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March 04, 2013

DNA 3D Nand Gate Bricks Would Be Able to Make a Computer with 1 million times the transistors of Intel Itanium Poulson Computers

Harvard researchers have used single strand DNA, to self assemble custom designed nano scale structures. Each of the bricks shown to the left is, 25-nanometers on a side, they are composed of ~1,000 voxels (I think it is 500 DNA strand, 2 voxels per strand) unique single strands of DNA, each with 32 nucleotides. Each strand is like a jigsaw puzzle piece and can only bind in one location. This is due to the fact that nucleotides only bind to their opposites, A to T and G to C. These DNA strands can be designed to self assemble into pretty much any shape, as shown in the image.

David Fuchs at Hephastus Project outlines what kind of computing would be possible with 25 nanometer 3D Nand bricks.


A one inch cube could hold 1,000,000,000,000,000,000 of these 25 nm bricks.

Using two simple techniques, you can build much larger structures out of smaller ones. The first technique is to create binding sites, on each of the six sides of the brick. The second technique is to create a spacer-binder with matching but opposite nucleotides to bind to.

NOTE - Limiting factors.
* cost to produce this much DNA is still out of reach
It costs $2 billion to synthesize the billions of base pairs for the human genome. There are some approaches which could lower the cost by 10,000 to 100,000 times but that is still $20,000 for a human genome. Even if short sequence DNA brick synthesis is a lot cheaper in massively parallel production that has to be very cheap synthesis of 260 billion billion 25 nanometer bricks.

* connecting it and making the structure and logic for useful work and providing the skeleton for massive number of bricks seems to pretty much need full blown molecular nanotechnology.

* there is also the heat management issues



The NAND logic gate is the universal gate, with it you can build all other logic gates, NOT, AND, OR, NOR, XOR, and XNOR. By extension, using only NAND gates you can build any logic circuit imaginable, processor, memory, and any other logic circuit you can conceive of or need.

6 Inch cube of DNA 3D Nand Bricks

The concept for the Three Dimensional Configurable NAND Gate is simple. It is a cube with a NAND gate inside. The cube NAND gate has the following specifications.

* A cube NAND gate has six sides, each side can be individually turned on for input, output, or set as unused.
* A used cube NAND gate, must have at least one input and one output.
* When only one input is used, the gate acts as a NOT gate.
* All outputs of a single cube NAND gate output the same signal.
* A cube NAND gate can either be in use and logically connected to other cube NAND gates, or unused and not logically connect to any other NAND gates.

216,000,000,000,000,000,000 individual NAND gates. This does not take into account the spacer binders, the need for cooling, long range (over 1,000 nm) communications, and power. David chose to ignore them because this is a speculative piece. Adding all the missing pieces listed above takes about half the volume and ~halves the number of NAND gates, again we are ignoring that. We just want to see roughly what can be done.

A system consist of

* An Intel 8-Core Itanium Poulson
* 2 Terabytes of RAM
* 1 Terabyte hard drive

Would need about 128 trillion transistors.

A six inch cube of 3D NAND would be able to fit ~1.8 million maxed out Intel 8 core systems.
Roughly halving it for the cooling and communication and power would be about 1 million systems.

The ability to selectively attach or bind to specific nano-scale structures or specific chemicals and move them into position, with atomic precision, will more than likely occur within the next 3 to 6 years. By combining the technology of DNA bricks and selective manipulation of nano-scale objects, devices such as the configurable 3D NAND gate can be constructed. This is just one small step away from full blown nanotechnology (Drexlerian or other).






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