Power/Performance Bits: April 2

DNA programming; multi-function sensor; soft logic.


DNA programming
Computer scientists at California Institute of Technology, University of California, Davis, Maynooth University, and Harvard University created a library of DNA molecules that can self-assemble to compute a variety of algorithms.

Each molecule represents a six-bit binary number. The library created by the team is made up of around 700 short pieces, or tiles, of DNA. Each DNA tile consists of 42 bases (A, C, G or T) arranged in four domains of 10-11 bases. Each domain can represent a 1 or 0 and can stick to some of the domains on other tiles. No two tiles are a complete match.

Two of the four domains on each tile are “input,” and two “output.” Depending on which tiles the researchers selected to begin their program, they could get a known output at the other end.

“We were surprised by the versatility of algorithms we were able to design, despite being limited to six-bit inputs,” said David Doty, assistant professor of computer science at UC Davis. “When we began experiments, we had only designed three programs. But once we started using the system, we realized just how much potential it has. It was the same excitement we felt the first time we programmed a computer, and we became intensely curious about what else these strands could do. By the end, we had designed and run a total of 21 circuits.”

Starting with the original six bits of input, the system adds row after row of molecules, progressively running the algorithm. Instead of electricity flowing through circuits, rows of DNA strands sticking together perform the computation.

The end result is read with an atomic force microscope, which detects a marker molecule attached to the DNA. The system can be reprogrammed to run a different algorithm by simply selecting a different subset of strands.

Completed DNA algorithms. (Credit: Winfree Lab/Caltech)

The team was able to demonstrate algorithms for a variety of tasks, including counting exercises, random walks and drawing patterns in the DNA.

“Think of them as nano apps,” said Damien Woods, professor of computer science at Maynooth University. “The ability to run any type of software program without having to change the hardware is what allowed computers to become so useful. We are implementing that idea in molecules, essentially embedding an algorithm within chemistry to control chemical processes.”

Doty added, “The ultimate goal is to use computation to grow structures and enable more sophisticated molecular engineering.”

Multi-function sensor
Researchers from Linköping University and RISE Bioeconomy developed a cellulose-based multi-function sensor capable of measuring pressure, temperature, and humidity at the same time. The sensor is created from an elastic aerogel of polymers that conducts both ions and electrons and takes advantage of the thermoelectric effect.

The device starts as nanofibers of cellulose mixed with the conducting polymer PEDOT:PSS in water. The mixture is then freeze-dried under vacuum, which results in a sponge-like aerogel structure. To make the sponge elastic, polysilane was added.

Applying electrical potential across the material gives a linear current increase, but when the material is subject to a pressure, its resistance falls. Since the material is thermoelectric, it is also possible to measure temperature changes: the larger the temperature difference between the warm and cold sides, the higher the voltage developed. Humidity affects how rapidly the ions move from the warm side to the cold one. If the humidity is zero, no ions are transported.

“What is new is that we can distinguish between the thermoelectric response of the electrons (giving the temperature gradient) and that of the ions (giving the humidity level) by following the electrical signal versus time. That is because the two responses occur at different speeds,” said Xavier Crispin, professor in the Laboratory of Organic Electronics at Linköping University. “This means that we can measure three parameters with one material, without the different measurements being coupled.”

The researchers say the sensor could be a lower complexity, lower cost option for IoT applications such as security and medical monitoring, as well tracking the condition of sensitive goods.

Soft logic
Researchers at Harvard University built an entirely soft robot using a pressurized air computing system. Soft robots using silicone grippers are appealing for applications where hard metal parts could damage delicate or fragile objects, such as fruits and vegetables, or be a safer option in places where humans work in close proximity to machinery. However, most soft robots still rely on metal valves to open and close the channels of air that operate the rubbery grippers and a computer that tells those valves when to move.

To make such soft robots even softer, the team developed a computing system that uses only silicone tubing and pressurized air. “We’re emulating the thought process of an electronic computer, using only soft materials and pneumatic signals, replacing electronics with pressurized air,” said Daniel J. Preston, a postdoctoral researcher at Harvard.

To create NOT, AND, and OR gates, soft valves are programmed to react to different air pressures. For the NOT logic gate, for example, if the input is high pressure, the output will be low pressure. With these three logic gates, Preston says, “you could replicate any behavior found on any electronic computer.”

A demonstration created by the team is a submersible robot that bobs up and down in a water tank. The robot uses an environmental pressure sensor (a modified NOT gate) to determine what action to take. When the circuit senses low pressure at the top of the tank, the robot dives, then surfaces when it senses high pressure at depth. The robot can also surface on command if someone pushes an external soft button.

Beyond handling of delicate parts, the team says such soft robots are generally cheaper, simpler to make, and more durable. They could also operate in conditions that are challenging for electronics, such as high radiation areas, or in situations in which they might be crushed. Additionally, the circuits controlling the robot need no power when dormant.

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