4 ms·

To correctly model a cell you would need to simulate every atom and there are about 10^11 to 10^14 (!) of them in a single cell. I think an interesting number

• jevinskie 13y ago
  Aren't you modeling a subset of the universe at that level? Isn't a model supposed to provide a higher level understanding/abstraction?
  • deletes 13y ago
    Atom is still an abstraction of sub particles ( that may be made of even lower ones, we don't know ) and their physical interactions so i think it is a model. And a reasonably good one.
  • frozenport 13y ago
    In cases where qualitative meaning is nontrivial, you don't know 100% what is going on, it is nevertheless possible to implement parametric studies for some target parameter.
• lvs 13y ago
  Your point is valid, but many people are trying to "correctly model a cell" without making a total atomistic simulation (which is clearly not going to happen any time soon). It's all about what questions you're looking to ask of a model.
• foobarbazqux 13y ago
  Usually people modeling cells don't consider molecular dynamics, they consider concentrations of proteins, ions, and metabolites. A full MD simulation would obviously be superior, but useful predictions could be made without it. It's hard to say which is the better approach. On the one hand you have MD from which you could technically build an accurate model "from scratch", folding all of your own proteins as part of the simulation, but it is exceedingly expensive to do that. On the other hand, you have a model built at the level of biochemical reactions and molecular biology, which is computationally feasible, but then you don't have enough information from bench work to flesh it out.
  • Osmium 13y ago
    It depends what you mean by "full MD" too. That term can cover a multitude of sins. Truly accurate MD would be even more computationally expensive.
  • dekhn 13y ago
    I used to do explicit MD with waters, etc, the whole shebang. Massive waste of cycles. Never gonna make a useful prediction. Reduced representations that contain the minimum of complexity to express the phenomena of interest are far more useful.
• jfoutz 13y ago
  What would you get from simulating both hydrogen atoms and the oxygen atom that you wouldn't get from simulating plain old water? The vast majority of a cell is just water, seems like you could cut your complexity in half with that abstraction. I'm no molecular biologist, so i'll happily agree if you say there are some fraction of water molecules broken down, or formed by various cellular processes, but that must be a tiny fraction of the total, and could just be special cased. It just seems like you're willfully ignoring everything physics has to say about how the universe works so you can get a big number for your calculation.
  • moocowduckquack 13y ago
    How would you plan on simulating all the variety of states, reactions and solutions involving plain old water without worrying about hydrogen and oxygen atoms?
    • jfoutz 13y ago
      Again, i would assert that a cell is 70% water. some tiny fraction of water that's actually used in a reaction would just be special cased, and modeled independently. My understanding of "solution" is stuff floating in water. If there's some value in breaking out each atom, i'm all for it, but i kind of suspect the spherical cow is good enough in that case. Even if i'm wrong there, each atom would introduce at least 6 degrees of freedom. IIRC, water is slightly polarized, and that's likely relevant to at least some reactions. Replacing the 18 degrees of freedom with 6 to represent a rigid water, or perhaps 10 or so to represent a flexible version, modeling as the molecule will dramatically lower complexity.
      • moocowduckquack 13y ago
        "My understanding of "solution" is stuff floating in water." In that case, don't even bother with trying to work out what it would take to mathematically model biochemistry yet. Go study some basic physics and chemistry for a few years instead.