause disease.

          This sounds like it is meant more as a proof of concept, not a complete simulation.

        • MD is sexy for the journals. The real beauty of the simulation is that it provides a picture as to how something occurs over short timesteps. You can peek in at a protein as it moves, and watch what the computer thinks will happen. MD is also nice because you can change out molecules and run with modified conditions.

          As far as force field calculations go, it depends on the protein, however I'd jump up and down for an efficient and accurate force field system. I'm betting that as the simulation gets large

        • Then can you tell me why significant useful science (understanding about solidification at the atomic level) was found with this even larger MD simulation: http://pda.physorg.com/lofi-news-simulations-natio nal-nuclear_8651.html [physorg.com]
    • But now someone needs to go the next step and come up with an experiment that can, perhaps, indirectly, look at the fluid nature of the viral particle. While it stands to reason that the virus is not simply a static box envisioned in classic pictures, I would like to see some exprimental evidence of this "pulsing" phenomena.

      But pretty cool nontheless. Your tax dollars at work (finally).
    • So, by doing this simulation of a tiny span of time, the team was able to get new insight into the process of viral replication that would be extremely difficult to come by with experimental techniques.

      The fact that DNA is a structural part of viruses and often required for their assembly and stability has been well know for a long time. So, this result is not novel. It's also not hard to demonstrate this experimentally in many cases.
  • by markov_chain (202465) on Tuesday March 14, 2006 @05:39PM (#14919361) Homepage
    They will be writing computer simulations of spores!
  • by Anonymous Coward on Tuesday March 14, 2006 @05:43PM (#14919404)
    a McAfee AntiVirus update immediately wiped this program and all associated files from the face of the earth.
  • Exchange... (Score:5, Funny)

    by fahrbot-bot (874524) on Tuesday March 14, 2006 @05:48PM (#14919455)
    Later that day, the virus infected their simulation of a MS Exchange server. Fortunately, it was so slow that it was discovered before infecting all the simulated Outlook users.

    The virus later choked to death on a SMTP configuration file.

  • by Amonimous Coward (778781) on Tuesday March 14, 2006 @05:49PM (#14919460)
    Dear Sir or Madam: This letter is to notify you, pursuant to the provisions of the Digital Millennium Copyright Act, that we believe one of your humans is infringing God's copyrighted materials. Specifically, God is the owner of the copyright and trademarked materials, wich includes all life forms. The aforementioned human reverse engineered a virus without authorization, thereby infringing upon God's copyrights and trademarks. Accordingly, God demands that you act expeditiously immediatelly stop and remove all acquired data from that procedure in order for you to claim a safe harbor under the DMCA from liability for contributory and vicarious copyright infringement. Sincerely, God
    • Specifically, God is the owner of the copyright and trademarked materials, wich includes all life forms. The aforementioned human reverse engineered a virus without authorization, thereby infringing upon God's copyrights and trademarks.

      Jesus Christ on a pogo stick, God! I thought that you of all people would know that those copyrights expired millions of years ago. And as for your trademarks? You have done nothing lately to protect them, so I'm pretty sure that you are SOL on those as well.

      Have a nice da

      • ...those copyrights expired millions of years ago.

        Thousands. Thousands of years ago. HTH.

      • "You have done nothing lately to protect them..."

        In other news - Authorities suspect arson in the WTO fire but are still no closer to explaining the source of the brimstone.
    • by Urusai (865560) on Tuesday March 14, 2006 @06:13PM (#14919682)
      ...on finding a lawyer. I hear most of them end up downstairs.
    • by brianerst (549609) on Tuesday March 14, 2006 @06:19PM (#14919741) Homepage
      Dear God,

      Thank you for your letter, dated 14 March, 2006, in which you expressed concern in re:possible DMCA copyright violations in our research activities. On the advise of counsel, we have concluded that your copyrights and/or patent applications on "life" are invalid due to prior art, namely, yourself. In that you stand outside of time, you infinitely predate your subsequent creations (rendering any patent claims moot) and any copyrights on your works predate English Common Law, which form the sole basis for your tort.

