Debora Rodrigues, Ezekiel Cullen Professor of Engineering at the University of Houston Cullen College of Engineering, in collaboration with Francisco C. Robles Hernandez, professor at the UH College of Technology and Ellen Aquino Perpetuo, professor at the University of Sao Paulo, Brazil offered conclusive research for understanding how bacteria found in copper mines convert toxic copper ions to stable single-atom copper.

In their co-authored paper, “Copper Mining Bacteria: Converting toxic copper ions into a stable single atom copper,” their research demonstrates how copper-resistant bacterium from a copper mine in Brazil convert copper sulfate ions into zero-valent metallic copper.

“The idea of having bacteria in mines is not new, but the unanswered question was: what are they doing in the mines?” Robles said. “By putting the bacteria inside an electronic microscope, we were able to figure out the physics and analyze it. We found out the bacteria were isolating single atom copper. In terms of chemistry, this is extremely difficult to derive. Typically, harsh chemicals are used in order to produce single atoms of any element. This bacterium is creating it naturally that is very impressive.”

As useful as copper is, the process of mining the metal often leads to toxic exposures and challenges on drawing out substantial volume for commercial use. Approximately one billion tons of copper are estimated in global reserves, according to the Copper Development Association Inc., with roughly 12.5 million metric tons per year mined. This aggregates to roughly 65 years of remaining reserves. Part of the supply challenge comes from limited available copper in high concentration in the earth’s crust, but the other challenge is the exposure to sulfur dioxide and nitrogen dioxide in the copper smelting and production process to concentrate the metal into useful quantities.

“The novelty of this discovery is that microbes in the environment can easily transform copper sulfate into zero valent single atom copper. This is a breakthrough because the current synthetic process of single atom zerovalent copper is typically not clean, it is labor intensive and expensive,” Rodrigues said.

“The microbes utilize a unique biological pathway with an array of proteins that can extract copper and convert it into single-atom zero-valent copper. The aim of the microbes is to create a less toxic environment for themselves by converting the ionic copper into single-atom copper, but at the same time they make something that is beneficial for us too.”

With a focus in electronic microscopy, Robles examined samples from Rodrigues’ findings in Brazilian copper mines and he determined the single atom nature of the copper. Rodrigues and Aquino’s groups further identified the bacterial process for converting copper sulfate to elemental copper — a rare find.

Research results demonstrate this new conversion process as an alternative to produce single atoms of metallic coper is safer, and more efficient versus current methods (i.e. chemical vapor deposition, sputtering and femtosecond laser ablation).

“We have only worked with one bacterium, but that may not be the only one out there that performs a similar function,” Rodrigues concluded. “The next step for this particular research is harvesting the copper from these cells and using it for practical applications.”

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Materials provided by University of Houston. Note: Content may be edited for style and length.

This new code to model stellar collisions is more expeditious than the established code used for numerical simulations. The research came from a unique collaboration between experimental computer scientists and astrophysicists in the Louisiana State University Department of Physics & Astronomy, the LSU Center for Computation & Technology, Indiana University Kokomo and Macquarie University, Australia, culminating in over of a year of benchmark testing and scientific simulations, supported by multiple NSF grants, including one specifically designed to break the barrier between computer science and astrophysics.

“Thanks to a significant effort across this collaboration, we now have a reliable computational framework to simulate stellar mergers,” said Patrick Motl, professor of physics at Indiana University Kokomo. “By substantially reducing the computational time to complete a simulation, we can begin to ask new questions that could not be addressed when a single-merger simulation was precious and very time consuming. We can explore more parameter space, examine a simulation at very high spatial resolution or for longer times after a merger, and we can extend the simulations to include more complete physical models by incorporating radiative transfer, for example.”

Recently published in Monthly Notices of the Royal Astronomical Society, “Octo-Tiger: A New, 3D Hydrodynamic Code for Stellar Mergers That Uses HPX Parallelisation,” investigates the code performance and precision through benchmark testing. The authors, Dominic C. Marcello, postdoctoral researcher; Sagiv Shiber, postdoctoral researcher; Juhan Frank, professor; Geoffrey C. Clayton, professor; Patrick Diehl, research scientist; and Hartmut Kaiser, research scientist, all at Louisiana State University — together with collaborators Orsola De Marco, professor at Macquarie University and Patrick M. Motl, professor at Indiana University Kokomo — compared their results to analytic solutions, when known and other grid-based codes, such as the popular FLASH. In addition, they computed the interaction between two white dwarfs from the early mass transfer through to the merger and compared the results with past simulations of similar systems.

