“When you see a scurrying centipede, you're basically seeing an animal that inhabits a world that is very different than our world of movement,” said Daniel Goldman, the Dunn Family Professor in the School of Physics. “Our movement is largely dominated by inertia. If I swing my leg, I land on my foot and I move forward. But in the world of centipedes, if they stop wiggling their body parts and limbs, they basically stop moving instantly.”

Intrigued to see if the many limbs could be helpful for locomotion in this world, a team of physicists, engineers, and mathematicians at the Georgia Institute of Technology are using this style of movement to their advantage. They developed a new theory of multilegged locomotion and created many-legged robotic models, discovering the robot with redundant legs could move across uneven surfaces without any additional sensing or control technology as the theory predicted.

These robots can move over complex, bumpy terrain — and there is potential to use them for agriculture, space exploration, and even search and rescue.

The researchers presented their work in the papers, “Multilegged Matter Transport: A Framework for Locomotion on Noisy Landscapes,” in Science in May and “Self-Propulsion via Slipping: Frictional Swimming in Multilegged Locomotors,” in Proceedings of the National Academy of Sciences in March.

A Leg Up

For the Science paper, the researchers were motivated by mathematician Claude Shannon’s communication theory, which demonstrates how to reliably transmit signals over distance, to understand why a multilegged robot was so successful at locomotion. The theory of communication suggests that one way to ensure a message gets from point A to point B on a noisy line isn’t to send it as an analog signal, but to break it into discrete digital units and repeat these units with an appropriate code.

“We were inspired by this theory, and we tried to see if redundancy could be helpful in matter transportation,” said Baxi Chong, a physics postdoctoral researcher. “So, we started this project to see what would happen if we had more legs on the robot: four, six, eight legs, and even 16 legs.”

A team led by Chong, including School of Mathematics postdoctoral fellow Daniel Irvine and Professor Greg Blekherman, developed a theory that proposes that adding leg pairs to the robot increases its ability to move robustly over challenging surfaces — a concept they call spatial redundancy. This redundancy makes the robot’s legs successful on their own without the need for sensors to interpret the environment. If one leg falters, the abundance of legs keeps it moving regardless. In effect, the robot becomes a reliable system to transport itself and even a load from A to B on difficult or “noisy” landscapes. The concept is comparable to how punctuality can be guaranteed on wheeled transport if the track or rail is smooth enough but without having to engineer the environment to create this punctuality.

“With an advanced bipedal robot, many sensors are typically required to control it in real time,” Chong said. “But in applications such as search and rescue, exploring Mars, or even micro robots, there is a need to drive a robot with limited sensing. There are many reasons for such sensor-free initiative. The sensors can be expensive and fragile, or the environments can change so fast that it doesn’t allow enough sensor-controller response time.”

To test this, Juntao He, a Ph.D. student in robotics, conducted a series of experiments where he and Daniel Soto, a master’s graduate in the George W. Woodruff School of Mechanical Engineering, built terrains to mimic an inconsistent natural environment. He then tested the robot by increasing its number of legs by two each time, starting with six and eventually expanding to 16. As the leg count increased, the robot could more agilely move across the terrain, even without sensors, as the theory predicted. Eventually, they tested the robot outdoors on real terrain, where it was able to traverse in a variety of environments.

“It's truly impressive to witness the multilegged robot's proficiency in navigating both lab-based terrains and outdoor environments,” Juntao said. “While bipedal and quadrupedal robots heavily rely on sensors to traverse complex terrain, our multilegged robot utilizes leg redundancy and can accomplish similar tasks with open-loop control.”

Next Steps

The researchers are already applying their discoveries to farming. Goldman has co-founded a company that aspires to use these robots to weed farmland where weedkillers are ineffective.

“They’re kind of like a Roomba but outside for complex ground,” Goldman said. “A Roomba works because it has wheels that function well on flat ground. Until the development of our framework, we couldn’t confidently predict locomotor reliability on bumpy, rocky, debris-ridden terrain. We now have the beginnings of such a scheme, which could be used to ensure that our robots traverse a crop field in a certain amount of time.”

The researchers also want to refine the robot. They know why the centipede robot framework is functional, but now they’re determining the optimal number of legs to achieve motion without sensing in a way that is cost-effective yet still retains the benefits.

“In this paper, we asked, ‘How do you predict the minimum number of legs to achieve such tasks?’” Chong said. “Currently we only prove that the minimum number exists, but we don't know that exact number of legs needed. Further, we need to better understand the tradeoff between energy, speed, power, and robustness in such a complex system.”

CITATION:

Baxi Chong et al., Multilegged matter transport: A framework for locomotion on noisy landscapes.Science380,509-515(2023).DOI:10.1126/science.ade4985

Fermented foods like kimchi have been an integral part of Korean cuisine for thousands of years. Since ancient times, Korean chefs have used onggi — traditional handmade clay jars — to ferment kimchi. Today, most kimchi is made through mass fermentation in glass, steel, or plastic containers, but it has long been claimed that the highest quality kimchi is fermented in onggi.

Kimchi purists now have scientific validation, thanks to recent research from David Hu, professor in the George W. Woodruff School of Mechanical Engineering and the School of Biological Sciences at Georgia Tech, and Soohwan Kim, a second-year Ph.D. student in Hu’s lab.

In a combined experimental and theoretical study, Hu and Kim measured carbon dioxide levels in onggi during kimchi fermentation and developed a mathematical model to show how the gas was generated and moved through the onggi’s porous walls. By bringing the study of fluid mechanics to bear on an ancient technology, their research highlights the work of artisans and provides the missing link for how the traditional earthenware allows for high quality kimchi.

