Tag Archives: Geobacter

Neuromorphic computing with voltage usage comparable to human brains

Part of neuromorphic computing’s appeal is the promise of using less energy because, as it turns out, the human brain uses small amounts of energy very efficiently. A team of researchers at the University of Massachusetts at Amherst have developed function in the same range of voltages as the human brain. From an April 20, 2020 news item on ScienceDaily,

Only 10 years ago, scientists working on what they hoped would open a new frontier of neuromorphic computing could only dream of a device using miniature tools called memristors that would function/operate like real brain synapses.

But now a team at the University of Massachusetts Amherst has discovered, while on their way to better understanding protein nanowires, how to use these biological, electricity conducting filaments to make a neuromorphic memristor, or “memory transistor,” device. It runs extremely efficiently on very low power, as brains do, to carry signals between neurons. Details are in Nature Communications.

An April 20, 2020 University of Massachusetts at Amherst news release (also on EurekAlert), which originated the news items, dives into detail about how these researchers were able to achieve bio-voltages,

As first author Tianda Fu, a Ph.D. candidate in electrical and computer engineering, explains, one of the biggest hurdles to neuromorphic computing, and one that made it seem unreachable, is that most conventional computers operate at over 1 volt, while the brain sends signals called action potentials between neurons at around 80 millivolts – many times lower. Today, a decade after early experiments, memristor voltage has been achieved in the range similar to conventional computer, but getting below that seemed improbable, he adds.

Fu reports that using protein nanowires developed at UMass Amherst from the bacterium Geobacter by microbiologist and co-author Derek Lovely, he has now conducted experiments where memristors have reached neurological voltages. Those tests were carried out in the lab of electrical and computer engineering researcher and co-author Jun Yao.

Yao says, “This is the first time that a device can function at the same voltage level as the brain. People probably didn’t even dare to hope that we could create a device that is as power-efficient as the biological counterparts in a brain, but now we have realistic evidence of ultra-low power computing capabilities. It’s a concept breakthrough and we think it’s going to cause a lot of exploration in electronics that work in the biological voltage regime.”

Lovely points out that Geobacter’s electrically conductive protein nanowires offer many advantages over expensive silicon nanowires, which require toxic chemicals and high-energy processes to produce. Protein nanowires also are more stable in water or bodily fluids, an important feature for biomedical applications. For this work, the researchers shear nanowires off the bacteria so only the conductive protein is used, he adds.

Fu says that he and Yao had set out to put the purified nanowires through their paces, to see what they are capable of at different voltages, for example. They experimented with a pulsing on-off pattern of positive-negative charge sent through a tiny metal thread in a memristor, which creates an electrical switch.

They used a metal thread because protein nanowires facilitate metal reduction, changing metal ion reactivity and electron transfer properties. Lovely says this microbial ability is not surprising, because wild bacterial nanowires breathe and chemically reduce metals to get their energy the way we breathe oxygen.

As the on-off pulses create changes in the metal filaments, new branching and connections are created in the tiny device, which is 100 times smaller than the diameter of a human hair, Yao explains. It creates an effect similar to learning – new connections – in a real brain. He adds, “You can modulate the conductivity, or the plasticity of the nanowire-memristor synapse so it can emulate biological components for brain-inspired computing. Compared to a conventional computer, this device has a learning capability that is not software-based.”

Fu recalls, “In the first experiments we did, the nanowire performance was not satisfying, but it was enough for us to keep going.” Over two years, he saw improvement until one fateful day when his and Yao’s eyes were riveted by voltage measurements appearing on a computer screen.

“I remember the day we saw this great performance. We watched the computer as current voltage sweep was being measured. It kept doing down and down and we said to each other, ‘Wow, it’s working.’ It was very surprising and very encouraging.”

Fu, Yao, Lovely and colleagues plan to follow up this discovery with more research on mechanisms, and to “fully explore the chemistry, biology and electronics” of protein nanowires in memristors, Fu says, plus possible applications, which might include a device to monitor heart rate, for example. Yao adds, “This offers hope in the feasibility that one day this device can talk to actual neurons in biological systems.”

That last comment has me wondering about why you would want to have your device talk to actual neurons. For neuroprosthetics perhaps?

Here’s a link to and a citation for the paper,

Bioinspired bio-voltage memristors by Tianda Fu, Xiaomeng Liu, Hongyan Gao, Joy E. Ward, Xiaorong Liu, Bing Yin, Zhongrui Wang, Ye Zhuo, David J. F. Walker, J. Joshua Yang, Jianhan Chen, Derek R. Lovley & Jun Yao. Nature Communications volume 11, Article number: 1861 (2020) DOI: https://doi.org/10.1038/s41467-020-15759-y Published: 20 April 2020

This paper is open access.