“A test on Australia’s fastest supercomputer, Gadi (#25 in the World’s Top 500 list), showed that Octo-Tiger, running on a core count over 80,000, displays excellent performance for large models of merging stars,” De Marco said. “With Octo-Tiger, we cannot only reduce the wait time dramatically, but our models can answer many more of the questions we care to ask.”

Octo-Tiger is currently optimized to simulate the merger of well-resolved stars that can be approximated by barotropic structures, such as white dwarfs or main sequence stars. The gravity solver conserves angular momentum to machine precision, thanks to a correction algorithm. This code uses HPX parallelization, allowing the overlap of work and communication and leading to excellent scaling properties to solve large problems in shorter time frames.

“This paper demonstrates how an asynchronous task-based runtime system can be used as a practical alternative to Message Passing Interface to support an important astrophysical problem,” Diehl said.

The research outlines the current and planned areas of development aimed at tackling a number of physical phenomena connected to observations of transients.

“While our particular research interest is in stellar mergers and their aftermath, there are a variety of problems in computational astrophysics that Octo-Tiger can address with its basic infrastructure for self-gravitating fluids,” Motl said.

The animation (https://www.youtube.com/watch?v=hg9MQNLLJw4) was prepared by Shiber, who says: “Octo-Tiger shows remarkable performance both in the accuracy of the solutions and in scaling to tens of thousands of cores. These results demonstrate Octo-Tiger as an ideal code for modeling mass transfer in binary systems and in simulating stellar mergers.”

Scientists have attempted for years to balance the potent pain-relieving properties of opioids with their numerous negative side effects — with mostly mixed results.

Work by John Traynor, Ph.D., and Andrew Alt, Ph.D., and their team at the University of Michigan Edward F. Domino Research Center, funded by the National Institute on Drug Abuse, seeks to side-step these problems by harnessing the body’s own ability to block pain.

All opioid drugs — from poppy-derived opium to heroin — work on receptors that are naturally present in the brain and elsewhere in the body. One such receptor, the mu-opioid receptor, binds to natural pain-killers in the body called endogenous endorphins and enkephalins. Drugs acting on the mu-opioid receptor can cause addiction as well as unwanted side effects like drowsiness, problems with breathing, constipation and nausea.

“Normally, when you are in pain, you are releasing endogenous opioids, but they’re just not strong enough or long lasting enough,” says Traynor. The team had long hypothesized that substances called positive allosteric modulators could be used to enhance the body’s own endorphins and enkephalins. In a new paper published in PNAS, they demonstrate that a positive allosteric modulator known as BMS-986122 can boost enkephalins’ ability to activate the mu-opioid receptor.

What’s more, unlike opioid drugs, positive allosteric modulators only work in the presence of endorphins or enkephalins, meaning they would only kick in when needed for pain relief. They do not bind to the receptor in the way that opioids do instead binding in a different location that enhances its ability to respond to the body’s pain-relieving compounds.

“When you need enkephalins, you release them in a pulsatile fashion in specific regions of the body, then they are metabolized quickly,” explains Traynor. “In contrast, a drug like morphine floods the body and brain and sticks around for several hours.”

The team demonstrated the modulator’s ability to stimulate the mu-opioid receptor by isolating the purified receptor and measuring how it responds to enkephalins. “If you add the positive allosteric modulator, you need a lot less enkephalin to get the response.”

Additional electrophysiology and mouse experiments confirmed that the opioid receptor was more strongly activated by the body’s pain-relieving molecules leading to pain relief. In contrast the modulator showed much reduced side effects of depression of breathing, constipation and addiction liability.

Their next goal is to measure their ability to enhance activation of endogenous opioids under conditions of stress or chronic pain, explains Traynor, to ensure that they are effective but don’t lead to more dangerous responses like depression of breathing.

