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Supercomputer Sets Protein-Folding Record

Posted by Soulskill on from the here's-your-chance-to-top-the-folding@home-stat-boards dept.

Nicros writes with this snippet from Nature News: "A specially designed supercomputer named Anton has simulated changes in a protein's three-dimensional structure over a period of a millisecond — a time-scale more than a hundred-fold greater than the previous record. ... The simulations revealed how the proteins changed as they folded, unfolded and folded again. 'The agreement with experimental data is amazing,' says Chandra Verma, a computational structural biologist at the Bioinformatics Institute of the Agency for Science, Technology and Research in Singapore. Simulating the basic pancreatic trypsin inhibitor over the course of a millisecond took Anton about 100 days — roughly as long as computers spent toiling over previous simulations that only spanned 10 microseconds."

63 comments

  1. Even though it was published in Nature News... by blind+biker · · Score: 4, Interesting

    ..it's a rather poor article. It talks in very basic terms about proteins and their folding, talks a bit more about the scientist who founded the institute behind the computer, and says fuck-all about the construction of the computer itself.

    Bah. For a publishing house of Nature Publishing Group's (intellectual and economic) muscle, one should expect more.

    --
    "The agriculture ministry is not in charge of Gundam" - Japanese ministry official.
    1. Re:Even though it was published in Nature News... by Anonymous Coward · · Score: 0

      I've come to expect less of Nature in recent years. A lot less.

    2. Re:Even though it was published in Nature News... by ikkonoishi · · Score: 4, Informative

      Here this should give you more information.

      http://en.wikipedia.org/wiki/Anton_(computer)

      I think the article was alright though. It told what was going on, and why it could be important. It wasn't written for a computer nerd demographic so the exact specs weren't really relevant.

    3. Re:Even though it was published in Nature News... by kestasjk · · Score: 1

      What I want to know is how they verify the accuracy of the results.

      --
      // MD_Update(&m,buf,j);
    4. Re:Even though it was published in Nature News... by Anonymous Coward · · Score: 2, Funny

      It wasn't written for a computer nerd demographic so the exact specs weren't really relevant.

      You are writing for a nerd demographic though so you should have said "It wasn't written for a computer nerd demographic so it missed out all the most important information."

    5. Re:Even though it was published in Nature News... by anguirus.x · · Score: 5, Informative

      The best way is to just compare them to the actual structure which is known from x-ray crystallography and NMR studies. They could do isotopic replacement studies to get ideas about which hydrogrens or nitrogens or carbons were kinetically involved in the folding process and see whether the same atoms were important in the simulation. If they're the same it could just be a coincidence, or it could be an indication that the folding itself is accurate on the computer, not just the final structure. This is truly amazing, but we've still got a long ways to go. MOAR COMPUTERS PRZ!

    6. Re:Even though it was published in Nature News... by Anonymous Coward · · Score: 1

      It wasn't written for a computer nerd demographic so the exact specs weren't really relevant.

      You are writing for a nerd demographic though so you should have said "It wasn't written for a computer nerd demographic so it missed out all the most important information."

      A true computer nerd demographic wouldn't need to have it written out for them. They would just figure it out for themselves.

    7. Re:Even though it was published in Nature News... by serviscope_minor · · Score: 2, Insightful

      ..it's a rather poor article. It talks in very basic terms

      That's because it's in nature news, which does rather high-level, short coverage of a wide range of topics for a very broad scientific audience. It's meant to be a "hey look this is cool" article, that you can read up more about if you are interested and have the right kind of background. Perhaps you were thinking it was a ahort or regular article?

      --
      SJW n. One who posts facts.
    8. Re:Even though it was published in Nature News... by imsabbel · · Score: 2, Interesting

      Nature and Science are not for hard science.

      If you just get articles from citation search its not obvious why, but if you ever see a print issue it becomes obvious:

      They cover a _huge_ range of fields. You can have articles about egyptian mummies, rainforrest status in south america, neutron scattering and virus chrystallography within 20 pages or so.

      So people have to write the arcticles in a way that at least readers from most of the fields involved can understand it and see why it is important. Otherwise, it would better to publish it in a publication of a narrower scope.

      --
      HI O WISE PRINCE. WHT TOOK U SO DAM LONG?
    9. Re:Even though it was published in Nature News... by the+gnat · · Score: 2, Insightful

      The best way is to just compare them to the actual structure which is known from x-ray crystallography and NMR studies.