      Sincerely,

      Orobouros Corporation
      What goes around, comes around

  • possible? (Score:5, Interesting)

    by spectrokid (660550) on Tuesday March 14, 2006 @05:52PM (#14919494) Homepage
    I once read that if you converted all the sand of the earth into processors, it would still take ages to accurately simulate the folding of a protein. Is this just "zooming out" and ignoring things like protein folding?
  • Just a few billion more molecules worth of computing power to go!
  • by Frumious Wombat (845680) on Tuesday March 14, 2006 @05:56PM (#14919545)
    Bigger problems, and bigger computers to solve them on. This is certainly a fun example, and aesthetically pleasing as well.

    Unfortunately, we're still a few generations of supercomputer off from being able to simulate ribosomes (at which point most of the cellular machinery will be suitable for in-silicio biochemical investigation), but this is an excellent step along the way. It's also a good to showcase Schulten's group's work on efficient parallelization of complex simulations. He's had to solve a lot of algorithmic issues in order to be able to run that simulation, so this is not just an example of "wait for a bigger computer". If you check out their web-page http://www.ks.uiuc.edu/ [uiuc.edu], you'll find discussions of the underlying technology, which has required collaboration between biophysicists and computer science. My hat is off to them, especially as they not only achieved the proof of concept (we can simulate a small virus), but also gained biochemical insights (we didn't know they collapsed without the genetic payload). Bully for the Biophysicists!

    Note: I don't work for them, but I admire the scale of simulations they do, and their willingness to make available to the community the tools they use.
  • by Anonymous Coward on Tuesday March 14, 2006 @06:00PM (#14919579)
    From TFA the virus so simple as to need a second more complex virus in order to replicate. Even so, the simulation only covered 50 billionths of a second, or about 50,000 frames. The Nature article stated that in the next 5 years it may be possible to simulate more complex viruses. Its amazing to see how complex life is that even the most powerful computers we have come up short.
  • by pimpimpim (811140) on Tuesday March 14, 2006 @06:01PM (#14919591)
    FTA:
    The simulations followed the life of the satellite tobacco mosaic virus, but only for a very brief time,

    The nature article mentions a runtime of 50 times a billionth of a second, which I guess is 50 nanosecond, or 50 femtosecond, depending on how you define 'billion'. 50 nanoseconds is pretty good for a simulation nowadays, especially for a system of that size.

    Look, it al seems very nice that they did this, fancy pictures and nature paper garantueed, but this really won't help us much further. This is no big scientific step forward. Virus processes happen at least in the micro/millisecond timescale, there's a lot of protein diffusion and refolding going on. Since the short simulation done here was an immense effort, it means that going to the timescales studying the real important processes is still way too far away. But who knows, maybe in ten years.

    Right now, you could better use the same computer power used for this single project to study a lot more smaller projects that actually will give us insight into real molecular processes. Or maybe I'm just jealous ;)

  • Chuckle! (Score:4, Funny)

    by MyLongNickName (822545) on Tuesday March 14, 2006 @06:14PM (#14919694) Journal
    They need a supercomputer to simulate a virus? Crap, just get an XP box, give one of my coworkers admin rights, and you'll have the real thing in 15 minutes!

    Futher proof of Windows' superiority.
  • by Sebilrazen (870600) <blahsebilrazen@blah.com> on Tuesday March 14, 2006 @06:21PM (#14919758)
    FTFA: This particular virus can only replicate in a cell which has already been infected by another virusthe tobacco mosaic viruswhich commonly attacks tomato plants.

    Tomacco.
  • by sidney (95068) on Tuesday March 14, 2006 @06:22PM (#14919767) Homepage
    Finally, I can say this for real: Imagine a Beowulf cluster [nih.gov] (link is to Biowulf) of these!