“While these molecules won’t solve the opioid crisis,” says Traynor, “they could slow it and prevent it from happening again because patients in pain could take this type of a drug instead of a traditional opioid drug.”

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Materials provided by Michigan Medicine – University of Michigan. Original written by Kelly Malcom. Note: Content may be edited for style and length.

A new study sequencing the genome of four species of sifakas, a genus of lemurs found only in Madagascar’s forests, reveals that these animals’ taste for leaves runs all the way to their genes, which are also more diverse than expected for an endangered species.

Sifakas are folivores, meaning that the bulk of their diet is composed of leaves. Leaves can be difficult to digest and full of toxic compounds meant to prevent them from being eaten. Unlike our carefully selected spinach, tree leaves also don’t taste great, and are not very nutritious.

Because of that, leaf-eaters typically have all sorts of adaptations, such as a longer digestive tract with special pouches where bacteria help break down the food.

In a new study appearing April 23 in Science Advances, researchers sequenced genomes from Coquerel’s (Propithecus coquereli), Verreaux’s (P. verreauxi), golden-crowned (P. tattersalli), and diademed (P. diadema) sifakas. The individuals sequenced had been wild-born but were housed at the Duke Lemur Center, with the exception of two Verreaux’s sifakas, one wild and one born in captivity.

These four species are found in different habitats in Madagascar, ranging from arid deciduous forests to rainforests, but share a similar diet.

The genomes showed molecular evidence for adaptations to neutralize and eliminate leaves’ toxic compounds, optimize the absorption of nutrients, and detect bitter tastes. Their genome shows patterns of molecular evolution similar to those found in other distantly related herbivores, such as the colobus monkeys from Central Africa, and domestic cattle.

Yet despite being such fine-tuned leaf-eating machines, sifakas can eat more than just leaves. They eat lots of fruits when those are in season and will also happily munch on flowers.

“Sifakas can take advantage of foods that are higher energy and are more nutrient dense, and can fall back and subsist on leaves in times of scarcity,” said Elaine Guevara, assistant research professor of Evolutionary Anthropology at Duke University and lead author of the study.

This dietary flexibility may have given them an advantage over their strictly leaves-only or fruit-only cousins in the face of threats such as forest fragmentation and disturbance.

Indeed, the analysis also showed that sifakas are genetically more diverse than would be expected for a critically endangered species on an island of shrinking habitats.

“These animals do seem to have very healthy levels of genetic diversity, which is very surprising,” said Guevara

Guevara and her team gauged genome heterozygosity, which is a measure of genetic diversity and an indicator of population size. Species at high risk for extinction tend to have only small populations left, and very low heterozygosity.

Sifakas do not follow this pattern and show far higher heterozygosity than other primates or other species of critically endangered mammals. Heterozygous populations tend to be more resilient to threats such as climate change, habitat loss, and new pathogens.

However, sifakas have very long generation times, averaging 17 years, so the loss of genetic diversity may take decades to become obvious. Guevara says that the genetic diversity found in this study may actually reflect how healthy populations were 50 years ago, prior to a drastic increase in deforestation rates in Madagascar.

“Sifakas are still critically endangered, their population numbers are decreasing, and habitat loss is accelerating drastically,” said Guevara.

There is still room for optimism. By not being picky eaters, sifakas may be less sensitive to deforestation and habitat fragmentation than primates with more restricted diets, allowing them to survive in areas with less-than-pristine forests.

“I’ve seen sifakas at the Lemur Center eat dead pine needles,” said Guevara. “Their diet is really flexible.”

Their greater genetic diversity may therefore mean that there is still hope for sifakas, if their habitats receive and maintain protection and strategic management.

“Sifakas still have a good chance if we act. Our results are all the more reason to do everything we can to help them,” said Guevara.

This work was funded by the Center for the Advanced Study of Human Paleobiology at The George Washington University, Duke University, and the Wenner-Gren Foundation. Genome sequencing and assembly were funded by National Human Genome Research Institute grant U54 HG003273 to Richard Gibbs (HGSC, Baylor College of Medicine).