      And so far, this is the only way that most researchers are willing to trust. There is a very good reason why these folding studies tend to focus on a small group of well-defined model systems, because the folded native structure is already very well understood, and it provides an essential constraint on the interpretation of results. Using ab initio physics calculations like this for truly blind structure prediction would be a complete waste of time, and the entire field figured this out decades ago.

    10. Re:Even though it was published in Nature News... by the+gnat · · Score: 4, Informative

      Nature and Science are not for hard science.

      The actual research articles are hard science - this was just a news story for a general audience. The official publication of the results in Science magazine appears to be a pretty serious piece of work, and it's significant enough that the editors allowed them to make it reasonably long instead of a (severely compressed) three- or four-page summary article like most of what they publish. There are lots of valid criticisms of those two journals, starting with their length requirements, but they're not Scientific American, and publishing in one of these is practically a prerequisite for getting a faculty position in biosciences at a major research university.

    11. Re:Even though it was published in Nature News... by modmans2ndcoming · · Score: 1

      if the computer does a simulation on a known structure, then you can compare its accuracy to that of the known experimental results.

    12. Re:Even though it was published in Nature News... by matt4077 · · Score: 1

      That's quite misguided. Both Science and Nature have "magazine" parts written by science journalists that cover current research at a level suitable for a general but well-educated scientific public. The real meat is in the articles that use the traditional scientific publication method (i.e. written by scientists, peer-reviewed). These articles come from all areas of science, but they're not written to be understood by outsiders or anything like that. In essence, if the system works a breakthrough in any field will be covered in these journals (or PNAS), articles of lower importance will find their place in more specialized journals. Thus Nature published papers such as the discovery of X-Rays (physics), plate tectonics (geo) or the structure of DNA (biology).

      --
      Fleur de Sel
    13. Re:Even though it was published in Nature News... by ElektronSpinRezonans · · Score: 3, Informative

      This was not an ab initio, calculation. It's all atom MD, which itself is an approximation. People have done ab initio calculations on 10-15 residue peptides, but that's about all you can do with current computational power.

      I believe the article is published in Science not because of its computer utilization (i.e. using a bad-ass super computer), but because of its biological relevance. They managed to characterize not only the peptides conformations, but also their mutant's behavior in silico.

    14. Re:Even though it was published in Nature News... by the+gnat · · Score: 3, Insightful

      This was not an ab initio, calculation. It's all atom MD, which itself is an approximation

      Sorry, I meant "ab initio MD", although I realize that to a chemist or physicist this is a total oxymoron. (My background is molecular biology and bioinformatics, where we try not to think about quantum chemistry.) I should have written "physically-based", if you prefer, as opposed to the knowledge-based approaches that have been most successful for de novo structure prediction. (I think most MD "force fields" are ultimately based on genuinely ab initio QM calculations.)

    15. Re:Even though it was published in Nature News... by Anonymous Coward · · Score: 1, Informative

      Here ya go, whinger:

      David E. Shaw, et al "Anton, A Special-Purpose Machine for Molecular Dynamics Simulation," Communications of the ACM, vol. 51, no. 7, 2008, pp. 91–97. http://mags.acm.org/communications/200807/?folio=91

      Jeffrey S. Kuskin, et al "Incorporating Flexibility in Anton, a Specialized Machine for Molecular Dynamics Simulation," Proceedings of the 14th Annual International Symposium on High-Performance Computer Architecture (HPCA '08), Salt Lake City, Utah, February 16–20, 2008. http://www.cs.utah.edu/hpca08/papers/6A_2_Kuskin.pdf

      Richard H. Larson, et al "High-Throughput Pairwise Point Interactions in Anton, a Specialized Machine for Molecular Dynamics Simulation," Proceedings of the 14th Annual International Symposium on High-Performance Computer Architecture (HPCA '08), Salt Lake City, Utah, February 16–20, 2008. http://www.cs.utah.edu/hpca08/papers/6A_1_Larson.pdf

    16. Re:Even though it was published in Nature News... by Anonymous Coward · · Score: 0

      I find your comment on this article rather mundane, and lacking eloquence. You provided no further information about the substance that the original article apparently lacks, nor did you aspire to the level of intellectualism you accused them of discarding. It would seem to me that their article panders exactly to someone like you, if only to give you a reason to gripe about something on a Sunday morning.

    17. Re:Even though it was published in Nature News... by Hatta · · Score: 0, Redundant

      It's Nature News, not Nature. It's not supposed to be a research article. If you want that, there's a citation at the bottom. That's more than you can say for 99.99% of the popular science reporting out there.

