Power/Performance Bits: April 12

Digital storage in DNA

Computer scientists and electrical engineers from University of Washington and Microsoft detailed one of the first complete systems to encode, store and retrieve digital data using DNA molecules, which can store information millions of times more compactly than current archival technologies.

Progress in DNA storage has been rapid: in 1999, the state-of-the-art in DNA-based storage was encoding and recovering a 23 character message; in 2013, researchers successfully recovered a 739 kB message. Growth in sequencing productivity eclipses even Moore’s Law, said the team, fueled by exponential reduction in synthesis and sequencing cost and latency.

In one experiment the team successfully encoded digital data from four image files into the nucleotide sequences of synthetic DNA snippets. More significantly, they were also able to reverse that process, retrieving the correct sequences from a larger pool of DNA and reconstructing the images without losing a single byte of information.

To accomplish this, the researchers developed a novel approach to convert the long strings of ones and zeroes in digital data into the four basic building blocks of DNA sequences — adenine, guanine, cytosine and thymine.

“How you go from ones and zeroes to As, Gs, Cs and Ts really matters because if you use a smart approach, you can make it very dense and you don’t get a lot of errors,” said Georg Seelig, a UW associate professor of electrical engineering and of computer science and engineering. “If you do it wrong, you get a lot of mistakes.”

All the movies, images, emails and other digital data from more than 600 basic smartphones (10,000 gigabytes) can be stored in the faint pink smear of DNA at the end of this test tube. (Source: Tara Brown Photography/University of Washington)

The digital data is chopped into pieces and stored by synthesizing a massive number of tiny DNA molecules, which can be dehydrated or otherwise preserved for long-term storage. Compared to tape, which has a lifetime of 10-30 years, synthetic DNA sequences have an observed half-life of over 500 years in harsh environments.

Advances in DNA storage rely on techniques pioneered by the biotechnology industry, but also incorporate new expertise. The team’s encoding approach, for instance, borrows from error correction schemes commonly used in memory, which hadn’t previously been applied to DNA.

Currently, the largest barrier to viable DNA storage is the cost and efficiency with which DNA can be synthesized and sequenced on a large scale. But the researchers say there’s no technical barrier to achieving those gains if the right incentives are in place.

Debugging energy harvesting

Researchers at Carnegie Mellon University and Disney Research developed a hardware-software tool for finding bugs in small energy harvesting devices that are subject to intermittent power failures.

Whether these devices harvest energy from radio waves, solar energy, heat or vibration, it’s anticipated that they all will lose power from time to time and be forced to reboot. This unpredictable power cycling can result in code execution errors rarely if ever seen in continuously powered systems, which are difficult to diagnose with conventional debugging tools.

“The use of energy-harvesting devices will only proliferate as increasing numbers of sensor networks are deployed and other devices such as solar-powered microsatellites are invented,” said Jessica Hodgins, vice president at Disney Research. “Creating reliable software for these devices is vital. To do that, we need tools to help us detect and correct bugs.”

The energy-interference-free system for monitoring and debugging energy-harvesting devices, attached to a WISP (purple PCB) in Panel A and shown in detail in Panel B. (Source: Alexei Colin, Graham Harvey, Brandon Lucia, and Alanson P. Sample)

Most existing tools provide power to the device being monitored, making it impossible to search for errors associated with intermittent power, said Alanson P. Sample, research scientist at Disney Research and head of its wireless systems group. Mixed-signal oscilloscopes can passively monitor a device’s energy level, but don’t provide any information about the internal state of its software – and are expensive.

The new system can passively monitor an energy-harvesting device for its energy level, input/output events, and program events. But it also has the capability to manipulate the amount of energy stored on the device, making it possible for an engineer to inject or remove power based on code execution, to aid in finding intermittent bugs.

Bacteria and solar panels

A team at Binghamton University connected nine biological-solar cells into the first bio-solar panel. Then they continuously produced electricity from the panel and generated the most wattage of any existing small-scale bio-solar cells – 5.59 microwatts.

“Once a functional bio-solar panel becomes available, it could become a permanent power source for supplying long-term power for small, wireless telemetry systems as well as wireless sensors used at remote sites where frequent battery replacement is impractical,” said Seokheun “Sean” Choi, an assistant professor of electrical and computer engineering at Binghamton University.

The current research is the latest step in using cyanobacteria (which can be found in almost every terrestrial and aquatic habitat on the planet) as a source of clean and sustainable energy. Last year, the group took steps toward building a better bio-solar cell by changing the materials used in anodes and cathodes (positive and negative terminals) of the cell and also created a miniature microfluidic-based single-chambered device to house the bacteria instead of the conventional, dual-chambered bio-solar cells.

However, this time the group connected nine identical bio-solar cells in a 3×3 pattern to make a scalable and stackable bio-solar panel. The panel continuously generated electricity from photosynthesis and respiratory activities of the bacteria in 12-hour day-night cycles over 60 total hours.

The bio-solar panel. (Source: Seokheun “Sean” Choi/ Binghamton University)

Even with the breakthrough, a typical “traditional” solar panel on the roof of a residential house, made up of 60 cells in a 6×10 configuration, generates roughly 200 watts of electrical power at a given moment. The cells from this study, in a similar configuration, would generate only about 0.00003726 watts.

So, it isn’t efficient just yet, but the team hopes the findings will open the door to future research of the bacteria itself.

“It is time for breakthroughs that can maximize power-generating capabilities/energy efficiency/sustainability,” Choi said. “The metabolic pathways of cyanobacteria or algae are only partially understood, and their significantly low power density and low energy efficiency make them unsuitable for practical applications. There is a need for additional basic research to clarify bacterial metabolism and energy production potential for bio-solar applications.”