4 ms·

I really miss the days of increasing clock speeds. I attended a conference on molecular dynamics simulations two weeks ago (FOMMS), and more than one person la

I really miss the days of increasing clock speeds. I attended a conference on molecular dynamics simulations two weeks ago (FOMMS), and more than one person lamented the fact that long timescale (> millisecond) simulations are going to be difficult to attain now that clock speeds have stalled. GPUs are great for simulating more atoms, but they are in fact worse at performing longer simulations. If no more effort is put into making processors faster, then the only ways forward are to either build special purpose machines (like Anton) or to invent some clever mathematical techniques.

montecarl 11y ago
Long timescale atomic simulations of liquids is a really challenging problem. Most of the well developed accelerated dynamics methods only work well for solids where there is a well defined time scale separation between atomic lattice vibrations and reactive events. In liquids (e.g. protein folding) the timescale separation is not as well defined. There seems to be complexity at every level (vibrations, small rotations, dihedral angle changes, etc). Liquid like systems have a very rough potential energy landscape with an enormous number of shallow minima that must be explored to understand the dynamics. I look forward to the clever algorithms that will be developed that will enable modeling liquid systems on the experimental timescale. This is recently become possible in some solid-state systems, but it will take some time and effort before it happens for liquids. Then it will be much easier to do first principal studies of organic/bio chemistry.
- j-pb 11y ago
  Maybe a stupid question, but isn't it require to run these long-time simulations multiple times anyways? So one could evaluate these all at once by introducing randomness (vibrations, small rotations, dihedral angle changes, etc) once an interesting point in time is reached, and then simulating in parallel from then onward.
cmdrfred 11y ago
A bit off topic but I often think about if we developed the technology to simulate in real time a mass of about 4 pounds and the technology to do a cat scan (or something similar) with atomic granularity. We could sort of cheat when it came to AI and just take a human who already knows what we are trying to do, scan him, and simulate his brain. Never the less it seems we are very far from that possibility.
- blacksmith_tb 11y ago
  It's a very large unknown if a disembodied simulated human brain, even if it was a perfect copy, wouldn't be screamingly insane. All human brains we know of are embodied. Now, if you could also simulate (or at least stub out) the entire body, that might help, but that's a lot more than "four pounds"...
  - dragonwriter 11y ago
    > It's a very large unknown if a disembodied simulated human brain, even if it was a perfect copy, wouldn't be screamingly insane. What does "disembodied" mean here? Whatever you use to emulate a human brain is going to have a physical substrate and support system (body). It may be differently bodied, but its not going to be disembodied. (Certainly we know -- and in some cases even have some understanding of the mechanisms -- that parts of the body besides the brain are relevant in controlling how the brain works, so any cognition simulation intended to approximate human thought is likely to need simulation of those parts as well as the brain in the narrow sense, whether through direct physical analogs or simulations of the effects through alternative means.)
    - coldtea 11y ago
      >What does "disembodied" mean here? Whatever you use to emulate a human brain is going to have a physical substrate and support system (body). It may be differently bodied, but its not going to be disembodied. If we surgically implanted a human head on a cow it would be "differently bodied" too, but it's obviously not what the parent means. The casual use of "physical substrate and support system" as if it means the very specific "body" parent talks about, which is obviously the human body the simulated brain originated in, is bizarro. A PC box won't cut it as "body".
T-A 11y ago
Speaking of the devil: http://www.innoget.com/D.1224/Seeking-Ways-to-increase-calculation-speed-of-non-linear-partial-differential-equations-algorithmically-by-a-factor-of-1000 http://www.innoget.com/D.1224/Seeking-Ways-to-increase-calcu...

montecarl 11y ago

Long timescale atomic simulations of liquids is a really challenging problem. Most of the well developed accelerated dynamics methods only work well for solids where there is a well defined time scale separation between atomic lattice vibrations and reactive events. In liquids (e.g. protein folding) the timescale separation is not as well defined. There seems to be complexity at every level (vibrations, small rotations, dihedral angle changes, etc). Liquid like systems have a very rough potential energy landscape with an enormous number of shallow minima that must be explored to understand the dynamics. I look forward to the clever algorithms that will be developed that will enable modeling liquid systems on the experimental timescale. This is recently become possible in some solid-state systems, but it will take some time and effort before it happens for liquids. Then it will be much easier to do first principal studies of organic/bio chemistry.

j-pb 11y ago
Maybe a stupid question, but isn't it require to run these long-time simulations multiple times anyways? So one could evaluate these all at once by introducing randomness (vibrations, small rotations, dihedral angle changes, etc) once an interesting point in time is reached, and then simulating in parallel from then onward.

cmdrfred 11y ago

A bit off topic but I often think about if we developed the technology to simulate in real time a mass of about 4 pounds and the technology to do a cat scan (or something similar) with atomic granularity. We could sort of cheat when it came to AI and just take a human who already knows what we are trying to do, scan him, and simulate his brain. Never the less it seems we are very far from that possibility.

blacksmith_tb 11y ago
It's a very large unknown if a disembodied simulated human brain, even if it was a perfect copy, wouldn't be screamingly insane. All human brains we know of are embodied. Now, if you could also simulate (or at least stub out) the entire body, that might help, but that's a lot more than "four pounds"...
- dragonwriter 11y ago
  > It's a very large unknown if a disembodied simulated human brain, even if it was a perfect copy, wouldn't be screamingly insane. What does "disembodied" mean here? Whatever you use to emulate a human brain is going to have a physical substrate and support system (body). It may be differently bodied, but its not going to be disembodied. (Certainly we know -- and in some cases even have some understanding of the mechanisms -- that parts of the body besides the brain are relevant in controlling how the brain works, so any cognition simulation intended to approximate human thought is likely to need simulation of those parts as well as the brain in the narrow sense, whether through direct physical analogs or simulations of the effects through alternative means.)
  - coldtea 11y ago
    >What does "disembodied" mean here? Whatever you use to emulate a human brain is going to have a physical substrate and support system (body). It may be differently bodied, but its not going to be disembodied. If we surgically implanted a human head on a cow it would be "differently bodied" too, but it's obviously not what the parent means. The casual use of "physical substrate and support system" as if it means the very specific "body" parent talks about, which is obviously the human body the simulated brain originated in, is bizarro. A PC box won't cut it as "body".

T-A 11y ago

Speaking of the devil: http://www.innoget.com/D.1224/Seeking-Ways-to-increase-calculation-speed-of-non-linear-partial-differential-equations-algorithmically-by-a-factor-of-1000 http://www.innoget.com/D.1224/Seeking-Ways-to-increase-calcu...