      --
      Give me Classic Slashdot or give me death!
    18. Re:Even though it was published in Nature News... by blind+biker · · Score: 1

      It's Nature News, not Nature.

      I know, and I think I wrote so myself in the OP. I read Nature News rather regularly at work (at the coffee table, believe it or not) and this article was, in comparison to the ones I read, sub par. It wasn't quite the kind of shite BBC News would publishes (online) regarding science and technology, but it deviated into that sad direction.

      --
      "The agriculture ministry is not in charge of Gundam" - Japanese ministry official.
  2. Re:Bigger computer or simplified model? by Anonymous Coward · · Score: 1, Insightful

    It's about someone (a rich someone) building a really big computer to tackle a really, really, really, really, really, really, really complex physical/chemical problem that we currently know dick all about.

    If protein folding was equivalent to fluency in English, we'd be at "bwawubda?"

  3. Hundred-fold greater? by Anonymous Coward · · Score: 1, Insightful

    over a period of a millisecond — a time-scale more than a hundred-fold greater than the previous record

    This phrasing always confuses me where they say "It's this much faster so it's x times greater!"

    So they're a hundred fold greater and they're a millisecond...? Does that mean the other guy took 1/100ths of a millisecond?

    1. Re:Hundred-fold greater? by Samantha+Wright · · Score: 4, Informative

      No, Anton simulated one millisecond over the course of a hundred days. The previous recordholder took roughly the same time to do a hundredth of the work. (This was probably the RIKEN MDGRAPE-3, but again, documentation is le sparse.)

      --
      Bio questions? Ask me to start a Q&A journal. Computer analogies available for most topics!
    2. Re:Hundred-fold greater? by Anonymous Coward · · Score: 0

      I believe the previous record holder was Klaus Schulten (sp?) at UIUC, using an x86 Linux cluster.

    3. Re:Hundred-fold greater? by Anonymous Coward · · Score: 0

      . . .documentation is le sparse.

      Pepe Le Pew, is that you?

  4. Processing power by cjfs · · Score: 2, Funny

    The performance of a 512-node Anton machine is over 17,000 nanoseconds of simulated time per day for a protein-water system consisting of 23,558 atoms

    So... how many libraries of congress per second??

    1. Re:Processing power by Anonymous Coward · · Score: 0

      Can it run slashdot?

    2. Re:Processing power by rubycodez · · Score: 1

      since each of the 512 chips has six two-way links, one-way being 50 GBit/sec, we have roughly 6 * 50 * 512 Gbit/sec through each chip, or 154 Tbit/sec or about 19 Tbytes/sec.

      If the printed LOC is 10TB, then almost two Library of Congress' worth of data being processed per second.

  5. applause! by StripedCow · · Score: 2, Insightful

    This research is extremely important for finding new drugs, and therefore I applaud the originators of the project, especially D.E. Shaw who apparently put also a lot of funding into it. I wish more (rich) people put their money into such immensely useful projects. It is not just a noble thing to do, it is also smart, since we all could one day benefit from this kind of research.

    --
    If Pandora's box is destined to be opened, *I* want to be the one to open it.
  6. The folly of folding@home by Anonymous Coward · · Score: 0, Interesting

    Results like this just prove (as if scientists with half a brain couldn't reason it out themselves, but our audience here is the plebes I think) that distributed scientific computing using home computers is a fundamentally bad idea; a waste of natural resources.

    Why? Think about it. This computer using specialized ASICs is both vastly faster and more efficient (measured in calculations-per-watt-hour) than running the simulations on general-purpose CPUs.

    Now most people don't buy home computers just to run F@H, but we must also consider the fractional purchased induced by the public's desire to participate in "science" (and fractional replacements because of wear, although it's probably not the CPU itself that gets worn in any appreciable amount).

    Electricity must be generated to run home computers at full capacity that would otherwise have been turned of or idle. This energy could have "bought" a hundred-fold more simulations had it been put into specialized simulation machines like this one. Too bad.

    Populist science at its worst..

    1. Re:The folly of folding@home by Leynos · · Score: 1

      So where do I send my cheque?

