The cure for all bacteria-caused diseases

Which minimal order of magnitude is required to simulate single cells and microorganisms in cyberspace?

In an utopian future, people will be possibly able to rapidly design new cures, be their realization a new chemical substance, a nanobot or a synthetic antibody.

"Today we will learn how people built the first super computer which helped to eliminate all human deceases caused by microorganisms", teacher said. "All started with that question on the world building Q&A site.."

Could be this a quote from a hard sci-fi story, if the teacher would go deeper into how that legendary supercomputer had been engineered?

Possibly, a "hard" sci-fi requirement for that would be a need for physically possible supercomputers which can perfectly model and simulate pathogens, more than just a fictional positron brain with endless flops.

Coming to computational performance, as of 2019 we have supercomputers reaching orders of possible operations on peta- and coming close to exascale. Some research is also ongoing to assess what will be required to build a zettascale computer.

But how much is actually enough to have a simulation where a bacteria attacks a human cell and starts to self-replicate?

Relevant figures are:

• Simulation of viruses like HIV either poliovirus is not a big problem as they have less than 10-100M atoms which seems feasible since some years (which very likely has helped to design the AIDS cure!). Though, a virus is not "life" and there are also "giant" viruses;
• a bacterial organella has been recetnly simulated leading to a scientific discovery with 100M atoms;
• an E.coli bacteria has about 10¹¹ atoms;
• a recent non-biological simulation with fixed molecules allows for simulation of 20x10¹² atoms;
• a "typical" human cell is referred to have 10¹⁴ atoms.

The challenges which I could identify so far, but also the according state of the art approaches as of late 2019, look like the following (while atom by atom simulation seems to have good development, anyway):

• detail of simulation: is Newtonian molecular dynamics simulation enough or is it better to have a quantum-mechanical field interaction which is computationally more expensive?

• size of simulation: pathogens can differ by orders of magnitude in their size and complexity. This means, between being able to simulate two different species decades might pass. As of today, we can simulate some virus capsids either bacterial organellas on petascale computers.

• time frame: current petascale simulations allow up to ~45ns/day time frames which is really not much given that many bacteria need hours for one cycle.

That is, will it be anyhow possible, from physical/economical points of view, to build a computer smaller than the Earth and run such simulations?

What I've not considered yet are quantum computers, but today we as it seems actually do not know yet if we will be able to build such systems scaled enough to really compete with large non-quantum ones.

posted almost 5 years ago

J. Doe‭

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