There is an illustration of the work

Caption: A graphic depiction of protein nanowires (green) harvested from microbe Geobacter (orange) facilitate the electronic memristor device (silver) to function with biological voltages, emulating the neuronal components (blue junctions) in a brain. Credit: UMass Amherst/Yao lab

Synthetic biowire for nanoelectronics

Apparently this biowire derived by synthetic biology processes can make nanoelectronics a greener affair. From a July 14, 2016 news item on ScienceDaily,

Scientists at the University of Massachusetts Amherst report in the current issue of Small that they have genetically designed a new strain of bacteria that spins out extremely thin and highly conductive wires made up of solely of non-toxic, natural amino acids.

A July 14, 2016 University of Massachusetts at Amherst news release (also on EurekAlert), which originated the news item, provides more information,

Researchers led by microbiologist Derek Lovley say the wires, which rival the thinnest wires known to man, are produced from renewable, inexpensive feedstocks and avoid the harsh chemical processes typically used to produce nanoelectronic materials.

Lovley says, “New sources of electronic materials are needed to meet the increasing demand for making smaller, more powerful electronic devices in a sustainable way.” The ability to mass-produce such thin conductive wires with this sustainable technology has many potential applications in electronic devices, functioning not only as wires, but also transistors and capacitors. Proposed applications include biocompatible sensors, computing devices, and as components of solar panels.

This advance began a decade ago, when Lovley and colleagues discovered that Geobacter, a common soil microorganism, could produce “microbial nanowires,” electrically conductive protein filaments that help the microbe grow on the iron minerals abundant in soil. These microbial nanowires were conductive enough to meet the bacterium’s needs, but their conductivity was well below the conductivities of organic wires that chemists could synthesize.

“As we learned more about how the microbial nanowires worked we realized that it might be possible to improve on Nature’s design,” says Lovley. “We knew that one class of amino acids was important for the conductivity, so we rearranged these amino acids to produce a synthetic nanowire that we thought might be more conductive.”

The trick they discovered to accomplish this was to introduce tryptophan, an amino acid not present in the natural nanowires. Tryptophan is a common aromatic amino acid notorious for causing drowsiness after eating Thanksgiving turkey. However, it is also highly effective at the nanoscale in transporting electrons.

“We designed a synthetic nanowire in which a tryptophan was inserted where nature had used a phenylalanine and put in another tryptophan for one of the tyrosines. We hoped to get lucky and that Geobacter might still form nanowires from this synthetic peptide and maybe double the nanowire conductivity,” says Lovley.

The results greatly exceeded the scientists’ expectations. They genetically engineered a strain of Geobacter and manufactured large quantities of the synthetic nanowires 2000 times more conductive than the natural biological product. An added bonus is that the synthetic nanowires, which Lovley refers to as “biowire,” had a diameter only half that of the natural product.

“We were blown away by this result,” says Lovley. The conductivity of biowire exceeds that of many types of chemically-produced organic nanowires with similar diameters. The extremely thin diameter of 1.5 nanometers (over 60,000 times thinner than a human hair) means that thousands of the wires can easily be packed into a very small space.

The added benefit is that making biowire does not require any of the dangerous chemicals that are needed for synthesis of other nanowires. Also, biowire contains no toxic components. “Geobacter can be grown on cheap renewable organic feedstocks so it is a very ‘green’ process,” he notes. And, although the biowire is made out of protein, it is extremely durable. In fact, Lovley’s lab had to work for months to establish a method to break it down.

“It’s quite an unusual protein,” Lovley says. “This may be just the beginning” he adds. Researchers in his lab recently produced more than 20 other Geobacter strains, each producing a distinct biowire variant with new amino acid combinations. He notes, “I am hoping that our initial success will attract more funding to accelerate the discovery process. We are hoping that we can modify biowire in other ways to expand its potential applications.”

As it often does, funding provides some notes of interest,

This research was supported by the Office of Naval Research, the National Science Foundation’s Nanoscale Science and Engineering Center and the UMass Amherst Center for Hierarchical Manufacturing.

Caption: Synthetic biowire are making an electrical connection between two electrodes. Researchers led by microbiologist Derek Lovely at UMass Amherst say the wires, which rival the thinnest wires known to man, are produced from renewable, inexpensive feedstocks and avoid the harsh chemical processes typically used to produce nanoelectronic materials. Credit: UMass Amherst

Caption: Synthetic biowire are making an electrical connection between two electrodes. Researchers led by microbiologist Derek Lovely at UMass Amherst say the wires, which rival the thinnest wires known to man, are produced from renewable, inexpensive feedstocks and avoid the harsh chemical processes typically used to produce nanoelectronic materials. Credit: UMass Amherst

Here’s a link to and a citation for the paper,

Synthetic Biological Protein Nanowires with High Conductivity by Yang Tan, Ramesh Y. Adhikari, Nikhil S. Malvankar, Shuang Pi, Joy E. Ward, Trevor L. Woodard, Kelly P. Nevin, Qiangfei Xia, Mark T. Tuominen, and Derek R. Lovley. Small DOI: 10.1002/smll.201601112 Version of Record online: 13 JUL 2016

© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

This paper is behind a paywall.