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Scientists create first billion-atom biomolecular simulation

89 点作者 respinal超过 5 年前

6 条评论

jryb超过 5 年前
Biologist&#x27;s perspective: this paper is <i></i>not<i></i> 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&#x27;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.<p>There&#x27;s an inherent tension when doing a method development paper - if your result is too fantastical it&#x27;s hard to know whether it&#x27;s an artifact of your (potentially faulty) technique, and if the thing you&#x27;re studying is well-understood then it serves as a good control, but it&#x27;s less interesting. I suspect they chose the latter path since it requires no validation via existing methodologies.
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AllegedAlec超过 5 年前
While very impressive, I&#x27;m not sure about their goal:<p>&gt; 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&#x2F;off switching.<p>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&#x27;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.<p>And that is before I start on whether this is an actually useful way to research gene expression in general, which I&#x27;d very much argue against.
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callesgg超过 5 年前
&quot;130,000 processor cores with 1 ns&#x2F;day&quot;<p>Still a bit to slow... I guess it is progress :)
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tlobes超过 5 年前
I’m curious to know how much room there is for optimization in their code
jayalpha超过 5 年前
Sounds great. Again, how many mols are that? ;-)
moonbug超过 5 年前
must be Gordon Bell prize time again.
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