About the size of a Rubik’s cube and encased in clear acrylic, the seismometer has a sleek, consumer-ready look. The device’s geophone detects incoming ground motion, while onboard hardware and software translate the geophone’s electrical signals into a digital waveform. The device has detected all earthquakes over magnitude 3.0 around Los Angeles since September 2020.

When earthquakes are stronger than the alert threshold set by the user, the device can sound the onboard alarm for on-site warning, send a text message to local subscribers of the regional warning service, and can be controlled from a smartphone.

He presented her research on the device at the Seismological Society of America (SSA)’s 2021 Annual Meeting.She also won a SSA Student Travel Grant, the only high school student among all recipients, to attend the conference free of charge. She is a student at Palos Verdes Peninsula High School in Rolling Hills Estates. He thanks her science research class teacher, Melissa Klose, for her guidance on scientific research methods and her support in pursuing research opportunities.

He researched, designed, built, and tested the entire device over a summer and fall spent at home under COVID-19 restrictions. Her home lab occupies a corner of a bedroom with “bedside drawers full of little wires and extra geophones and components.” she said.

There was also the bathroom she borrowed where the bright light was good for soldering. For acrylic laser cutting, her dad helped her drag a table out of the garage into the yard as a safety precaution.

“I did — don’t tell my mom — but I did one time have a little bit of a fire,” she admitted.

The seismometer device fills a gap in current earthquake early warning systems, He said, by providing a consumer-friendly, low-cost but built-for-purpose alternative to more expensive, scientific-grade systems like the West Coast’s ShakeAlert system. Her device offers a way for people in earthquake zones to gain a few to tens of seconds of warning to take action and automatically shut down utilities and machinery at work.

He has set up a nonprofit, Melior Earth, to help her get the device to those who need an inexpensive earthquake early warning system. “I do have hopes that I would be able to provide this to lower-income families and neighborhoods with less earthquake-proof infrastructure,” she said.

Quiet Under Quarantine

He got the idea for the seismometer after reading a paper about the unusual seismic “quiet” that descended over the earth when COVID-19 lockdowns brought a halt to much human activity. “I was wondering whether I would be able to measure that from my own home,” she recalled, “and then that quickly evolved into, I wonder if I can measure in my own home and apply it to earthquake early warning?”

She began reading about earthquake early warning and building a giant three-ring binder of highlighted papers, including many from SSA journals. One of her favorite researchers in the field was Richard M. Allen, director of the Berkeley Seismology Lab.

“I really enjoyed the way he explained earthquake early warning systems and the current systems’ limitations,” He said.

The research gave He the confidence that she could build a low-cost device for earthquake early warning, taking a consumer-based approach versus the conventional public station-based approach. After that, it was time to figure out the components, the programming and the design. She didn’t have much expertise going into the project, however, given much of the skills and knowledge needed were outside of school curriculum.

“I went to an MIT hackathon the other day, and what they said is that the secret for hackers is that they just google everything, right?” she said. “And that’s kind of like what I did for this project, like, oh, I don’t know how this works, just google it!'”

As He will discuss in her SSA presentation, the device evolved over time as her skills improved and she solved design problems along the way. Along with its alert and notification functions, the final design contains a data card that can hold up to four years’ worth of standard earthquake waveform files that can also be used for seismological studies.

“Hey, You Guys Hear That?”

He plugged in her first seismometer one night after midnight last September. “And then I went to sleep, and then the next day I woke up and there had been an earthquake in Los Angeles and I was like, oh, it’s fate!”

She compared the seismic signal captured by her device to one produced by a U.S. Geological Survey station near her house, “and the waveform looked the same,” she recalled.

One of the early successes of her testing period came when “my family was all in the living room and we were all talking and the device started beeping and I said, ‘Hey, you guys hear that?’ And they were like, ‘is it an earthquake?’ and then the pendant lights started shaking,” she said.

The seismometer has since successfully detected several recent earthquakes in Southern California, and He has competed in science fairs at her school district and Los Angeles County. There, she won the International Science and Engineering Fair (ISEF) Finalist award, which moves her on to compete at the international level next. In addition, she won the Association of Women Geoscientists Award, the Cheryl Saban Self-Worth Foundation for Women & Girls 1st Place Award and Scholarship, and the Professional Engineers in California Government’s Marylin Jorgenson-Reece Award of Excellence and Scholarship.

