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Scientists pave the way for large-scale storage at the atomic level

economist.com

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Re: Scientists pave the way for large-scale storage at the atomic level

#21

Post by [deleted] »

coldcode wrote: post #15
dexwiz wrote: post #8

From -269ºC to -196ºC is actually a huge improvement. Its the difference between liquid helium (expensive) to liquid nitrogen (cheap). Getting something that cold is hard, but keeping it there is just a matter of insulation. There seems to be a different kind of physics when you get that cold. Stable single atom structures, superconducting magnets, etc. It's all based around the idea that nanometer structures are now…

The problem I see is what happens if the temperature doesn't stay in the required range for whatever reason like power failures, earthquakes, sloppy maintenance - you lose the data. Having such an enormous storage that is so fragile seems to have limited usefulness. If they ever get it to room temperature and have it be stabile then it might be more interesting.

[deleted]

Re: Scientists pave the way for large-scale storage at the atomic level

#22

Post by mcarlise »

delibes wrote: post #18
dekhn wrote: post #14

Earlier quoted context omitted.

The storage in the article is 2D surface. DNA storage in viruses is highly compacted in 3D. Single atom storage is limited by the interatomic distance and the accessibility of the atoms (you could use a series of 2D surfaces stacked on each other to increase density). DNA storage is roughly 30 atoms/base or bit. So, probably the single atom method could ultimately be scaled further.

Well OK it spirals around, but isn't RNA/DNA really just linear? To access, you need an enzyme to walk it forwards or backwards and there are no other options that I know of. (I'm not a biologist)

> but isn't RNA/DNA really just linear

No, it's not. RNA/DNA contains 4D of information. You need hundreds of proteins (also to be clear not enzymes - all enzymes are proteins, not all proteins are enzymes). Additionally (along with proteins), you need to unpack the chromatin structures - which requires huge cellular state transitions (hence the 4th dimension). So what bases are available to be replicated (read?) is dependent on the chromatin structure and their current state (euchromatin/heterochromatin), then depending on local molecular concentrations, replication is dependented on what proteins are locally available (due to the nucleosome structure). This is the very essence to why a large number of traits and diseases do not follow mendelian inheritance.

Re: Scientists pave the way for large-scale storage at the atomic level

#23

Post by saiya-jin »

delibes wrote: post #18
dekhn wrote: post #14

Earlier quoted context omitted.

The storage in the article is 2D surface. DNA storage in viruses is highly compacted in 3D. Single atom storage is limited by the interatomic distance and the accessibility of the atoms (you could use a series of 2D surfaces stacked on each other to increase density). DNA storage is roughly 30 atoms/base or bit. So, probably the single atom method could ultimately be scaled further.

Well OK it spirals around, but isn't RNA/DNA really just linear? To access, you need an enzyme to walk it forwards or backwards and there are no other options that I know of. (I'm not a biologist)

yeah it's 1-dimensional and processing I know about is sequential, twist is there just to make it more flexible inside the cell similar to old telephone cord (something about putting 3-meter line into few tens of micrometer sized cell)

Re: Scientists pave the way for large-scale storage at the atomic level

#24

Post by danbruc »

stephanheijl wrote: post #7

While this is very intesting, the storage mentioned does seem somewhat small to me. The article compares the area covered by the text to be a little smaller than a HIV (Human Immunodeficiency Virus). However, the genome of HIV apparently stores approximately 9.2kb (kilo basepairs, not kilobytes, so ~18KiB) of information. It also doesn't need to be kept at -196C. Are there any viable tactics for atom-based storage th…

The van der Waals radius of chlorine is 0.175 nm and they use cells with 2 by 3 atoms - two positions for zero and one and one atom wide border as separation to the neighboring cells. This suggests a size of 0.735 nm² per bit or 136 Tbit/cm² which is within a factor of two from the 78 Tbit/cm² from the article and mostly due to the additional spacing between blocks.

They stored 8,128 bits in a plane, the virus contains about 18,400 bits but in a three-dimensional structure. If we could layer this technology - again with one layer for separation - we would get a density of 15.5 billion Tbit/cm³. You could store two years worth of global IP traffic (2015) in one cubic centimeter.

Re: Scientists pave the way for large-scale storage at the atomic level

#25

Post by dekhn »

delibes wrote: post #18
dekhn wrote: post #14

Earlier quoted context omitted.

