Supercomputer Performs Simulation of Virus

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.

This is why we do scientific computing

[macklin01]

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

Re:This is why we do scientific computing

[ZachPruckowski]

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.

Re:This is why we do scientific computing

[A beautiful mind]

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.

No, this is scientific showboating.

[Anonymous Coward]

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.

Re:No, this is scientific showboating.

[macklin01]

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

Re:No, this is scientific showboating.

[Chris Burke]

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.

Re:No, this is scientific showboating.

[AFairlyNormalPerson]

"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.

Re:No, this is scientific showboating.

[protovirus]

[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? :)

Re:No, this is scientific showboating.

[Decaff]

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.

Re:No, this is scientific showboating.

[Seanasy]

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.

Re:No, this is scientific showboating.

[Decaff]

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.

Re:No, this is scientific showboating.

[Salis]

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.

Re:No, this is scientific showboating.

[Decaff]

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.

Re:No, this is scientific showboating.

[Salis]

The folding process can take place over microseconds of time.

Many processes, such as conformational changes, ion flow, and ligand binding can occur much faster (1 to 100 nanoseconds).

So if you start to simulate an already folded protein and watch its dynamics you can still discover what sort of behaviors it may do. Without having folded the protein.

Re:No, this is scientific showboating.

[Decaff]

The folding process can take place over microseconds of time.

Exactly. So modelling a 'virus' (or rather a model of a virus) on a scale of mere femtoseconds isn't going to give you a clear idea of anything.

Re:No, this is scientific showboating.

[Salis]

It was 50 nanoseconds.

Re:No, this is scientific showboating.

[Decaff]

Yes, you are right. The individual calculations were for femtosecond timesteps. However, significant changes in individual protein structures can take thousands of times longer that the length of time of this simulation.

Re:No, this is scientific showboating.

[Salis]

Well, that is true. I had forgotten about that detail. (Big detail though!)

But, what about hypothesizing certain criteria for the state of a folded protein? Such as... minimization of free energies, auto/cross correlation functions (pair distribution functions) going to zero (likely shell values), ergodicity in ensemble of states (time average = ensemble average). These are all indications of a system gone to equilibrium. Now, that's not necessarily the folded state..but it is a stable state of the protein

Re:No, this is scientific showboating.

[Salis]

Ok, true true. This just means I (and every other person studying stat mech) will have a job for the forseeable future. :)

Re:No, this is scientific showboating.

[Decaff]

Folding is only one aspect of understanding proteins.

True, but if you can't understand that, you can truly say you have modelled a protein in detail.

Re:No, this is scientific showboating.

[afidel]

Huh? How does that follow. We haven't modeled protein folding yet we can model car crashes fine. Just because we can't get a good answer at a very small scale does not mean that we can't get a good one at a larger scale with more loosly defined criteria. I mean even after we model a large protein folding we still won't necessarily understand what is happening at the quark level in that same simulation but it won't make the results any less valid.

Re:No, this is scientific showboating.

[Decaff]

Huh? How does that follow. We haven't modeled protein folding yet we can model car crashes fine. Just because we can't get a good answer at a very small scale does not mean that we can't get a good one at a larger scale with more loosly defined criteria. I mean even after we model a large protein folding we still won't necessarily understand what is happening at the quark level in that same simulation but it won't make the results any less valid.

This is true, but my point is that you have to be very careful

Re:No, this is scientific showboating.

[nwbvt]

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.

Gotta love the warmth of a slashdot flame

[tempest69]

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

Re:No, this is scientific showboating.

[SeanAhern]

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]

Re:No, this is scientific showboating.

[Decaff]

Also, if you read the actual journal article (Structure, not Nature) you'll note that everything that was found in this study is consistent with experimental results.

Of course it is. I have worked in this field. When you do this kind of thing, you set up the parameters so that you already know that almost everything about it is going to be consistent with experimental results. There are other approaches - called 'ab initio' - in which you make no assumptions, but that involved a phenomenal amount of computing for very small systems. The point of this kind of thing is to set almost everthing to be realistic, with all sorts of approximations and fine-tunings, in order to test your assumptions about small parts of the model.

Re:No, this is scientific showboating.

[Decaff]

You're an idiot.

No, a scientist; and one who has worked in this area

Parameters are developed to reproduce very basic and general properties of molecules. Nothing is changed to go from one system to the next. So results that are reached are indeed unique and interesting and were certainly not built in to the system prior.

Nonsense. There are a range of parameter sets you use depending on the simulation you want to perform. For example, there are a wide range of models that are used for water alone! (such as SPC, TIP4 etc.) Each gives different results depending on the type of simulation, and things like the scale you are operating at. Then there are the different parameter sets you can choose to represent the protein surfaces.