      --
      "Did you exchange a walk on part in the war for a lead role in a cage?"
    2. Re:The folly of folding@home by the+gnat · · Score: 4, Informative

      That's a little unfair to Folding@Home. Shaw has a lot of resources to pour into this project - he's lured faculty members away from universities to work for him instead and has the equivalent of several large labs worth of advanced researchers. He also has an immensely larger budget than most non-profit labs, and he's self-employed so he doesn't have to answer to granting agencies or tenure committees. I think what he's doing is great but he's really one of the only people who could have pulled this off. It's difficult to know what approach will work best in advance, and both Shaw and Vijay Pande have been very innovative in approaching the problem from completely different angles.

      By the way, this approach has been tried before with less stellar results - I'm thinking of the MD-GRAPE project in Japan. You're also assuming that every problem is equally well suited towards custom ASICs, but actually, molecular dynamics is far easier to do this with than many other methods. For instance, Rosetta (Rosetta@Home and Fold.It) is doing structure prediction, not folding, using a mostly statistics-based energy function and Monte Carlo sampling, and this isn't something you can trivially offload to a specialized chip. In that case, distributed computing is by far the most efficient solution.

    3. Re:The folly of folding@home by blackraven14250 · · Score: 2, Insightful

      Good thing F@H runs on the GPU, which is many times faster than the CPU at these operations.

      Also, don't forget what it takes to build supercomputer capable of doing this, and that resources put into building supercomputers are then not available for the consumer market. Distributing this stuff allows for a compromise between absolute best performance and letting people have powerful computers at home.

    4. Re:The folly of folding@home by SoftwareArtist · · Score: 2, Insightful

      Actually, Folding@Home can also simulate these time scales by means of Markov state models. The trajectory is pieced together out of data collected from many short simulations, whereas the Anton trajectory is generated from a single MD run, but in practice that distinction is usually irrelevant. Protein dynamics are stochastic, so for any time scale longer than about 1 ns, both approaches given equally "realistic" or "valid" trajectories.

      That's not to criticize Anton. It's an amazing piece of hardware and they're doing amazing work with it. But of the two approaches, Markov state models are probably going to prove more valuable in the end. They make more efficient use of whatever computational resources you have available, they give more insight into the structure of the folding pathway, and they can be run on commodity hardware that many more people have access to. David Shaw has even admitted they'll eventually have to start using them. By the third generation of Anton, he expects to have hit limits on how far they can parallelize a single MD run, so Markov state models will be the only way they can keep adding processing power.

      --
      "I'm too busy to research this and form an educated opinion, but I do have time to tell everyone my uninformed opinion."
    5. Re:The folly of folding@home by stillnotelf · · Score: 1

      For instance, Rosetta (Rosetta@Home and Fold.It) is doing structure prediction, not folding, using a mostly statistics-based energy function and Monte Carlo sampling, and this isn't something you can trivially offload to a specialized chip. In that case, distributed computing is by far the most efficient solution.

      Right on the money. Because most of its applications use Monte Carlo as you mention, Rosetta requires lots of independent trajectories anyway. It's trivially parallelizeable (embarassingly parallel if you prefer) so distributed computing is the solution we use for pretty much everything. The Baker lab has the BOINC Rosetta@home and the rest of us use university-size clusters.

  7. not really by pigwiggle · · Score: 3, Insightful

    This has been the promise of computer simulation - "in silico" drug design - for decades. It hasn't panned out. And I say this as someone who makes a living doing exactly what these folks have done. High throughput bench work is far more efficient, time and money wise, than computer simulation. Hard to say when or if that will change.

    --
    46 & 2
    1. Re:not really by StripedCow · · Score: 2, Interesting

      According to the article, it now takes 100 days to do one simulation. If we had 100 times the processing power (maybe a little more accounting for overhead), then we could do it in one day. I'd say that would be possible today with sufficient financial support, or at least it could be a reality within a decade. In short, it still sounds promising to me..

      --
      If Pandora's box is destined to be opened, *I* want to be the one to open it.
    2. Re:not really by Anonymous Coward · · Score: 2, Interesting

      100 days is for a 'hero run', the bread and butter runs last 1-4 days apiece and account for more like 20-100 microseconds of simulated time. One of the big innovations of this machine is that those runs would otherwise take months on other machines.

    3. Re:not really by Anonymous Coward · · Score: 0

      ya, so the ran numeric computations for a long time. great. Where is the comparison against experiment that suggests the results are meaningful in any way? That's been the problem with these computer simulations- they tend not to match up to experiments well enough to provide any benefit for drug design.

