Prototype DNA computer ( MAYA-II)

Researchers say that they have developed a DNA-based computer that could lead to faster, more accurate tests for diagnosing West Nile Virus and bird flu. Representing the first “medium-scale integrated molecular circuit,” it is the most powerful computing device of its type to date, they say.

The new technology could be used in the future, perhaps in 5 to 10 years, to develop instruments that can simultaneously diagnose and treat cancer, diabetes or other diseases, according to a team of scientists at Columbia University Medical Center in New York and the University of New Mexico, Albuquerque. Their study is scheduled to appear in the November issue of the American Chemical Society’s Nano Letters, a monthly peer-reviewed journal.

“These DNA computers won’t compete with silicon computing in terms of speed, but their advantage is that they can be used in fluids, such as a sample of blood or in the body, and make decisions at the level of a single cell,” says the researcher, whose work is funded by the National Science Foundation.
Composed of more than 100 DNA circuits, MAYA-II is quadruple the size of its predecessor, MAYA-I, a similar DNA-based computer developed by the research team three-years ago. With limited moves, the first MAYA could only play an incomplete game of tic-tac-toe, the researcher says.

The experimental device looks nothing like today’s high-tech gaming consoles. MAYA-II consists of nine cell-culture wells arranged in a pattern that resembles a tic-tac-toe grid. Each well contains a solution of DNA material that is coded with “red” or “green” fluorescent dye.

The computer always makes the first move by activating the center well. Instead of using buttons or joysticks, a human player makes a “move” by adding a DNA sequence corresponding to their move in the eight remaining wells. The well chosen for the move by the human player responds by fluorescing green, indicating a match to the player’s DNA input. The move also triggers the computer to make a strategic counter-move in one of the remaining wells, which fluoresces red. The game play continues until the computer eventually wins, as it is pre-programmed to do, Macdonald says. Each move takes about 30 minutes, she says.

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80 core processor !!!

On Tuesday, Intel showed off an 80-core processor at its developer forum taking place in San Francisco this week and one of the prominent features of the chip is that each core is connected directly to a 256MB memory chip through a technology called Through Silicon Vias, or TSV.


The memory wedded to the processor cores could constitute the entire memory needed for a computer, Intel CTO Justin Rattner told News.com in an interview during the Intel Developer Forum. TSV could be used in a variety of chips, not just the 80-core monster. As a result, computer makers, when building a system, would get their memory when they bought their processors from Intel. They would not have to obtain memory chips separately from other companies like they do now.

Wedding memory directly to the processor would have huge performance benefits. Currently, memory and the processor in Intel-based computers exchange data through a memory controller, which moves at a far slower rate than the processor. It's one of the big bottlenecks in computer performance. TSV, which displaces the memory controller, would shuttle data far quicker.

Data coming out of memory also squeezes through an overcrowded port. TSV would effectively open up thousands of ports. Overall, Rattner said, TSV is by far a more notable accomplishment than putting 80 cores on the same piece of silicon.


The processor cores are not restricted to getting memory from the chip wedded to it, added Rattner. The cores are connected to each other through high-speed links controlled by a router integrated into each core.


Overall, the prototype 80-core chip has an aggregate memory bandwidth of 1 terabyte per second, meaning that it can shift a trillion bytes per second.

Conceivably, TSV would also put AMD on the hot seat. A good portion of the performance gains AMD achieved with the Opteron chip came from Opteron's integrated memory controller. Intel does not put integrated memory controllers on its chips.



Rattner, however, noted that implementing TSV will take time. The memory chips attached to the 80-core processor are SRAM, a relatively expensive memory that Intel still makes. The next step is to see how well DRAM works with TSV.


Engineers would also have to devise packages that would let the processor and memory live together. The processor typically generates more heat than the memory, which is one of the factors that would have to be considered. Although it doesn't get many headlines, packaging design is a huge challenge for chipmakers.

"It's still in the research stage," he said. "We will do a lot of work with it in the next several years."


Source : News.com