Scientists create first billion-atom biomolecular simulation
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Re: Scientists create first billion-atom biomolecular simulation
#2Sounds great. Again, how many mols are that? ;-)
Re: Scientists create first billion-atom biomolecular simulation
#3While very impressive, I'm not sure about their goal:
> Modeling genes at the atomistic level is the first step toward creating a complete explanation of how DNA expands and contracts, which controls genetic on/off switching.
That does not work in isolation like this: McGuffee and Elcock did some fantastic work in 2010 where they showed that protein stability is quite dependent on that the cytoplasm is insanely densely packed. The same is also true for the nucleus of a cell. You can't make any serious claims of a bottom-up explanation of gene regulation and expression unless you can model the entire nucleus, which is out of our reach for years and years to come.
And that is before I start on whether this is an actually useful way to research gene expression in general, which I'd very much argue against.
Re: Scientists create first billion-atom biomolecular simulation
#4While very impressive, I'm not sure about their goal: > Modeling genes at the atomistic level is the first step toward creating a complete explanation of how DNA expands and contracts, which controls genetic on/off switching. That does not work in isolation like this: McGuffee and Elcock did some fantastic work in 2010 where they showed that protein stability is quite dependent on that the cytoplasm is insanely dense…
Depending on how they model the simulation's fields, long range intra-atomic forces, and boundary conditions, I'd still say this kind of molecular dynamic simulation is better than doing nothing and waiting to simulate the whole nucleus. It could have accounted for these sorts of effects in a way that is cruder than whole nucleus simulation, but I haven't read any papers about this simulation.
Re: Scientists create first billion-atom biomolecular simulation
#5"130,000 processor cores with 1 ns/day"
Still a bit to slow... I guess it is progress :)
Re: Scientists create first billion-atom biomolecular simulation
#6must be Gordon Bell prize time again.
Re: Scientists create first billion-atom biomolecular simulation
#7While very impressive, I'm not sure about their goal: > Modeling genes at the atomistic level is the first step toward creating a complete explanation of how DNA expands and contracts, which controls genetic on/off switching. That does not work in isolation like this: McGuffee and Elcock did some fantastic work in 2010 where they showed that protein stability is quite dependent on that the cytoplasm is insanely dense…
Depending on how they model the simulation's fields, long range intra-atomic forces, and boundary conditions, I'd still say this kind of molecular dynamic simulation is better than doing nothing and waiting to simulate the whole nucleus. It could have accounted for these sorts of effects in a way that is cruder than whole nucleus simulation, but I haven't read any papers about this simulation.
Also the stochastic nature of the processes involved would seem to allow for some shortcuts in simulation.
Re: Scientists create first billion-atom biomolecular simulation
#8Biologist's perspective: this paper is not about the biology. The simulation performed here has zero biological interest - the point of the paper was to show how efficient and scalable their software is. This article about the paper is terrible, but honestly I feel like they should be given a pass - it's hard to justify to a lay audience that understands neither DNA nor memory bandwidth why you would choose to study something that is of no use to the field.
There's an inherent tension when doing a method development paper - if your result is too fantastical it's hard to know whether it's an artifact of your (potentially faulty) technique, and if the thing you're studying is well-understood then it serves as a good control, but it's less interesting. I suspect they chose the latter path since it requires no validation via existing methodologies.
Re: Scientists create first billion-atom biomolecular simulation
#9"130,000 processor cores with 1 ns/day" Still a bit to slow... I guess it is progress :)
This is the "hard part" with atom-level biological simulations. You need extremely tiny timesteps -- like, sub-picosecond, even -- but many interesting molecular events happen on the timescale of minutes.
Re: Scientists create first billion-atom biomolecular simulation
#10While very impressive, I'm not sure about their goal: > Modeling genes at the atomistic level is the first step toward creating a complete explanation of how DNA expands and contracts, which controls genetic on/off switching. That does not work in isolation like this: McGuffee and Elcock did some fantastic work in 2010 where they showed that protein stability is quite dependent on that the cytoplasm is insanely dense…
Depending on how they model the simulation's fields, long range intra-atomic forces, and boundary conditions, I'd still say this kind of molecular dynamic simulation is better than doing nothing and waiting to simulate the whole nucleus. It could have accounted for these sorts of effects in a way that is cruder than whole nucleus simulation, but I haven't read any papers about this simulation.
Fascinating discussion! Could any of you knowledgeable folks say a bit more about 1. why whole-nucleus simulation is so hard and out of reach, 2. what role simulation currently plays in understanding gene expression, 3. to what extent will simulation be important for understanding how genes translate to phenotypes over the long term?
I know next to nothing about this field or the relevant biology, but would love to learn more!