    The modeling software they used is called NAMD [uiuc.edu], free open source "parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems" that will run on commodity clusters of tens of Linux PCs on gigabit ethernet. In other words, you too can run the virus simulation on your own Beowulf cluster, if you don't mind it taking some years to run. According to NCSA's own press release [uiuc.edu] about the virus simulation, it "only" took 35 processor-years, so if you have a 100 fast Linux PCs on a gigabit network lying around you can do it yourself in not much more than 4 months.
    • by tskirvin (125859) on Tuesday March 14, 2006 @06:28PM (#14919830) Homepage
      Also of note: we've done a series of cluster-building workshops [uiuc.edu] specifically focusing on the software and hardware required to run these kinds of simulations. Copies of the presentations and tutorials are linked off of that page.

      And if you want to see how we designed our clusters, I've got full specifications up here [uiuc.edu].
    • NAMD doesn't scale well, so unless you have a low latency network fabric you won't even come close to cashing in with more than 2^5 nodes on gigE. It's not really beowulf friendly.

      Their Origin 2000 numbers show that the latest release had no speedup after 126 processors. That is an SMP...

  • by tskirvin (125859) on Tuesday March 14, 2006 @06:23PM (#14919782) Homepage
    1. The full research page for this project is here [uiuc.edu]. This is a lot better than the stuff linked through Nature and such.

    2. The image was actually generated by our group [uiuc.edu], and specifically Anton Arkhipov [uiuc.edu], using our software package VMD [uiuc.edu]. NCSA didn't have anything to do with it.
    • NCSA didn't have anything to do with it.

      So, the machine the simulation ran wasn't at NCSA?

      And just so people don't get the wrong idea, VMD just visualizes data. It isn't software for running simulations. I know that's not what you meant but some people might not understand that.

  • Living Things (Score:3, Interesting)

    by the linux geek (799780) on Tuesday March 14, 2006 @06:29PM (#14919846)
    What about the fact that virii aren't usually considered to be alive, not being capable of reproduction outside of a host cell?
    • Man, that statement would make a virologist puke.

      Ok I showed it to one, and she didn't actually puke, but I swear she was green.

      Virii is hypercorrect. which is a nice way of saying 'it makes you sound like an idiot'
      Viruses

      Also, as to whether or not a virus is alive is in debate. I have read both sides of this issue, and my conclusion is that it will take someone smarter then me to figure it out.
  • SKYNET not only simulated a virus but it actually infected computer systems.
  • A supercomputer that starts designing viri in an attempt to rid the planet of humans. The virus wipes out huge numbers of people, then the survivors counter-attack and the computer keeps spinning out new viri that allow the computer to control specific behaviors in people. It's a see-saw futuristic sci-fi smack down!

    You could have the surviving humans turn into creatures with hyper-reactive DNA to protect themselves against the constantly changing virus patterns. Call them muties or something. They ha

  • by Expert Determination (950523) on Tuesday March 14, 2006 @09:43PM (#14921116)
    Here [uiuc.edu]. They're just looking at what holds together the structure of the virus.
  • by repvik (96666)
    "moller writes to tell us that Red Herring is reporting that researchers ... have announced ..."

    Indeed.
  • Discuss. ;)

    (That's what I believe, anyway; at a fundamental level, life is something unique that cannot entirely be modeled via biochemical process modeling. Still can't wait to see the results once this gets better...)
    • For a virus, the line between living and non-living is an abstract one anyway. Same thing with those prion diseases. People want to start drawing these hard distinctions, and it's all an illusion. Words like "believe" and "feel" come into the picture, and objectivity goes out the window. What is life? "Unique" in what way?

      It's hard to structure a definition of "life" that includes things like viruses and prion diseases without including stuff like these simulations, cellular automata and even memes, imo.

      m-
  • In premed, I tried to produce a 4D graphic animation of a virus being reproduced from an RNA, protein by protein, in a host cell. My advisor told me it would be too hard - I should use the newfangled computer to instead process huge (1980s megabyte) datasets of genetic drift data. I thought he was too shortsighted based on his pessimism for the animation, so I just made PR animations of cameraviews flying around a double helix, which I reused as a lightshow for the psychedelic rock band I lived with.

    Turns o

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