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Background thoughts before this question: is it feasible to simulate a complete bacterium, atom by atom, in a computer simulation? On modern systems, either in an upcoming exascale computer?

In current research they've simulated an organella with 100M atoms but I don't know on which infrastructure.

On Quora, there is an estimation of E.coli to have about 9x1010 atoms. With 4m base pairs it is though still quite big and possibly would produce too high computational workload in a simulation.

See also: https://scicomp.stackexchange.com/questions/33941/is-a-complete-bacteria-simulation-with-an-exascale-supercomputer-possible

If they have simulated an organella with 100M atoms atom by atom, possibly you could already completely simulate some viruses, but they are not independent organisms.

So there has been an atom by atom simulation of the polio virus capsid in 2014 on the K computer with 10 petaflops. To include enough water molecules to fill and surround the capsid, Okazaki and colleagues needed to model the dynamics of nearly 6.5 million atoms, which they did for a simulated 200 ns.

Question - which order of magnitude would a small bacterium count on atoms? What about the smallest known bacterium Nasuia deltocephalinicola with its 112K base pairs? How many atoms has it got?

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    $\begingroup$ Do you perhaps mean pathogens? I imagine you can classify pathogens by dozens of criteria, but number of atoms strikes me as little more use than the day of the week in which they were discovered. Molecular science is past the descriptive phase today. It is concerned with mechanism. $\endgroup$ – David Dec 2 at 20:12
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    $\begingroup$ There are literally hundreds of "well known pathogens". Their molecular weight is known, but their pathogenesis is much more important. $\endgroup$ – anongoodnurse Dec 2 at 20:17
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    $\begingroup$ @tyersome I try to understand the physical complexity $\endgroup$ – J. Doe Dec 2 at 21:12
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    $\begingroup$ I'm not sure number of atoms really helps with that — for example, a diamond has many more atoms than a virus, but to me it seems clear that a virus is much more complicated ... You might find the wikipedia article on complexity helpful for organizing your thinking on this subject. $\endgroup$ – tyersome Dec 2 at 21:26
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    $\begingroup$ @J.Doe It can be calculated. It is not explicitly reported because nobody thinks that it would be useful. Your question is not broad but the purpose of it is not clear. It certainly is not very useful. Moreover, a cell can change its structure in response to the environment and can drastically alter the number of molecules it contains. The importance of the number of atoms in the context of the paper that you linked is because of the technique they use. MD involves calculation of intra/intermolecular interactions. It makes sense for molecules/supramolecular complexes, not organisms in general. $\endgroup$ – WYSIWYG Dec 3 at 10:18
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Let's take the example of the model bacterium E. coli, for which one can find the numbers for a wet cell of a dry mass of 0.28pg. If you have a feeling for how much smaller the smallest known bacterium is compared to E. coli, you can ballpark things.

  1. The number of carbon atoms in a single E. coli cell is approx. 7x10^9 carbon atoms.

  2. The ratio of elements in E. coli is C : H(1.77) : O(0.49) : N(0.24) .

More simply, if you multiply the ratios by 4, you get the ratios of approximately 4 carbons, 7 hydrogen, and 2 oxygen atoms for each nitrogen atom.

Taken together, there are approximately the following number of atoms in an E. coli cell:

C: 7 x 10^9

H: 1.23 x 10^10

O: 3.5 x 10^9

N: 1.75 x 10^9

That is around 2.4 x 10^10 individual atoms. As you may have noticed, these numbers do not have any bearing on the complexity of the system whatsoever. They also do not provide any insight into the intrinsic biological plasticity and dynamics of the system.

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  • $\begingroup$ but how many atoms does the supposedly much smaller Nasuia deltocephalinicola have? most references I can find refer to its genome size. $\endgroup$ – J. Doe Dec 3 at 14:22
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    $\begingroup$ @J.Doe as I mentioned before, the composition and size of a bacteria will not remain constant. The paper in the question talks about a supramolecular complex, not a cell. If you assume that composition of all bacteria is more or less the same then you can simply calculate the values for your bacterium by scaling the volume accordingly. $\endgroup$ – WYSIWYG Dec 3 at 14:59
  • $\begingroup$ @WYSIWYG so what is the size of the Nasuia deltocephalinicola compared to E.coli? $\endgroup$ – J. Doe Dec 3 at 15:02
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    $\begingroup$ @J.Doe that's a separate question and is also something that you can Google easily. $\endgroup$ – WYSIWYG Dec 3 at 15:02

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