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2 responses to “Simulating a Cell and what you can do with it.”
awesome!
and there I through that some of the cell membrane inner workings wer poorly understood.
perhaps now these proteins can be debugged in the simulation rather than femtosecond experiments?
That’s a good question. This isn’t a simulation from basic physics principles; it’s a simulation based on a lot of measured biochemical reaction rates. So, femtosecond experiments on membrane proteins are more of an input to the simulation than an output.
Another way of looking at it is that this simulated bacterium is basically a web of chemical reactions. The state of the bacterium is specified by a vector listing how many of this kind of molecule you have, and how many of that kind. So, when we start optimizing this kind of simulated bacterium, we’ll be optimizing reaction rates: how fast X reacts with Y to form Z, but we won’t be learning about how each reaction happens.
So, this kind of simulation and improvement won’t help you (much) if you want to understand how the reactions happen. We’ll need femtosecond experiments for that. It might eventually give better measurements of reaction rates, which could then (eventually, in principle) be used to constrain more detailed simulations of the individual reactions, but we’re not anywhere near that yet.
FYI: the simulations don’t include predictions of protein folding, and they certainly don’t allow for the bacterium to change its genes.