Their research was published in the Journal of the Royal Society Interface.

“We wanted to find the ‘secret sauce’ for how onggi make kimchi taste so good,” Hu said. “So, we measured how the gases evolved while kimchi fermented inside the onggi — something no one had done before.”

The porous structure of these earthenware vessels mimics the loose soil where lactic acid bacteria — known for their healthy probiotic nature — are found. While previous studies have shown that kimchi fermented in onggi has more lactic acid bacteria, no one knew exactly how the phenomenon is connected to the unique material properties of the container.

First, Kim obtained a traditional, handmade onggi jar from an artisan in his hometown in Jeju, South Korea, a region famous for onggi. Back at Georgia Tech, Hu and Kim first tested the permeability of the onggi by observing how water evaporated through the container over time.

Next, they installed carbon dioxide and pressure sensors into both the onggi and a typical, hermetically sealed glass jar. They prepared their own salted cabbage and placed it in both containers. They then used the sensors to measure and compare the change in carbon dioxide — a signature of fermentation.

Hu and Kim also developed a mathematical model based on the porosity of the onggi. The model allowed them to infer the generation rate of carbon dioxide, since the onggi lets carbon dioxide out gradually.

They concluded that the onggi’s porous walls permitted the carbon dioxide to escape the container, which accelerated the speed of fermentation. The onggi’s porosity also functioned as a “safety valve,” resulting in a slower increase in carbon dioxide levels than the glass jar while blocking the entry of external particles. Their data revealed that the carbon dioxide level in onggi was less than half of that in glass containers.

They also found that the beneficial bacteria in the onggi-made kimchi proliferated 26% more than in the glass counterpart. In the glass jar, the lactic acid bacteria became suffocated by their own carbon dioxide in the closed glass container. It turns out that, because the onggi releases carbon dioxide in small rates, the lactic acid bacteria are happier and reproduce more.

“Onggi were designed without modern knowledge of chemistry, microbiology, or fluid mechanics, but they work remarkably well,” Kim said. “It’s very interesting to get these new insights into ancient technology through the lens of fluid dynamics.”

Onggi’s semiporous nature is unique compared to other forms of earthenware. A clay container that leaks, but only slightly, is not easy to make. Terra cotta containers, for example, quickly leak water.

“It's amazing that, for thousands of years, people have been building these special containers out of dirt, but in many ways, they are very high tech,” Hu said. “We discovered that the right amount of porosity enables kimchi to ferment faster, and these onggi provide that.”

Kim said that some artisans still use ancient methods when making onggi, but their numbers are decreasing. Now, the market is flooded with inauthentic versions of the vessels.

“We hope this study draws attention to this traditional artisan work and inspires energy-efficient methods for fermenting and storing foods,” he said. “Also, the onggi are quite beautiful.”

Citation: Kim Soohwan and Hu David L. Onggi’s permeability to carbon dioxide accelerates kimchi fermentation. J. R. Soc. Interface. 2023.

DOI: https://doi.org/10.1098/rsif.2023.0034

This material was supported by the Woodruff Faculty fellowship and the NSF Physics of Living Systems student network.

These ecosystems cover just 3% of Earth’s land area, but “peatlands store over one-third of all soil carbon on the planet,” explains Joel Kostka, professor and associate chair of Research in the School of Biological Sciences at Georgia Tech.

This carbon storage is supported in large part by microbes. Two microbial processes in particular — nitrogen fixation and methane oxidation — strike a delicate balance, working together to give Sphagnum mosses access to critical nutrients in nutrient-depleted peatlands. 

The coupling of these two processes is often referred to as the “missing link” of nutrient cycling in peatlands. Yet, how these processes will respond to changing climates along northern latitudes is unclear.

“There are tropical peatlands — but the majority of peatlands are in northern environments.” notes Caitlin Petro, a research scientist who works with Kostka in Biological Sciences at Tech. “And those are going to be hit harder by climate change.”

Kostka and Petro recently led a collaborative study to investigate how this critical type of ecosystem (and the “missing link” of microbial processes that support it) may react to the increased temperature and carbon dioxide levels predicted to come with climate change. The team, which also includes researchers from the Oak Ridge National Laboratory (ORNL), Florida State University, and the University of Tennessee, Knoxville, just published their work in the scientific journal Global Change Biology.

By testing the effects of increasing temperature and carbon dioxide on the growth of Sphagnum moss, its associated microbiome, and overall ecosystem health, Kostka and Petro say computational models will be better equipped to predict the effects of climate change.

“Down the road,” Kostka added, “we hope the results can be used by environmental managers and governments to adaptively manage or geoengineer peatlands to thrive in a warmer world.”

Raising the heat

To see how northern peatlands will react to climate change, the team, which also included School of Earth and Atmospheric Sciences Associate Professor Jennifer Glass, turned to the ORNL Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment — a unique field lab in northern Minnesota where the team warms peat bogs and experimentally changes the amount of carbon dioxide in the atmosphere. 

Starting in 2016, the team exposed different parts of SPRUCE’s experimental peatlands to a gradient of higher temperatures ranging from an increase of 0°C to 9°C, capturing the Intergovernmental Panel on Climate Change models’ predicted 4°C to 6°C increase in northern regions by 2100.

The moss’s reaction was significant. Although nearly 100% of the bog’s surface was covered in moss at the beginning of the experiment, moss coverage dropped with each increase in temperature, plummeting to less than 15% in the warmest conditions.

Critically, the two microbial processes that had previously been consistently linked fell out of sync at higher temperatures. 

