inside google's futuristic quantum lab
Stanford creates biological transistors, the final step towards computers inside living cells By Sebastian Anthony on March 29, 2013 at 8:56 am
Bioengineers at Stanford University have created the first biological transistor made from genetic materials: DNA and RNA. Dubbed the “transcriptor,” this biological transistor is the final component required to build biological computers that operate inside living cells. We are now tantalizingly close to biological computers that can detect changes in a cell’s environment, store a record of that change in memory made of DNA, and then trigger some kind of response — say, commanding a cell to stop producing insulin, or to self-destruct if cancer is detected.
Stanford’s transcriptor is essentially the biological analog of the digital transistor. Where transistors control the flow of electricity, transcriptors control the flow of RNA polymerase as it travels along a strand of DNA. The transcriptors do this by using special combinations of enzymes (integrases) that control the RNA’s movement along the strand of DNA. “The choice of enzymes is important,” says Jerome Bonnet, who worked on the project. “We have been careful to select enzymes that function in bacteria, fungi, plants and animals, so that bio-computers can be engineered within a variety of organisms.”
Like a transistor, which enables a small current to turn on a larger one, one of the key functions of transcriptors is signal amplification. A tiny change in the enzyme’s activity (the transcriptor’s gate) can cause a very large change in the two connected genes (the channel). By combining multiple transcriptors, the Stanford researchers have created a full suite of Boolean Integrase Logic (BIL) gates — the biological equivalent of AND, NAND, OR, XOR, NOR, and XNOR logic gates. With these BIL gates (pun possibly intended), a biological computer could perform almost computation inside a living cell.
You need more than just BIL gates to make a computer, though. You also need somewhere to store data (memory, RAM), and some way to connect all of the transcriptors and memory together (a bus). Fortunately, as we’ve covered a few times before, numerous research groups have successfully stored data in DNA — and Stanford has already developed an ingenious method of using the M13 virus to transmit strands of DNA between cells. (See: Harvard cracks DNA storage, crams 700 terabytes of data into a single gram.) In short, all of the building blocks of a biological computer are now in place.
This isn’t to say that highly functional biological computers will arrive in short order, but we should certainly begin to see simple biological sensors that measure and record changes in a cell’s environment. Stanford has contributed the BIL gate design to the public domain, which should allow other research institutes, such as Harvard’s Wyss Institute, to also begin work on the first biological computer. (See: The quest for the $1000 genome.)
Moving forward, though, the potential for real biological computers is immense. We are essentially talking about fully-functional computers that can sense their surroundings, and then manipulate their host cells into doing just about anything. Biological computers might be used as an early-warning system for disease, or simply as a diagnostic tool (has the patient consumed excess amounts of sugar, even after the doctor told them not to?) Biological computers could tell their host cells to stop producing insulin, to pump out more adrenaline, to reproduce some healthy cells to combat disease, or to stop reproducing if cancer is detected. Biological computers will probably obviate the use of many pharmaceutical drugs.
Posted by Richard Mellor-Leeds on May 8, 2012
U. LEEDS (UK) -- Bacteria that make magnets and wires may someday help build environmentally friendly computers with larger hard drives and faster connections.
Researchers at the University of Leeds have used a bacterium that “eats” iron to create a surface of magnets, similar to those found in traditional hard drives, and wiring. As the bacterium ingests the iron it creates tiny magnets within itself.
In a process akin to potato-printing, but on a much smaller scale, this protein is attached to a gold surface in a checkerboard pattern and placed in a solution containing iron. (Credit: U. Leeds) The team has also begun to understand how the proteins inside these bacteria collect, shape, and position these “nanomagnets” inside their cells. As reported in the journal Small, the researchers can now replicate this behavior outside the bacteria.
Led by Sarah Staniland from the School of Physics and Astronomy, in a longstanding collaboration with the Tokyo University of Agriculture and Technology, the team hopes to develop a “bottom-up” approach for creating cheaper, more environmentally friendly electronics of the future.
“We are quickly reaching the limits of traditional electronic manufacturing as computer components get smaller. The machines we’ve traditionally used to build them are clumsy at such small scales. Nature has provided us with the perfect tool to circumvent this problem,” says Staniland.
The magnetic array was created by doctoral student Johanna Galloway, who used a protein that creates perfect nanocrystals of magnetite inside the bacterium Magnetospirillum magneticum.