    4. Re:not really by WrongMonkey · · Score: 2, Insightful

      I totally agree with you. I think it should always be pointed out the inherent limitation of these models. D.E. Shaw Research, Folding@home and many others use a force-field model that is fundamentally Newtonian. It doesn't take into account any quantum dynamics, it can't model the formation or dissociation of chemical bonds and most of the simulation parameters aren't much better than a wild guess. There used to be an implicit assumption in the computational chemistry community that all of those little errors would cancel out for large molecules, such as proteins. But, personally, I don't think that assumption has held up very well to experimental scrutiny.

    5. Re:not really by axismundi · · Score: 1

      You're absolutely right, though you're going to get a lot of abuse for your statement. While I think it's fine that they continue pushing research in this direction, its usefulness in drug design, etc. is often overstated, typically to get the funds necessary to pull off this kind of stuff. And yes, I was once a protein folder (in grad school), so I am qualified to make this statement.

    6. Re:not really by Anonymous Coward · · Score: 0

      What exactly do you work on? As far as I know the Anton is the only serious attempt at a dedicated Molecular Simulation processor. MD-GRAPE would be the next closest.

    7. Re:not really by pigwiggle · · Score: 1

      I suppose that depends on what you are doing. The kinds of potential energy surfaces these simulations use are extremely crude - ball and spring (sometimes one ball for many atoms), electrostatics, short range repulsion, and no chemical reactions. Only good for rough trends in docking and stuff. If you need reactivity, and you will for it to really compete with bench work, there are some severely limited classical force fields that work - but they are at least an order of magnitude more expensive. More accurate methods (quantum mechanics) are multiple orders of magnitude more expensive.

      --
      46 & 2
    8. Re:not really by pigwiggle · · Score: 1

      I do molecular dynamics. These are MD simulations. They are talking 2 orders of magnitude speedup. That's good, but not good enough to compete with bench work. Incidentally, people are claiming this sort of speedup by offloading some parts of the calculation to a GPU. NCSA has a cluster of GPUs for just this use - Lincoln if I recall correctly. MD is currently useful for a lot of stuff. Not drug design yet.

      --
      46 & 2
    9. Re:not really by StripedCow · · Score: 1

      Aren't these interactions only interesting at the small scale? If the bulk of the computation is in the long-range interactions, then I'm not sure if these more expensive computations will really increase the complexity that much... but I am not an expert.

      Also, I've seen once a documentary (forgot the name), in which a couple of students were trying to figure out the folding by crystallization, and they were seriously concerned that the folding of the proteins would not happen correctly in the solid state. So, unless there are methods to avoid this, this does seem to be an area where the "in silico" drug design could be really helpful.

      --
      If Pandora's box is destined to be opened, *I* want to be the one to open it.
    10. Re:not really by Anonymous Coward · · Score: 0

      so for no one has shown that even if you speed up the calculations 100 orders of magnitude and did a molecular-mechanics simulation on the order of seconds that it would correspond to some observable movement or experimentally interesting behaviour of a protein.

    11. Re:not really by pigwiggle · · Score: 1

      an 33 order of magnitude increase in a single typical MD timestep is of the order of the lifetime of the universe.

      --
      46 & 2
  8. But what kind of keyboard does it have? by Anonymous Coward · · Score: 0

    Dvorak?

  9. Ah, the human body by Anonymous Coward · · Score: 1, Insightful

    I love it how simple-minded tech geeks, usually IT guys, programmers and even people who should know better like electrical engineers, think that the internet is more complex than the human body... Here we have ONE molecule, simulated for a lousy millisecond, and it took more than THREE MONTHS. How many molecules in the human body? Our body is performing a truly staggering amount of computation. Actually, every bit of matter is, everything including "inanimate" matter, it's really all the same. We just happen to be more complex.

    I wonder how accurate this is? Information Processing in Human Body And when we do start uderstanding how the huge amount of molecules in one cell behaves, we can maybe start understanding how the huge number of cells becomes US. Including things like diseases and aging. Once that is done, hello life-extension! Isn't that more interesting than tin cans floating in a vacuum? I think so. But then again, I'm crazy; I think wanting to have more time is the same as wanting to have more space. It's humans exploring the universe, it's just that we need to live longer than we do if we think we really are going to explore the universe. After all, can a mayfly explore a city? It'll be dead in three days. That's us, in space.

    1. Re:Ah, the human body by HiThere · · Score: 4, Interesting

      It is complex, but you are ignoring the relative isolation between levels that exists in the human, and rat, body.