“Peatlands are extremely nutrient-poor and microbial nitrogen fixation represents a major nitrogen input to the ecosystem,” Kostka explained. Fixing nitrogen is the process of turning atmospheric nitrogen into an organic compound that the moss can use for photosynthesis, while methane oxidation allows the moss to use methane released from decomposing peat as energy. “Methane oxidation acts to fuel nitrogen fixation while scavenging a really important greenhouse gas before it is released to the atmosphere. This study shows that these two processes, which are catalyzed by the Sphagnum microbiome, become disconnected as the moss dies.”

“These processes occurring together are really important for the community,” Petro explained. Yet many microbes that are able to both fix nitrogen and oxidize methane were absent in the mosses collected from higher temperature enclosures. And while elevated carbon dioxide levels appeared to offset some of the changes in nitrogen cycling caused by warming, the decoupling of these processes remained.

“These treatments are altering a fairly well-defined and consistent plant microbiome that we find in many different environments, and that has this consistent function,” Petro explained. “It's like a complete functional shift in the community.” 

Though it’s not clear which of these changes — the moss dying or the altered microbial activity — is driving the other, it is clear that with warmer temperatures and higher carbon dioxide levels comes a cascade of unpredictable outcomes for peat bogs.

“In addition to the direct effects of climate warming on ecosystem function,” Petro adds, “it will also introduce all of these off-shooting effects that will impact peatlands in ways that we didn't predict before.”

This work was supported by the National Science Foundation (DEB grant no. 1754756). The SPRUCE project is supported by the U.S. Department of Energy's Office of Science, Biological, and Environmental Research (DOE BER) and the USDA Forest Service.

DOI: https://doi.org/10.1111/gcb.16651

Citation: Petro, C., et al. Climate drivers alter nitrogen availability in surface peat and decouple N2 fixation from CH4 oxidation in the Sphagnum moss microbiome. Global Change Biology. (2023).

Aerial Photo: Hanson, P.J., M.B. Krassovski, and L.A. Hook. 2020. SPRUCE S1 Bog and SPRUCE Experiment Aerial Photographs. Oak Ridge National Laboratory, TES SFA, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A. https://doi.org/10.3334/CDIAC/spruce.012 (UAV image number 0050 collected on October 4, 2020).

Inside a typical human cell are tens of thousands of proteins. We need so many because proteins are the skilled laborers of the cell with each one performing a specific job. Some lend firmness to muscle cells or neurons. Others bind to specific, targeted molecules, ferrying them to new locations. And there are others that activate the process of cell division and growth.

A protein’s specific function depends on its shape, and to achieve its functional shape – it’s native state – a protein folds.  A protein begins its life as a long chain of amino acids, called a polypeptide. The sequence of amino acids determines how the protein chain will fold and form a complex, 3D structure that allow the protein to perform an intended task.

In the lab of Loren Williams, researchers are using “creative destruction” as a model for protein fold evolution and innovation. The term, coined by Austrian economist and political scientist Joseph Schumpeter in the 1940s, describes the deliberate dismantling of an established thing, like the wired telephone, to develop a new thing, like the smart phone.

“We have protein structures that have evolved over almost four billion years, and we don’t really understand where they came from or how they came to be what they are,” said Claudia Alvarez-Carreño, a postdoctoral researcher in the Williams lab, which is called the Center for the Origin of Life, or COOL. “It’s a very complex process forming these structures, and there are many hypotheses on how they could have emerged in early evolution.”

Out with the Old, In with the New

Alvarez-Carreño is the lead author of the paper, “Creative Destruction: New Protein Folds from Old,” published recently in the journal Proceedings of the National Academy of Sciences, or PNAS. She and her co-authors (Williams, Rohan Gupta, and Anton Petrov) excavated the deepest evolutionary history found within the translation machinery – which resides within all cells in the ribosome and is the birthplace of all proteins.

The researchers provide evidence supporting the common origins of some of the simplest, oldest, and most common protein folds. It suggests a form of creative destruction at work, explaining how simple protein folds spawn more complex folds.

They discovered that once a protein can fold and achieve its 3D structure, when it is combined with another protein which has folded into a different 3D structure, that combination can easily become a new structure. “So maybe it’s not as difficult as we thought to go from one structure to another,” said Williams, professor in the School of Chemistry and Biochemistry. “And maybe this can explain the diversity of protein structures that we see today.”

In Schumpter’s creative destruction model, developing “daughter products” involves the destruction of ancestral products. “Daughter products can inherit features of ancestors but can in essence be different from them,” they write in the paper. In the smart phone example ancestral wired phones, computers, cameras, global positioning, and other technologies that are merged to create a daughter, i.e. the smart phone.

The daughter inherits many features of the ancestors. These features, which interact in specific ways in the daughter, create new functional niches that were not accessible, or even possible, in the ancestors.

“So, the creative destruction of protein folds might account for a lot of the diversity we see,” Williams said.

Molecular Mergers

Ever since the simplest and most ancient protein folds emerged on Earth billions of years ago, the number of folds has expanded to form the universe of protein function we see in modern biology.

But the origins of protein folds and the evolutionary mechanisms at play pose central questions in biology that Williams and his team considered. For instance, how did protein folds arise, and what led to the diverse set of protein folds in contemporary biological systems, and why did nearly four billion years of fold evolution produce fewer than 2,000 distinct folds?

The researchers believe that creative destruction can be generalized to explain a lot of this.

In creative destruction, they explain, one open reading frame – the span of DNA sequence that encodes a protein  – merges with another to produce a fused polypeptide. The merger forces these two ancestors into a new structure. The resulting polypeptide can achieve a form that was inaccessible to either of the independent ancestors, before the merger. But these new folds are not totally independent of the old. That is, a daughter fold inherits some things from the ancestral fold.

