5 ms·

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 tha

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 that could rival this density?

dexwiz 10y ago
Genetic storage is way more resistant to bit rot than conventional computers. DNA is not stable, has a full time support system fixing it, and still has a relatively high mutation rate. But biological systems on the whole are much more resistant to individual errors. Yes, single mutations can cause horrible diseases, but these mutations are either in the active site of proteins, or disrupt folding. A large portion of proteins are "bulk." If you look at protein simulations, only a small section of the protein is simulated, and the rest is just approximated as charged mass. Changes there are much less impactful and noticeable. As for it to be a disease, it had to be present at time of concept. If it happens during life (which is does, millions of times a day), the cell either ignores it or dies.
- dekhn 10y ago
  DNA kept cool and dry is stable for millenia. Any storage done with DNA would likely be done in a fixed environment outside of the cell.
  - choicewords 10y ago
    I thought natural radioactive decay was sufficient to mangle DNA.
    - dekhn 10y ago
      minimal shielding and non-radioactive storage elements suffice.
    - skykooler 10y ago
      Same for other storage devices.
Vraxx 10y ago
I am not entirely sure how the calculations are done in order to determine the information contained in the genome of HIV, but my suspicion is that the reason this is more dense is due to the genome containing more than binary bits. I'm guessing that in the genome, for every atom that could be at a certain location in the genome, that would represent a different information state. So each location corresponds to more than a binary possibility (atom A, atom B, atom C, etc.). I think this is not the current goal as our purposes with memory storage have more constraints that merely density, what might increase density significantly could potentially decrease read/write speeds or maybe even energy required to perform read/write operations. All of this is speculation and difficult for me to say for certain since I am not intimately knowledgeable on the topic, but that is my general guess.
y04nn 10y ago
DNA digital data storage
dekhn 10y ago
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.
- delibes 10y ago
  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)
  - mcarlise 10y ago
    > 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.
    - dekhn 10y ago
      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.
deleted 10y ago
[deleted]
danbruc 10y ago
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.
abecedarius 10y ago
There was a paper in the last few years proposing to make DNA a practical mass-storage technology, as the last and slowest level of the hierarchy. It'd need lots of error correction, and to be chunked up into small-enough strings to synthesize, and each string would need to carry address bits to match on (unless you want a content-addressable store). But IIRC the storage density and the cost trends made it at least kind of plausible. And of course there's http://e-drexler.com/d/06/00/Nanosystems/toc.html http://e-drexler.com/d/06/00/Nanosystems/toc.html chapter 12.

dexwiz 10y ago

Genetic storage is way more resistant to bit rot than conventional computers. DNA is not stable, has a full time support system fixing it, and still has a relatively high mutation rate. But biological systems on the whole are much more resistant to individual errors. Yes, single mutations can cause horrible diseases, but these mutations are either in the active site of proteins, or disrupt folding. A large portion of proteins are "bulk." If you look at protein simulations, only a small section of the protein is simulated, and the rest is just approximated as charged mass. Changes there are much less impactful and noticeable. As for it to be a disease, it had to be present at time of concept. If it happens during life (which is does, millions of times a day), the cell either ignores it or dies.

dekhn 10y ago
DNA kept cool and dry is stable for millenia. Any storage done with DNA would likely be done in a fixed environment outside of the cell.
- choicewords 10y ago
  I thought natural radioactive decay was sufficient to mangle DNA.
  - dekhn 10y ago
    minimal shielding and non-radioactive storage elements suffice.
  - skykooler 10y ago
    Same for other storage devices.

Vraxx 10y ago

I am not entirely sure how the calculations are done in order to determine the information contained in the genome of HIV, but my suspicion is that the reason this is more dense is due to the genome containing more than binary bits. I'm guessing that in the genome, for every atom that could be at a certain location in the genome, that would represent a different information state. So each location corresponds to more than a binary possibility (atom A, atom B, atom C, etc.). I think this is not the current goal as our purposes with memory storage have more constraints that merely density, what might increase density significantly could potentially decrease read/write speeds or maybe even energy required to perform read/write operations. All of this is speculation and difficult for me to say for certain since I am not intimately knowledgeable on the topic, but that is my general guess.

y04nn 10y ago

DNA digital data storage

dekhn 10y ago

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.

delibes 10y ago
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)
- mcarlise 10y ago
  > 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.
  - dekhn 10y ago
    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.

deleted 10y ago

[deleted]

danbruc 10y ago

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.

abecedarius 10y ago

There was a paper in the last few years proposing to make DNA a practical mass-storage technology, as the last and slowest level of the hierarchy. It'd need lots of error correction, and to be chunked up into small-enough strings to synthesize, and each string would need to carry address bits to match on (unless you want a content-addressable store). But IIRC the storage density and the cost trends made it at least kind of plausible. And of course there's http://e-drexler.com/d/06/00/Nanosystems/toc.html http://e-drexler.com/d/06/00/Nanosystems/toc.html chapter 12.