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Scientists create first billion-atom biomolecular simulation

lanl.gov

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Re: Scientists create first billion-atom biomolecular simulation

#11

Post by throwaway_law »

AllegedAlec wrote: post #3

While 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…

>And that is before I start on whether this is an actually useful way to research gene expression in general

Haven't we already reproduced existing bacteria/DNA from atoms which has allowed us to more easily study gene expression?

Moreover, we take a bacteria with 200 genes ( we understand a lot of the gene functions/expressions, but we don't understand what all these 200 genes do). Thus, we synthetically reproduce the bacteria from the atoms up while removing nearly half of the genes that we determine are not needed to sustain the living bacteria, and the resulting synthetic bacteria we created in the lab allows us to more readily isolate and study the individual genes we didn't previously understand.

Re: Scientists create first billion-atom biomolecular simulation

#13

Post by deugtniet »

throwaway_law wrote: post #11
AllegedAlec wrote: post #3

While 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…

>And that is before I start on whether this is an actually useful way to research gene expression in general Haven't we already reproduced existing bacteria/DNA from atoms which has allowed us to more easily study gene expression? Moreover, we take a bacteria with 200 genes ( we understand a lot of the gene functions/expressions, but we don't understand what all these 200 genes do). Thus, we synthetically reproduce t…

bacteria =/= eukaryotes. Gene expression in bacteria is very far away from gene expression in humans.

Re: Scientists create first billion-atom biomolecular simulation

#14

Post by stochastic_monk »

jryb wrote: post #8

Biologist'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…

I'm not familiar with this method, but NAMD and CHARM are a great way to inspect biological systems at greater resolution than experimental methods can measure. There was really cool work on fibrinogen about a decade ago showing how it provides elasticity.

Reference: https://www.ks.uiuc.edu/Highlights/?section=2008&highlight=2...

Re: Scientists create first billion-atom biomolecular simulation

#15

Post by phkahler »

jryb wrote: post #8

Biologist'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…

Maybe the problem is that these scientists aren't doing science, they did some engineering. That's great, but it doesnt fit their publishing model.

Re: Scientists create first billion-atom biomolecular simulation

#16

Post by safsafsafa »

krzat wrote: post #12
callesgg wrote: post #5

"130,000 processor cores with 1 ns/day" Still a bit to slow... I guess it is progress :)

Damn I hope they can optimize this away eventually. Game of life can be sped up with hash tables.

Game of life doesn't have long range interactions, and doesn't have to deal with electrostatic interactions (which, with parallel B.C., diverge and cannot be calculated in real space).

Re: Scientists create first billion-atom biomolecular simulation

#17

Post by saalweachter »

jpvelez wrote: post #10
cjslep wrote: post #4

Earlier quoted context omitted.

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 l…

Time is the problem.

Imagine you're doing a straight-forward computer simulation. You have a state-of-the-world, a time-step, and rules for how the world evolves during that time-step.

You might write your own orbital simulation; the positions of the various planets and asteroids are your state, you might use a time-step of a minute or an hour or a day, and your rules for how the state evolves during each time step might just be Newton's laws of gravity and motion. You can probably update your state in a fraction of a second, even if you are simulating hundreds or thousands of planetary bodies, and you can simulate eons in hours.

The problem with simulating biology on an atomic level is that your time-step needs to be in the femtosecond to picosecond range, because atoms can move fast, and small differences in their position make big differences, but interesting things like protein folding can take minutes of real time.

So to simulate anything interesting, you need to step through quadrillions of time steps.

Oh, and you're running this on more than one processor, so you need to do smart things so your simulation isn't trying to synchronize all of its processors on every step; oh, and we can't tell you the exact position of every atom in a cell to start with, or even necessarily all of the different types of molecules that are present. Oh, and all of these cells -- or pieces of cellular machinery -- behave in ways that are dependent upon the environment they are immersed in, so you also need to simulate that somehow.

There's a reason Randall Monroe described the difficulty of protein folding as "we may one day find a harder problem".

Re: Scientists create first billion-atom biomolecular simulation

#18

Post by safsafsafa »

moonbug wrote: post #6

must be Gordon Bell prize time again.

1E9 atoms / 130 000 cores = 8000 atoms/core

in 2011 I was building 40 000 atom models on a 2001 SGI Fuel simulating them on a single 8 core node at 1ns/week -> 8000 atoms/core. They're about 7 times faster then me 8 years later.

So from a computation point, meh.

From a tools point this is cool. It isn't trivial to build or analyze a model of 40 000 atoms, never mind 1E9 atoms.

Re: Scientists create first billion-atom biomolecular simulation

#19

Post by throwaway_law »

deugtniet wrote: post #13
throwaway_law wrote: post #11

Earlier quoted context omitted.

>And that is before I start on whether this is an actually useful way to research gene expression in general Haven't we already reproduced existing bacteria/DNA from atoms which has allowed us to more easily study gene expression? Moreover, we take a bacteria with 200 genes ( we understand a lot of the gene functions/expressions, but we don't understand what all these 200 genes do). Thus, we synthetically reproduce t…

bacteria =/= eukaryotes. Gene expression in bacteria is very far away from gene expression in humans.

Of course gene expression in bacterial isn't the same as humans...obviously when building synthetic life from atoms up we aren't going to just reproduce a human in our first effort, we start with a simple bacteria, and because of the complexity (and our lack of understanding of the gene expression in even simple bacteria) we purposely reproduced the bacteria with about 1/2 the genes for the sole purpose of studying those genes.

But maybe I am wrong and this is in no way helpful for studying gene expression.

Re: Scientists create first billion-atom biomolecular simulation

#20

Post by thatcat »

phkahler wrote: post #15
jryb wrote: post #8

Biologist'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…

Maybe the problem is that these scientists aren't doing science, they did some engineering. That's great, but it doesnt fit their publishing model.

What is the engineer publishing model?
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