This, broadly speaking, is what Williams and his team observed, and they think their creative destruction model has some application in studying disease – proteins that fold improperly can impact the health of the cells and the human comprised of those cells.

“For example, we think this process is important in the biology of cancer – there are many, many proteins that have fused and, we believe have refolded, in cancers,” said Williams. “And there’s the world of protein aggregation diseases, like Parkinson’s or Alzheimers, and proteins that have not folded correctly, or have refolded.”

But right now, Williams and his team are most interested in how their creative destruction model helps them understand some of the deepest questions of our evolution.

“Like, where did we come from,” Williams said. “Creative destruction could help us understand where the proteins in our body came and how we came to be what we are.”

CITATION: Claudia Alvarez-Carreño, Rohan J. Gupta, Anton S. Petrov and Loren Dean Williams. “Creative destruction: New protein folds from old.” PNAS Journal.

https://doi.org/10.1073/pnas.2207897119

“But I didn’t realize the role that real estate can play in that,” said Lawler, general manager of BioSpark Labs – the collaborative, shared laboratory environment taking shape at Science Square at Georgia Tech.

Sitting adjacent to the Tech campus and formerly known as Technology Enterprise Park, Science Square is being reactivated and positioned as a life sciences research destination. The 18-acre site is abuzz with new construction, as an urban mixed-use development rises from the property.

Meanwhile, positioned literally on the ground floor of all this activity is BioSpark Labs, located in a former warehouse, fortuitously adjacent to the Global Center for Medical Innovation. It’s one of the newer best-kept secrets in the Georgia Tech research community.

BioSpark exists because the Georgia Tech Real Estate Office,  led by Associate Vice President Tony Zivalich, recognized the need of this kind of lab space. Zivalich and his team have overseen the ideation, design, and funding of the facility, partnering with Georgia Advanced Technology Ventures, as well as the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University, and the core facilities of the Petit Institute for Bioengineering and Bioscience.

“We are in the middle of a growing life sciences ecosystem, part of a larger vision in biotech research,” said Lawler, who was hired on to manage the space, bringing to the job a wealth of experience as a former research scientist and lab manager with a background in molecular and synthetic biology.

Researchers’ Advocate

BioSpark was designed to be a launch pad for high-potential entrepreneurs. It provides a fully equipped and professionally operated wet lab, in addition to a clean room, meeting and office space, to its current roster of clients, five life sciences and biotech startup, a number certain to increase – because BioSpark is undergoing a dramatic expansion that will include 11 more labs (shared and private space), an autoclave room, equipment and storage rooms.

“We want to provide the necessary services and support that an early-stage company needs to begin lab operations on day one,” said Lawler, who has put together a facility with $1.7 million in lab equipment. “I understand our clients’ perspective, I understand researchers and their experiments, and their needs, because I have first-hand proficiency in that world. So, I can advocate on their behalf.”

CO2 incubators, a spectrophotometer, a biosafety cabinet, a fume hood, a -80° freezer, an inverted microscope, and the autoclave are among the wide range of apparatus. Plus, a virtual treasure trove of equipment is available to BioSpark clients off-site through the Core Facilities of the Petit Institute for Bioengineering and Bioscience on the Georgia Tech campus.

“One of the unique things about us is, we’re agnostic,” Lawler said. “That is, our startups can come from anywhere. We have companies that have grown out of labs at Georgia State, Alabama State, Emory, and Georgia Tech. And we have interest from entrepreneurs from San Diego, who are considering relocating people from mature biotech markets to our space.”

Ground Floor Companies

Marvin Whiteley wants to help humans win the war against bacteria, and he has a plan, something he’s been cooking up for about 10 years, which has now manifested in his start-up company, SynthBiome, one of the five startups based at BioSpark Labs.

“We can discover a lot of antibiotics in the lab but translating them into the clinic has been a major challenge – antibiotic resistance is the main reason,” said Whiteley, professor in the School of Biological Sciences at Georgia Tech. “Something might work in a test tube easily enough and it might work in a mouse. But the thing is, bacteria know that mice are different - and and so bacteria act differently in mice than in humans.”

SynthBiome was built to help accelerate drug discovery. With that goal in mind, Whiteley and has team set out to develop a better, more effective preclinical model. “We basically learned to let the bacteria tell us what it’s like to be in a human,” Whiteley said. “So, we created a human environment in a test tube.”

Whiteley has said a desire to help people is foundational to his research. He wants to change how successful therapies are made. The same can be said for Dr. Pooja Tiwari, who launched her company, Arnav Biotech, to develop mRNA-based therapeutics and vaccines. Arnav Biotech also serves as a contract researcher and manufacturer, helping other researchers and companies interested in exploring mRNA in their work.

“There are only a handful of people who have deep knowledge of working in mRNA research, and this limits the access to it” said Tiwari, a former postdoctoral researcher at Georgia Tech and Emory. “We’d like to democratize access to mRNA-based therapeutics and vaccines by developing accessible and cost-effective mRNA therapeutics for global needs”.

Arnav – which has RNA right there in the name – in Sanskrit means ‘ocean.’ An ocean has no discernible borders, and Tiwari is working to build a biotech company that eliminates borders in equitable access to mRNA-based therapeutics and vaccines.

With this mission in mind, Arnav is developing mRNA-based, broad-spectrum antivirals as well as vaccines against pandemic potential viruses before the next pandemic hits. Arnav has recently entered in a collaboration with Sartorius BIA Separations, a company based on Slovenia, to advance their mRNA pipeline. While building its own mRNA therapeutics pipeline, Arnav is also helping other scientists explore mRNA as an alternative therapeutic and vaccine platform through its contract services. 