In a process akin to potato-printing, but on a much smaller scale, this protein is attached to a gold surface in a checkerboard pattern and placed in a solution containing iron.
At a temperature of 80 degrees Celsius, similarly sized crystals of magnetite form on the sections of the surface covered by the protein. The researchers are now working to reduce the size of these islands of magnets, in order to make arrays of single nanomagnets.
They also plan to vary the magnetic materials that this protein can control. These next steps would allow each of these nanomagnets to hold one bit of information allowing the construction of better hard drives.
“Using today’s ‘top-down’ method—essentially sculpting tiny magnets out of a big magnet—it is increasingly difficult to produce the small magnets of the same size and shape which are needed to store data,” says Galloway.
“Using the method developed here at Leeds, the proteins do all the hard work; they gather the iron, create the most magnetic compound, and arrange it into regularly-sized cubes.”
While temporarily at Leeds from Tokyo University of Agriculture and Technology, Masayoshi Tanaka has used a different protein to create tiny electrical wires.
These “nanowires” are made of “quantum dots”—particles of copper indium sulphide and zinc sulphide that glow and conduct electricity—and are encased by fat molecules, or lipids.
The magnetic bacteria contain a protein that molds mini compartments for the nanomagnets to be formed in using the cell membrane lipids. Tanaka used a similar protein to make tubes of fat containing quantum dots—biological-based wiring.
“It is possible to tune these biological wires to have a particular electrical resistance. In the future, they could be grown connected to other components as part of an entirely biological computer,” says Tanaka, whose approach is also reported in Small.
The research group and the team in Japan led by Tadashi Matsunaga now plan to examine the biological processes behind the behavior of these proteins. “Our aim is to develop a toolkit of proteins and chemicals which could be used to grow computer components from scratch,” adds Staniland.
The research is funded by the Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council, and the Royal Society’s Newton International Fellowships Scheme.
Molecules as circuits Jan 23, 2014
Pursuit of silicon-based electronics has certain limits, in the physical sense: This type of circuit can never become "nano" because of the physical laws governing the flow of electrons. This imposes a halt to the process of miniaturization of electronic devices. One of the possible solutions is to use molecules as circuits, but their poor conduction capabilities make them unlikely candidates. There is, however, a possible way around this, which was investigated in a recent paper published in Proceedings of the National Academy of Sciences (PNAS) by an international research team that includes Ryan Requist, Erio Tosatti and Michele Fabrizio of the International School for Advanced Studies (SISSA) in Trieste.
The Kondo effect, first described last century by the Japanese physicist Jun Kondo, is observed when magnetic impurities, i.e., very few atoms (even only 1 in 1000) of magnetic material such as iron are added to metals like gold or copper. Even molecules like nitric oxide behave like magnetic impurities: when located between metal electrodes they give rise to a Kondo effect. This effect, as the study authors show, could be exploited to change the conductance between the two electrodes. Requist and Tosatti created a computer model of the Kondo effect under these conditions and formulated predictions on the behaviour of the molecules. These were then tested in experiments carried out by the experimental physicists involved in the study.
The results are encouraging: "Our work demonstrates for the first time that we can predict the Kondo effect quantitatively and it offers a theoretical basis for similar calculations with larger and more complex molecules. In the future it might be helpful when searching for the most appropriate molecules for these purposes", commented Requist.
The research collaboration that carried out the study saw the participation of SISSA, CNR-IOM Democritos, ICTP, the University of Trieste, the University of Technology of Dresden and the French Alternative Energies and Atomic Energy Commission (CEA).
The Kondo effect occurs when the presence of a magnetic atom (an impurity) causes the movement of electrons in a material to behave in a peculiar way.
"Every electron has a mechanical or magnetic rotation moment, termed spin", explains Erio Tosatti. "Kondo is a phenomenon related to the spin of metal electrons when they encounter a magnetic impurity. The free metal electrons cluster around the impurity and "screen it out" so that it can no longer be detected, at least so long as the temperature is sufficiently low". This results in specific properties of the material, for example an increase in electrical resistance.
"Conversely, in conditions involving very small size scales (the tip of a tunnelling electron microscope) such as those used in this study, the result is instead an increase in conductivity", explains Requist.