If you want to do a large-scale model of a virus in water, you pick the parameter sets that you already know from similar simulations (large protein clusters in water etc.) that will give good results. So, of course it is going to be realistic.

Re:No, this is scientific showboating.

[Decaff]

By the way, this study at least didn't use long range electrostatic cutoffs; they use a (fairly common, now) technique that allows calculation of full electrostatics of a system in N log N time as long as it is periodic.

So save me looking this up, could you let me know what this is? When I was doing molecular simulation, the issue of long-range electrostatic interactions was a major one. I would be interested to know how things have advanced (though my systems were not periodic, so it might not apply).

Re:No, this is scientific showboating.

[AFairlyNormalPerson]

If your system is pure MM and described by point charges (no higher order multipole moments included, e.g. the TINKER force field), then particle mesh ewald will get you the interaction energy between the "real" unit cell and all possible images of that cell. There is still, of course, the real space interactions WITHIN the cell and these either use a cutoff function or some people use recursive bisection/fast mutipole methods (which is much better and can be applied to non-periodic systems -- Look for pap

Re:No, this is scientific showboating.

[Decaff]

You say "of course it is going to be realistic", but isn't that the point?

Well, yes, but I was trying to counter statements of surprise that the results were indeed realistic. I am not critical of MD. My point is that one should not be surpised if the simulation is realistic - it is designed to be! That is a good thing - there would not be much point in running it otherwise.

Re:No, this is scientific showboating.

[Decaff]

That's fair enough; your comments elsewhere had lead me to believe you were more critical of the technique as a whole.

No, not at all... I have worked in the past with MD people and seen some fantastic work done. My only concern with this particular project is the way it is being publicised - the idea that it is really simulating a virus accurately is a bit too much for me; it seems more like a 'look what we can do' sort of thing rather than good science. When I was doing molecular simulation researchers w

Re:No, this is scientific showboating.

[Decaff]

So this certainly doesn't seem like it is coming out of nowhere, as you might be concerned -- there have been a lot of other big simulations done recently in the 100,000 atom and up range.

Looks like I am way out of date! When I was dealing with these things, it was on a scale more of hundreds of atoms rather than hundreds of thousands.

Re:This is why we do scientific computing

[ColdWetDog]

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).

Re:This is why we do scientific computing

[idlake]

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.

Next thing you know...

[markov_chain]

They will be writing computer simulations of spores!

Re:Next thing you know...

[ToasterofDOOM]

I want to see someone frop a fork bomb on one of those calculators!

And within minutes....

[Anonymous Coward]

a McAfee AntiVirus update immediately wiped this program and all associated files from the face of the earth.

Exchange...

[fahrbot-bot]

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.

And God spoke:

[Amonimous Coward]

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

Re:And God spoke:

[Scarletdown]

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

Re:And God spoke:

[wanerious]

...those copyrights expired millions of years ago.

Thousands. Thousands of years ago. HTH.

Re:And God spoke:

[TapeCutter]

"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.

Re:And God spoke:

[Scarletdown]

Ah, but His/Her copyright would have been under the old laws, which was 14 years plus an optional 14 year renewal, like most of the stuff on Project Gutenberg.

And if He/She still wanted to claim copyright under the Sonny Bono Act, then technically, expiration would have occurred in 100 CE in the U.S. or 75 CE everywhere else according to Christian mythology. :p

Times may vary according to other religious beliefs.

Good luck, God...

[Urusai]

...on finding a lawyer. I hear most of them end up downstairs.

Re:Good luck, God...

[slavemowgli]

Doesn't that actually make finding them easier?

Re:Good luck, God...

[dodobh]

God has Chuck Norris. He doewn't need lawyers

Re:And God spoke:

[brianerst]

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

Re:And God spoke:

[BlueHands]

Orobouros Corporation
What goes around, comes around

i don't know if the tag line on that was yours or not, but if it was it was VERY well done.....

Re:And God spoke:

[brianerst]

Afraid it's all mine. Just seemed apropos.

possible?

[spectrokid]

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?

Re:possible?

[A beautiful mind]

Easy. We just have to make processors subatomic. Problem solved.

I doubt it will happen soon though.

Yes.

[ichigo 2.0]

Folding@Home [wikipedia.org].

Re:possible?

[geekoid]

"If our computational power keep increasing that way it has for the last 2 years,"..

err 20 years. Sorry, I got a cold.

Beam Me Up Scotty!

[PortHaven]

Just a few billion more molecules worth of computing power to go!