“I think of the vaccine scientist who makes his medicine using proteins, but would like to explore the mRNA option,” Tiwari posits. “Maybe he doesn’t want to make the full jump into it. That’s where we come in, helping to drive interest in this field and help that scientist compare his traditional vaccines to see what mRNA vaccines looks like.”

She has all the equipment and instruments that she needs at BioSpark Labs and was one of the first start-ups to put down roots there. So far, it’s been the perfect partnership, Tiwari said, adding, “It kind of feels like BioSpark and Arnav are growing up together.”

Jennifer Glass and Chris Reinhard are in the first class of grant winners in the Scialog: Signatures of Life in the Universe program, sponsored by Research Corporation for Science Advancement and the Heising-Simons Foundation. Additional sponsorship comes from NASA and the Kavli Foundation.

Scialog®, short for “science + dialog,” was formed in 2010 “to bring together early career scientists to advance basic science in areas of global importance, and to write proposals for high risk, high reward collaborative research projects,” according to the organization’s website. The Signatures of Life program first met virtually this June with the founding organizations providing facilitators from a variety of disciplines: Earth and planetary science, chemistry and physics, astronomy and astrobiology, microbiology and biochemistry, and data science.

Eight teams of researchers — a total of 20 scientists — are the result of that June brainstorming session, proposing research projects “with the potential to transform our understanding of the habitability of planets, of how the occurrence of life alters planets and leaves signatures, and of how to detect such signatures beyond Earth, both within our solar system and on exoplanets,” according to a Scialog® news release. Each of the 20 scientists receives an individual award of $55,000.

Jennifer Glass: Methane and False Biosignature Positives

“I am thrilled to start working on a new problem related to my favorite molecule (methane),” says Glass. “I am excited to have a Georgia Tech student, Camille Butkus, who has already made great headway helping with this project. This is great timing because the James Webb Space Telescope is launching this December and will be able to detect methane in exoplanet atmospheres.”

Glass’s research proposal is “Methane from Nontraditional Abiotic Sources and Potential for False Biosignature Positives” and her team includes colleagues from the University of Chicago and University of California, Los Angeles.

“Methane is one of the only gases with a dominant biological source on Earth that can be readily detected in exoplanet atmospheres with the new generation of space telescopes,” Glass explains. As space telescopes begin to characterize exoplanet atmospheres, scientists are looking to firm up what can confidently be termed a biosignature gas — and rule out false positives in the imminent findings of methane-containing rocky exoplanets within the habitable zone of their solar system. 

“A common assumption in previous models of methane production from abiotic sources (nonliving parts of an environment, like climate and chemistry) is that other rocky exoplanets have a crustal composition similar to Earth. Yet we now know that many rocky exoplanets will be richer in carbon than Earth,” Glass says. “How would more carbon in a planet’s crust affect abiotic methane production? Could it lead to production of false biosignature methane biosignatures?” Glass asks. “How can we rule these out to avoid false positive biosignatures, and to capture signs of methane-cycling life on exoplanets? These are the types of questions my group is excited to explore with this new funding.”

Chris Reinhard: Modeling Planetary Biosphere Evolution

Reinhard says he is humbled and grateful to receive support from the inaugural year of the Scialog® initiative. “The Scialog model for catalyzing novel interdisciplinary research is one of a kind — and to be honest, just being involved in the initial workshop was an incredibly enriching and useful experience for me,” Reinhard says. “But I am very excited to have the opportunity to embark on the project in earnest and see where it leads.”

That project, “Stochastic Simulation of Evolving Planetary Biospheres”, is based on the premise that the metabolic networks that drive the large-scale impacts of a biosphere are in many ways path-dependent — which is to say their development will depend on often random trajectories of environmental evolution and on the existing suite of metabolic pathways available at any given time. “Our goal is to systematically explore the likelihood and long-term viability of biospheres that are very different from our own, and the signatures they might leave behind in the local environment, or on the scale of a planetary atmosphere,” Reinhard notes. His project team includes scientists from the University of Chicago and the University of Oregon.

AGU Awards,  Honors, Appreciation

Glass and Reinhard also join School of Earth and Atmospheric Sciences assistant professor Frances Rivera-Hernández and School of Civil and Environmental Engineering associate professor Jingfeng Wang in receiving annual American Geophysical Union (AGU) accolades.

Reinhard is among those receiving the organization’s “highest honors for excellence in scientific research, education, communication, and outreach” and Glass is recognized for “meritorious work or service toward the advancement and promotion of discovery and solution science”:

2021 AGU Union Medal, Award, and Prize Recipients
James B. Macelwane Medal
Christopher T. Reinhard, Georgia Institute of Technology

2021 AGU Section Awardees and Named Lecturers
Thomas Hilker Early Career Award for Excellence in Biogeosciences
Jennifer B. Glass, Georgia Institute of Technology

In Appreciation of AGU’s Outstanding Reviewers of 2020
Frances Rivera-Hernández
Georgia Institute of Technology
Andrew Dombard
Geophysical Research Letters

In Appreciation of AGU’s Outstanding Reviewers of 2020
Jingfeng Wang
Georgia Institute of Technology
Earth and Space Science editors
Earth and Space Science

To collect and transport pollen, honey bees mix pollen particles with regurgitated nectar and form it into a pellet, which clings to each of their hind legs. The honey bees then deposit the pellets into a cell within the hive by carefully scraping them off using their other legs. 

The study, from the lab of George W. Woodruff School of Mechanical Engineering Professor David Hu, sought to better understand the mechanics of this process which could inspire new ways to manufacture and manipulate soft materials. Hu holds a joint appointment in the School of Biological Sciences.