The storage in the article is 2D surface. DNA storage in viruses is highly compacted in 3D. Single atom storage is limited by the interatomic distance and the accessibility of the atoms (you could use a series of 2D surfaces stacked on each other to increase density). DNA storage is roughly 30 atoms/base or bit. So, probably the single atom method could ultimately be scaled further.

Well OK it spirals around, but isn't RNA/DNA really just linear? To access, you need an enzyme to walk it forwards or backwards and there are no other options that I know of. (I'm not a biologist)

My point is that while DNA is linear, using 3D structure makes packing density far higher.

Re: Scientists pave the way for large-scale storage at the atomic level

#26

Post by dekhn »

mcarlise wrote: post #22
delibes wrote: post #18

Earlier quoted context omitted.

Well OK it spirals around, but isn't RNA/DNA really just linear? To access, you need an enzyme to walk it forwards or backwards and there are no other options that I know of. (I'm not a biologist)

> but isn't RNA/DNA really just linear No, it's not. RNA/DNA contains 4D of information. You need hundreds of proteins (also to be clear not enzymes - all enzymes are proteins, not all proteins are enzymes). Additionally (along with proteins), you need to unpack the chromatin structures - which requires huge cellular state transitions (hence the 4th dimension). So what bases are available to be replicated (read?) is…

More likely, complex traits are influenced by gene regulation, which is affected by chromatin structure, but chromatin is just one form of regulation.

Complex traits are more likely just due to many interaction elements (promoters, enhancers affecting multiple genes in a nonlinear way) and the complex feedback mechanisms and redundancy mechanisms.

Chromatin state is completely abolished and recovered (in a non-deterministic way) in egg and sperm, which places some limits on which it can influence inheritence.

Re: Scientists pave the way for large-scale storage at the atomic level

#27

Post by ska »

Sharlin wrote: post #20
coldcode wrote: post #15

Earlier quoted context omitted.

The problem I see is what happens if the temperature doesn't stay in the required range for whatever reason like power failures, earthquakes, sloppy maintenance - you lose the data. Having such an enormous storage that is so fragile seems to have limited usefulness. If they ever get it to room temperature and have it be stabile then it might be more interesting.

There is an existing engineering discipline centered around keeping a lot of precious fragile data at liquid nitrogen temperatures for decades without malfunction. Say what you want about cryonics but the storage part is proven technology.

As I understand it the tract record isn't actually that good.

Re: Scientists pave the way for large-scale storage at the atomic level

#28

Post by camelNotation »

Sharlin wrote: post #20
coldcode wrote: post #15

Earlier quoted context omitted.

The problem I see is what happens if the temperature doesn't stay in the required range for whatever reason like power failures, earthquakes, sloppy maintenance - you lose the data. Having such an enormous storage that is so fragile seems to have limited usefulness. If they ever get it to room temperature and have it be stabile then it might be more interesting.

There is an existing engineering discipline centered around keeping a lot of precious fragile data at liquid nitrogen temperatures for decades without malfunction. Say what you want about cryonics but the storage part is proven technology.

"Say what you want about cryonics but the storage part is proven technology"

I've always wanted to say that cryonics as a field of study gives me indigestion. I would also like to say that all who study cryonics are villains and fiends. There. I said it. I feel so much better, thank you.

Re: Scientists pave the way for large-scale storage at the atomic level

#29

Post by smellf »

> Dr Otte reports read speeds of 1-2 minutes per block. He reckons he could boost those speeds drastically, to about a megabit per second. That would be a big improvement, but still thousands of times slower than modern hard drives.

Try tens of times slower. There would absolutely be applications for nonvolatile memory that reads at 1 Mbps but has this kind of insane memory density. For most applications you'd probably have to make the technology stable at room temperature though.

Re: Scientists pave the way for large-scale storage at the atomic level

#30

Post by saganus »

nik61 wrote: post #3

http://trillian.mit.edu/~jc/humor/Ms_fnd_in_a_Lbry.html

Wow! Excellent read!.

It's even more impressive since the footnote says:

"This story first appeared in the Magazine of Fantasy and Science Fiction, December 1961"

Fifty-five years ago!

It reminds me of a recent hn article (if anyone has a link it would be great!) that I believe it was about how Dropbox tests it's storage system, layer by layer, and the final error graph is always a flat line at "0", since every error is caught and corrected in one of the layers below.

Will it ever reach the case where it will be impossible to really guarantee that we have the right data?

PS: I can't seem to find the article using Algolia or even Google... maybe it was not Dropbox but other storage company? I really would like to find this story but for some reason never marked it as favorite or even upvoted it! (maybe I wasn't logged in).

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