      Protein folding may be complex, but most of it is irrelevant detail. What's usually important is the final shape that one ends up with, e.g. But when wants to modify that process, then the details of that process become important. This is roughly equivalent to...at the level that I work, I pay no attention to how the compiler is going to optimize my code. If I wanted to modify that I'd need to pay attention to things at a much finer level of detail.

      It *is* true that people tend to oversimplify things they aren't dealing with directly. But to make it a fair statement it needs to be made fully *that* general. (This doesn't make you original assertion false, but observationally it *is* false. I've never known a knowledgeable geek that oversimplified the biochemistry of life in the way that you painted. I'm sure they exist, but they aren't, as you implied, common. If they are common among your friends, well, then you have some uncommon friends.)

      --

      I think we've pushed this "anyone can grow up to be president" thing too far.
    2. Re:Ah, the human body by shougyin · · Score: 1

      After all, can a mayfly explore a city? It'll be dead in three days. That's us, in space.

      That's a horrible analogy IMHO. I don't see any need for humans to live longer than we do. We can pass on our knowledge to anyone that wishes to have it, and now have entire decades worth of knowledge, all at our finger tips. The only thing that matters is a persons thirst for such exploration. I'd much rather delve in something that stops the aging process (yes, i know, very far fetched) not to keep us alive for longer, but to keep us young till we die. Then you wouldn't have to worry about 80 year old people driving down the road, or unable to make a contribution to society, and could get rid of "old folks homes."

    3. Re:Ah, the human body by Ginger+Unicorn · · Score: 1

      I love it how simple-minded tech geeks, usually IT guys, programmers and even people who should know better like electrical engineers, think that the internet is more complex than the human body..

      I love it how you think that the moon is made of cheese. Oh you don't? Ah that must be because I just made up some bullshit strawman to make a point.

      --
      (1.21 gigawatts) / (88 miles per hour) = 30 757 874 newtons
  10. There's other stuff too by Anonymous Coward · · Score: 1, Interesting

    From experimental evidence we know the folding rates of certain proteins at various temperatures, we know the flow rates for ion channels, and so on. A lot of these macro-properties can't be tested in the short simulations that current computers can do, but they can easily be reached by the DE Shaw machine.

  11. Folding by Anonymous Coward · · Score: 0

    Haven't they folded all the proteins in existence by now? This is like a laundry day from hell.

  12. every great thing that has ever been done by Anonymous Coward · · Score: 0

    there was a time immediately before it was done when there had been many failed attempts.

  13. We are protein based quantum computers by Anonymous Coward · · Score: 0

    Well, i didnt know proteins did this. The image i get is that of animals being protein and dna based quantum computers designed to model and respond to the external world. add a human sized brain to that, and Im amazed we havent punched a hole in reality with the information density of our bodies. And the horrible waste: 7 billion of us, with so much idle time. Would it be so bad to be plugged into a server at night that feeds our bodies problems to calculate? or is that to matrixy?

  14. Re:Bigger computer or simplified model? by Anonymous Coward · · Score: 1, Insightful

    The physicists have been doing protein folding for decades now. We know the basics of the physics but it requires a lot of computer power to perform useful simulations. This article is probably just another small step along the way. But if they cannot explain exactly what they have done that is new, then they probably haven't done so much that is new.

  15. Here by Anonymous Coward · · Score: 1, Informative

    I didn't RTFA since I've already heavily researched these guys. D.E Shaw is the kind of billionaire I would be.

    Summary: The actual atomic interaction equations are simulated very fast. Distributing the results of a local interaction to the rest of the simulation quickly, is hard.

    http://www.deshawresearch.com/publications/Simulation%20and%20Embedded%20Software%20Development%20for%20Anton,%20a%20Parallel%20Machine%20with%20Heterogeneous%20Multicore%20ASICs.pdf
    http://cacs.usc.edu/education/cs653/Shaw-msMD-SC09.pdf

  16. Future Computing Speeds by catchblue22 · · Score: 1

    The fact that it takes 100 days to simulate a few milliseconds of molecular activity hints at the potential speed of future computers. I know the actual process isn't precisely analogous to the computation, but I suspect there are more elegant ways to compute than the methods we use today. Our brains "outperform" the best supercomputers, with energy requirements supplied by a bowl of oatmeal for a few hours of activity. The mind boggles at the possibilities.

    --
    This and no other is the root from which a tyrant springs; when first he appears as a protector - Plato (423 to 327 BC)
  17. heh by Anonymous Coward · · Score: 0

    Why do we need this? Lab rats fold proteins real-time...