The paper, “Biomechanics of Pollen Removal By the Honey Bee,” is published in the Journal of the Royal Society Interface. 

“We measured the viscoelastic material properties of a pollen pellet,” said Marguerite Matherne, a recent Georgia Tech mechanical engineering Ph.D. graduate who now teaches at Northeastern University. “We found that the pellets have a really long relaxation time, which means they remain mostly in a solid form during the transport process. This is good because it keeps the pellet from melting or falling apart from vibration during flight.”

Matherne and the Georgia Tech research team also tried to replicate how honey bees remove the pellets from their hind legs in the lab. They built a device that scraped adhered pollen pellets from bee legs. The invention produced two discoveries. The first was that the honey bees were much more efficient in removing the pellet than the scraping device they built (the device left much more pollen residue on the leg). They also found that slower removal speeds reduce the force and work required to remove pellets under shear stress. 

“If you remove it slowly, you can avoid applying the excessive force required to remove it quickly,” said Hu, Matherne’s former Georgia Tech advisor. “Removing a pollen pellet is like the opposite of ripping off a Band-Aid.”

Matherne said that there are two key components to the efficiency of the honey bees transporting these pellets. First, the pellets are gooey, allowing them to stick to the hind legs. But, she said, the bees also have a special structure on their legs called the corbicula. It’s fringed with long, curved hairs and becomes embedded into the pellet, allowing for adhesion.

In addition, honey bees can collect pollen particles in various shapes and sizes, while also developing a way to transport them. This is different from other species of bees, which only collect and carry specific types of pollen that are similar in size. They also use different transport techniques.

“Honey bees collect from flowers miles and miles away,” said Hu. “The pollen can change in size by a factor of 10. They must collect all these individual particles and bring it back to one place. And they must do a dozen foraging trips each day, all while keeping their bodies clean. They solve it all by this special method they created to exploit the pellet’s soft material properties.”

The research team believes further studies could lead to new developments in medical patches or fastener applications for soft materials.

“It’s kind of like smart gooey Velcro for soft materials,” said Hu. “It could be a fastener and it knows when you’re trying to remove it so that you don’t have to use an excessive amount of force.”

Matherne suggests that it’s also important to understand the pollinating process since 35% of the world’s crop production depends on pollinators.

“Honey bees are really important pollinators,” said Matherne. “If we want to create a world where we can keep up our pollinators, I think it’s important to understand exactly what they’re doing.”

CITATION: Matherne, M., et.al., "Biomechanics of pollen pellet removal by the honey bee." (Journal of the Royal Society Interface) https://doi.org/10.1098/rsif.2021.0549

Three Ph.D. students — two from the College of Sciences — have been announced as the inaugural cohort for a new Georgia Tech training program designed to give biomedical researchers a deeper dive into quantitative, data-intensive studies. 

The trainees for the 2021 class of the Integrative and Quantitative Biosciences Accelerated Training Environment (InQuBATE) program, areas of study, and their advisors are:

• Kathryn (Katie) Wendorf MacGillivray, Quantitative Biosciences Interdisciplinary Graduate Program (advised by Will Ratcliff)
• Gabriella Chebli, Biological Sciences (advised by Julia Kubanek)
• Maxfield (Max) Comstock, Computational Science and Engineering (advised by Elizabeth Cherry)

As noted in the summer announcement of the program, the three students are part of a new five-year, $1.27 million grant from the National Institutes of Health (NIH) that creates the InQuBATE program to help transform the study of quantitative- and data-intensive biosciences at Georgia Tech. InQuBATE is designed to train a new generation of biomedical researchers and thought leaders to harness the data revolution.

“We want to improve and enhance the training of students to focus on biological questions while leveraging modern tools, and in some cases developing new tools, to address foundational challenges at scales from molecules to systems,” noted Joshua Weitz, professor and Tom and Marie Patton Chair in the School of Biological Sciences, in that announcement. Weitz is co-leading the program with Peng Qiu, associate professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University.

Biology is undergoing a transformation, added Weitz and Qiu, requiring a new educational paradigm that integrates quantitative approaches like computational modeling and data analytics into the experimental study of living systems.

“Our intention is to develop a training environment that instills a quantitative, data-driven mindset, integrating quantitative and data science methods into all aspects of the life science training pipeline,” added Weitz, founding director of Tech’s Interdisciplinary Graduate Program in Quantitative Biosciences (QBioS).

Meet the inaugural InQuBATE cohort

Kathryn (Katie) Wendorf MacGillivray
Quantitative Biosciences Interdisciplinary Graduate Program (advised by Will Ratcliff)

Katie Wendorf MacGillivray received a Master’s in Biology from New York University where she worked on phenotypic heterogeneity of antibiotic susceptibility in the lab of Edo Kussell. She is now a Ph.D. student in the Quantitative Biosciences program at Georgia Tech. In the Ratcliff Lab, she is interested in engineering yeast that can switch between life cycles – unicellular, clonal, and aggregative. Outside of the lab, she likes to knit, garden, and take road trips with her husband Ian. "I have a biology and chemistry background, and believe strongly that all biosciences research could benefit from the addition of computational modeling and/or data science approaches. That's why I chose QBioS for my PhD program in the first place," she says.

Gabriella Chebli
Biological Sciences (advised by Julia Kubanek)

Gabriella Chebli graduated from Agnes Scott College with a Bachelor of Science in Biology and Chemistry. While an undergraduate, she conducted research under the direction of Chemistry professor Thomas Morgan to revise the structure of a class of natural products called “hyloins” that are found in the frog species Boana punctata. Chebli also worked in the lab of Biology professor, Iris Levin, studying telomere length in adult barn swallows. Chebli first joined the Kubanek Lab as an REU participant, working on a metabolomics-based project on harmful algal blooms. After graduating from Agnes Scott, she took a gap year, where she volunteered with ecotourism kayak tours with Seaside Adventure in Kachemak Bay, Alaska and interned at the Lammi Biological Station in Lammi, Finland. In the Kubanek Lab, Chebli is researching chemical ecology and assisting with an algal biofuel ponds project and maintenance of phytoplankton cultures.