He, who turned 17 in February, is working on getting a utility patent for the device. She plans to use her nonprofit to drive consumer adoption for the device, especially making earthquake early warning accessible for the lower-income countries, regions and population.

“The whole point of it is that it would be a consumer product, but I’m not focused on the monetary gain of it,” she explained. “I’m more focused on the science of it and just the impact in general on people and on earthquake disaster prevention.”

The exoskeleton is externally powered by motors and controlled by an algorithm. When the researchers optimized it for speed, participants walked, on average, 42 percent faster than when they were wearing normal shoes and no exoskeleton. The results of this study were published April 20 in IEEE Transactions on Neural Systems and Rehabilitation Engineering.

“We were hoping that we could increase walking speed with exoskeleton assistance, but we were really surprised to find such a large improvement,” said Steve Collins, associate professor of mechanical engineering at Stanford and senior author of the paper. “Forty percent is huge.”

For this initial set of experiments, the participants were young, healthy adults. Given their impressive results, the researchers plan to run future tests with older adults and to look at other ways the exoskeleton design can be improved. They also hope to eventually create an exoskeleton that can work outside the lab, though that goal is still a ways off.

“My research mission is to understand the science of biomechanics and motor control behind human locomotion and apply that to enhance the physical performance of humans in daily life,” said Seungmoon Song, a postdoctoral fellow in mechanical engineering and lead author of the paper. “I think exoskeletons are very promising tools that could achieve that enhancement in physical quality of life.”

Walking in the loop

The ankle exoskeleton system tested in this research is an experimental emulator that serves as a testbed for trying out different designs. It has a frame that fastens around the upper shin and into an integrated running shoe that the participant wears. It is attached to large motors that sit beside the walking surface and pull a tether that runs up the length of the back of the exoskeleton. Controlled by an algorithm, the tether tugs the wearer’s heel upward, helping them point their toe down as they push off the ground.

For this study, the researchers had 10 participants walk with five different modes of operation. They walked in normal shoes without the exoskeleton, with the exoskeleton turned off and with the exoskeleton turned on with three different modes: optimized for speed, optimized for energy use, and a placebo mode adjusted to make them walk more slowly. In all of the tests, participants walked on a treadmill that adapts to their speed.

The mode that was optimized for speed — which resulted in the 42 percent increase in walking pace — was created through a human-in-the-loop process. An algorithm repeatedly adjusted the exoskeleton settings while the user walked, with the goal of improving the user’s speed with each adjustment. Finding the speed-optimized mode of operation took about 150 rounds of adjustment and two hours per person.

In addition to greatly increasing walking speed, the speed-optimized mode also reduced energy use, by about 2 percent per meter traveled. However, that result varied widely from person to person, which is somewhat expected, given that it was not an intentional feature of that exoskeleton mode.

“The study was designed to specifically answer the scientific question about increasing walking speed,” Song said. “We didn’t care too much about the other performance measures, like comfort or energy. However, seven out of 10 participants not only walked faster but consumed less energy, which really shows how much potential exoskeletons have for helping people in an efficient way.”

The settings that were optimized specifically for energy use were borrowed from a previous experiment. In the current study, this mode decreased energy use more than the speed-optimized settings but did not increase speed as much. As intended, the placebo mode both slowed down participants and boosted their energy use.

Better, faster, stronger

Now that the researchers have attained such significant speed assistance, they plan to focus future versions of the ankle exoskeleton emulator on reducing energy use consistently across users, while also being more comfortable.

In considering older adults specifically, Collins and his lab wonder whether future designs could reduce pain caused by weight on joints or improve balance. They plan to conduct similar walking tests with older adults and hope those provide encouraging results as well.

“A 40 percent increase in speed is more than the difference between younger adults and older adults,” said Collins. “So, it’s possible that devices like this could not only restore but enhance self-selected walking speed for older individuals and that’s something that we’re excited to test next.”

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Materials provided by Stanford University. Original written by Taylor Kubota. Note: Content may be edited for style and length.