And *That* is what computers are for!

[Frumious Wombat]

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.

Re:And *That* is what computers are for!

[Dachannien]

And here I thought doing our business is what computers are for.

Re:And *That* is what computers are for!

[budgenator]

I tried to go there but the site was already slashdotted... just kidding, neat stuff there.

shows how far off we are from simulating life

[Anonymous Coward]

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.

Big PC + Fancy Virus/cancer stuff = nature paper

[pimpimpim]

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 ;)

Re:Big PC + Fancy Virus/cancer stuff =nature paper

[MonaLisa]

I agree. It's just another "computer stunt" paper. The supercomputer centers love these things, as they (sort of) justify their existence. I think if they tore apart these big parallel machines and gave a small piece to small research groups around the country, a lot more science would get done. It takes a _lot_ of simulations to really learn anything, not just one moon shot hero run. The idea of these grand challenge computational problems soaking up all of the resources is so 80's. You can load up a

Re:Big PC + Fancy Virus/cancer stuff =nature paper

[budgenator]

It takes a _lot_ of simulations to really learn anything,
still you have to do one before you can do a lot. Maybe those opterons would even exist with out people grand-standing on a super-computer a decade ago.

Re:Big PC + Fancy Virus/cancer stuff = nature pape

[pimpimpim]

Ah thanks, you're right, and I am deeply ashamed of myself ;)

I already figured it would most likely be 50 nanoseconds, but of course they might have used the wrong one on purpose to make it look like a bigger number :)
In the process I also found a very nice wiki on the history of the word 'billion': http://en.wikipedia.org/wiki/Billion [wikipedia.org]

Re:Big PC + Fancy Virus/cancer stuff = nature pape

[pimpimpim]

oh, and another error: the actual paper was not in nature but in structure. I wonder if they tried Nature first...

Chuckle!

[MyLongNickName]

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.

These scientists must be Simpsons fans.

[Sebilrazen]

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.

Re:These scientists must be Simpsons fans.

[Maxo-Texas]

You say tamacco, I say tamakeo

Re:These scientists must be Simpsons fans.

[ultramk]

If memory serves, both tobacco and tomato are in the nightshade family (along with peppers, potatoes and petunias). It's not surprising that the same virus would affect both or even all of these plants.

m-

You can run this yourself (theoretically)

[sidney]

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.

Re:You can run this yourself (theoretically)

[tskirvin]

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].

Re:You can run this yourself (theoretically)

[Mad Hughagi]

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...

Re:You can run this yourself (theoretically)

[Mad Hughagi]

Don't get me wrong, I know very little about MD. Why doesn't NAMD scale near-linearly?

Re:You can run this yourself (theoretically)

[budgenator]

each node has to get data and coordinate with the other nodes, eventualy you get to a point where the computer power brought by a new node is equal to the communication overhead. Too many nodes can actualy make the whole thing slower, its a property of computer clusters in general. there is a point where it noticeable that its not scaling linearly.

Re:You can run this yourself (theoretically)

[dlapine]

Scaling capability for most parallel programs has a lot to do with how "large" of a simulation you run. If you run a 100,000 atom simulation on more than 100 nodes (let's assume perfect spatial decomposition), you've got less than 1,000 atoms of force evaluation work per node, it becomes quite challenging to scale well once the amount of work per processor gets very small. If you simulate 1,000,000 atoms, then you have more work per processor, and the GigE system will fare much better than it would with 100

More/better information...

[tskirvin]

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.

Re:More/better information...

[Seanasy]

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

[the linux geek]

What about the fact that virii aren't usually considered to be alive, not being capable of reproduction outside of a host cell?

Re:Living Things

[geekoid]

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.

Apparently they never saw Terminator 3

[Gary Destruction]

SKYNET not only simulated a virus but it actually infected computer systems.

Great idea for a sci-fi story

[HangingChad]

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

A Poster Giving an Overview of the Whole Thing

[Expert Determination]

Here [uiuc.edu]. They're just looking at what holds together the structure of the virus.

Huh?

[repvik]

"moller writes to tell us that Red Herring is reporting that researchers ... have announced ..."

Indeed.

A simulation of life will never equal life.

[5n3ak3rp1mp]

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...)

Re:A simulation of life will never equal life.

[ultramk]

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-

Polypeptide Polytechnic

[Doc Ruby]

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

Re:I dunno...

[LunaticTippy]

I realize your colecovision is a formidable computer, but the model is pretty complex.

There are millions to hundreds of millions of atoms in a typical virus. Here is interesting virus simulation info [indiana.edu]

Oh yeah, I know (hope?) you're joking, but modelling millions of atomic interactions is, as they say, nontrivial.