Maxfield (Max) Comstock
Computational Science and Engineering (advised by Elizabeth Cherry)

Comstock, originally from Seattle, Washington, received his undergraduate degrees in Math and Computer Science from Harvey Mudd College. “I'm honored to be part of the inaugural InQuBATE cohort, and am looking forward to working with all the amazing people involved with the program," he says. "I hope to gain experience collaborating with researchers from different backgrounds who may approach problems from a different perspective, and to learn new ways to apply computational techniques to important biomedical problems. I intend to continue tackling medical problems using these skills throughout the rest of my career.”

Joshua Weitz, professor and Tom and Marie Patton Chair in the School of Biological Sciences, and co-director of the Interdisciplinary Ph.D. in Quantitative Biosciences, is one of four 2021 recipients of the Blaise Pascal International Chair of Excellence. Weitz will be based at the Institute of Biology at the École Normale Supérieure (IBENS) in Paris. Previous winners of the Pascal Chair of Excellence include several Nobel Prize recipients. 

Weitz’s work in Paris, which will last one year, will involve research and educational components that will bring attention to Georgia Tech in the global science community. 

“Altogether, this integrative research and educational program will help connect initiatives developed in the College of Sciences with a broad, international community,” Weitz says. 

“The central aim of my project is to deepen understanding of the entangled fates of viruses and their hosts. In doing so, my research program spans viral ecology, evolution, and epidemiology. It will also be shaped by necessity, as a significant amount of my time — and that of my group — remains directed towards developing mathematical models, real-time dashboards, and public health-centered intervention tools to understand and mitigate the spread of SARS-CoV-2.“

Background on rapid testing, Covid-19 Event Risk Assessment Planning Tool

Weitz came up with the concept for the Covid-19 Event Risk Assessment Planning Tool, which measures the risk that one or more individuals infected with COVID-19 are present in an event of various sizes. Weitz, along with Clio Andris, assistant professor in the College of Design, and researchers from the Applied Bioinformatics Laboratory, Duke University, and Stanford University developed the Tool’s website and dashboard. Weitz says the tool has helped more than 8 million visitors make tens of millions of risk estimates since its July 2020 launch.

Weitz is also part of the team that developed a rapid saliva-based asymptomatic surveillace testing program for the Georgia Tech community — a program credited with keeping infection levels low on campus.

“I am proud of having served, along with Greg Gibson, and many faculty and staff colleagues, as part of an interdisciplinary team to implement an asymptomatic testing program in the 2020-21 academic year in support of the Institute’s response efforts to protect the safety of our community – and support ongoing efforts to ensure that science and public health evidence shapes response policy at Georgia Tech and throughout the University System of Georgia,” Weitz says. Gibson is also a Georgia Tech School of Biological Sciences professor and Tom and Marie Patton Chair, and was recently named a Regents’ Professor for his service in research and teaching.

“Moving ahead, the ongoing spread of the Delta variant, and potential spread of variants to come, necessitates a sustained response, bridging fundamental models with public-facing interventions,” Weitz adds. “To this end, I look forward to continuing to work with a network of colleagues to advance a rigorous, data-driven, and open approach to pandemic response, mitigation, and prevention. This will be a long-term effort and I have already begun the process to engage with international colleagues to share approaches and lessons learned.”

Joining international scientists in researching viruses — and how to beat them

The Blaise Pascal Research Chair award will aid in that effort. According to its website, the program “is intended to bring international researchers to French institutions in the Ile de France region (Paris and nearby) for year-long research stays, to facilitate research collaboration with French-based teams, and to support the training of the next generation of France-based junior researchers.” 

Weitz was selected as part of the 2019 cohort, which includes scientists from the Massachusetts Institute of Technology, the University of Connecticut, and the University of Glasgow. The 2020 cohort was postponed due to the pandemic.

Weitz will work with his colleagues at the Institute of Biology at the École Normale Supérieure to advance foundational understanding of viral infections of single cell microbes, including the study of infections that don’t necessarily lead to the death of the infected cell. “Latent (or chronic) infections of single-celled microbes can paradoxically provide benefits to both viruses and infected cells, yet the relationship can be tenuous,” Weitz says. “Understanding virus-microbe interactions on a continuum from antagonistic to mutualistic has implications for improving human health and the health of the environment.”

On the human health side, Weitz will be collaborating with Laurent Debarbieux of the Institut Pasteur in Paris to advance the use of bacteriophage for therapeutic treatment of antibiotic resistant bacterial infections. Bacteriophages (also called phages) are viruses that exclusively infect and eliminate bacteria, and they are increasingly being used in therapeutic contexts given the potential for elimination of targeted pathogens. “I am currently the principal investigator, along with Professor Debarbieux, of a National Institutes of Health R01 grant on phage treatment of acute respiratory infections caused by bacterial pathogens. In the coming year, I intend to explore the potential to utilize phage to target pathogens that persist in chronic infections as part of complex microbiomes.”

Environment and education round out Weitz’s work in France

The environmental aspect of Weitz’s work in France will see him build on his group’s existing relationship with a global network of researchers to advance understanding of viral impacts on surface ocean ecosystems. This work, supported by the National Science Foundation and the Simons Foundation, aims to understand how viral infections of key bacteria in surface ocean ecosystems modulates the fate of microbes and ecosystem functioning, including global carbon and biogeochemical cycles.  