Re:I dunno...

[Scarletdown]

My colecovision does whole ATOM sims.

Are you sure you didn't mean Adam sims, considering it's a ColecoVision you are talking about? ;)

Re:You don't need a supercomputer...

[Anonymous Coward]

You don't need a supercomputer, just a Windows box.

Not quite:

Windows Box: lol this is not a virus
Supercomputer: LOL THIS IS NOT A VIRUS

Re:You don't need a supercomputer...

[sexyrexy]

Thank you Randall, that was the joke.

Re:And thus God spoke:

[whitehatlurker]

God threatens to sue over DMCA Violations

As the Devil said, "where's He going to find the lawyers?"

Re:how about dark matter

[geekoid]

It's there, you just can't detect it....

Re:ATTENTION EVERYONE

[Toba82]

Sorry, but I don't see how this is insightful. Anyone...?

Re:Philosophical question

[gansch]

What is your evidence that life is completely deterministic atlarge scales? If you've figured that out, you've solved problems for a lot of scientists, philosophers, and theologists.

Most large-scale patterns and processes in nature are stochastic and the outcome is one of a distribution of possibilities, similarly to quantum mechanics. In general, the same pattern can result from diverse processes (e.g., banded patterns of vegetation from dispersal dependence or topographical variation), while a single pr

Re:Philosophical question

[svkal]

Your argument hinges on the assumption that "the world is quite deterministic in any large enough scale", which tends not to be true, quite a few natural systems exhibit chaotic behaviour at any reasonable scale, and quantum mechanics dictate that we will always have incomplete information about the world. Currently, the "Oracle supercomputer" seems infeasible from a scientific point of view: there are simply too many factors to track(in infinite detail, if perfect accuracy is required) to run accurate simulations of complex systems on extreme scales. Note that this simulation of a virus is probably not "perfect": there are errors, and however small and insignificant they may be at this scale, they may introduce crippling inaccuracies the moment you try to simulate a larger system with a certain number of viruses(each introducing their own error factors), or one system over a more significant amount of time.

Philosophically, however, the question is interesting and has, as most interesting philosophical questions, been discussed before. Look up "Laplace's demon" sometime(the demon being the closest thing an 18th century mathematician could imagine to a supercomputer with access to infinite information): if one assumes that the world is inherently deterministic(from our point of view, this assumes the "hidden variables" interpretation of quantum mechanics) and proposes that some kind of being could in theory have access to unlimited information about it, then concepts such as time lose much of their meaning, since things are "destined" to happen before they actually do happen(and in what absolute sense can they then be said not to have happened already?).

Obviously, free will in the absolute sense is also non-existent from this point of view.

Re:Philosophical question

[Slashcrap]

Note that this simulation of a virus is probably not "perfect": there are errors, and however small and insignificant they may be at this scale, they may introduce crippling inaccuracies the moment you try to simulate a larger system with a certain number of viruses(each introducing their own error factors), or one system over a more significant amount of time.

This is an excellent point. An example I once heard concerned simulating a game of Snooker (for our Leftpondian cousins, think Pool). The basic premi

Re:Philosophical question

[budgenator]

world is quite deterministic in any large enough scale
Sensitive dependence on intial conditions will kill you here, and the best you can do with a digital computer is estimate. This means calculating a system with 80 bit of accuracy gives a different (often wildly given enough interations), than a 81 bits of accuracy one would. The Real world is often irrational as in pi or e. I'm amazed weather prediction works as well as it does.

"Computing life" is possible

[this great guy]

This is an interesting coincidence because I used to reflect deeply on this exact subject a few years ago: what if a supercomputer could simulate a human ? I'll be honest here: I am literally _astounded_ to discover that this scientific team has successfuly simulated a virus. I didn't thought supercomputers were powerful enough for such a task. I just finished reading some articles about the experience and I now understand why this has been possible: they used some empirical functions instead of implementi

Re:Philosophical question

[Ihlosi]

Since the world is quite deterministic in any large enough scale,

A simple three-body-problem is completely deterministic, but since no exact solution has been found, predicting the behavior of the system is limited by the accuracy of the simulation (which will never be 100%). So, while you may be able to quite accurately predict what the system will be doing for a short time, your predictions will become more and more inaccurate as they go farther into the future.

Re:I can do my own computer virus simulation...

[jack_csk]

Excuse me, but why is the parent modded as a troll?

Re:But

[budgenator]

it seems to run any everything I can think of.

Re:Soviet

[Slashcrap]

Infected Pus.

Dude, at least try and use the correct terminology. It's called Windows.