“Collaborations with researchers in Israel and in France will help expand study sites for our ongoing work to integrate mathematical models of viral dynamics, along with time-series observations collected in ocean-going research expeditions,” he says. 

The educational component revolves around two major initiatives, one of which could end up on Georgia Tech’s campus. In the fall, Weitz will be co-teaching a short course on quantitative viral dynamics “as part of an effort to characterize how viral infections at cellular scales transform the fate of cells, organisms, and populations. I hope to bring this course back to Georgia Tech as part of an effort to introduce short-form summer courses affiliated with the Quantitative Biosciences Ph.D. Program, and the Center for Microbial Dynamics and Infection.”

Weitz is also in the process of developing a larger winter school and workshop for spring 2022, part of a joint project with the Q-Life Institute of Paris Sciences et Lettres University (PSL). “In many ways, the Q-Life Institute shares some of the same guiding principles of the Quantitative Biology Ph.D. program at Georgia Tech, and I look forward to learning more of their approach to integrate mechanisms, models, and data analytics into the principled study of living systems across scale.” The planned theme for the winter school/workshop will be viral dynamics, with more information to come later this fall.

One factor V. cholerae uses to cause disease is a toxin-loaded “nano-harpoon,” in the words of Brian Hammer, associate professor in the School of Biological Sciences. “Many pathogenic bacteria, including V. cholerae, are successful in the environment and human body because they compete for food and space by lancing their neighbors with that harpoon. The harpoon’s toxic ‘contact-antibiotics’ kill bacteria from the inside. Thwarting human pathogens will require an understanding of these arsenals.”

Now, Hammer is on a team of scientists from Georgia Tech who have found a previously unknown weapon in the arsenal of cholera bacteria: a toxin that impairs a cell’s membrane and looks like none described prior — hence the title of the team’s research study: “A New Contact Killing Toxin Permeabilizes Cells and Belongs to a Broadly Distributed Protein Family,” published July 21 in mSphere, part of the American Society of Microbiology Journals.

Team members include Hammer (the study’s corresponding author), his graduate student Christian Crisan (the study’s lead author), and undergraduate researcher Catherine Everly; along with assistant professor Peter Yunker and his postdoctoral student Gabi Steinbach of the School of Physics; and professor Raquel Lieberman and her postdoctoral student Shannon Hill in the School of Chemistry and Biochemistry. Hammer and Yunker are members of Georgia Tech’s Center for Microbial Dynamics and Infection; and Hammer, Lieberman, and Yunker are also members of the Parker H. Petit Institute for Bioengineering and Bioscience. 

The technical term for V. cholerae’s “nano-harpoon” is a Type 6 Secretion System, (T6SS). “While many microbiologists have focused their efforts on a few toxins made by V. cholerae obtained from patients, we sequenced the DNA of Vibrios from non-human environmental sources and developed computational tools to find new contact-antibiotic toxin genes,” Hammer says of his lab’s work. “In doing so, my student Cristian Crisan, who just defended his Ph.D., discovered a new T6 toxin that doesn't look like any other protein characterized prior. He showed this toxin” — which the team named TpeV (type VI permeabilizing effector Vibrio) — “kills competitors by altering their cell membranes.” Doing so results in cell damage or death.

Hunting through a database, Crisan also discovered that hundreds of other bacteria, including pathogens like Salmonella and Proteus, also carry this novel toxin. “Our current work is studying exactly how this contact-antibiotic works, and ways that bacteria can adapt to become resistant to it and other T6 toxins,” Hammer says. 

Cholera remains a well-studied disease since it touches many disciplines including microbiology, epidemiology, aquatic ecology, and water resource management, Hammer says. Outbreaks still occur in places such as Bangladesh, Yemen, and Haiti.

Learning more about V. cholerae’s toxins, and their antimicrobial abilities, could mean more effective ways to deal with antibiotic resistance, now an area of concern for microbiologists. 

“We demonstrate that TpeV has antimicrobial activity by permeabilizing cells, eliminating membrane potentials, and causing severe cytotoxicity,” the team writes in its study. “We propose that TpeV-like toxins contribute to the fitness of many bacteria. Finally, since antibiotic resistance is a critical global health threat, the discovery of new antimicrobial mechanisms could lead to the development of new treatments against resistant strains.”

The School of Biological Sciences, the National Science Foundation, the U.S.-Israel Binational Science Foundation, and the German National Academy of Natural Sciences Leopoldina contributed to this research study.

But, what about more complex terrain? The capability that would allow land-based search-and-rescue robot swarms to navigate buildings and other disaster areas does not yet exist. Researchers at the Georgia Institute of Technology are working to develop simple, low-cost, legged robots capable of linking and unlinking to accomplish tasks, such as gap traversal, stair climbing, and object transport over uneven terrains.

Working with Daniel Goldman, Dunn Family professor in the School of Physics at Georgia Tech, Yasemin Ozkan-Aydin, a former postdoc in Goldman’s lab and now an assistant professor at the University of Notre Dame, developed “quadruped” robots using easily acquired off-the-shelf technology. Each unit has a 3D-printed, two-segmented chassis and body, four flexible legs, a “passive tail” appendage for additional balance and directional control, touch and light sensors, and a central-body-mounted microprocessor. A magnetic connector allows for docking and cooperative behaviors. The research team recently published its work in Science Robotics.

Reconfigurable swarm robots have been used in prior research into terrain solutions. But these units have limited motive abilities, require human intervention, and lack the desired ease of scale-up for manufacturing and use in a timely and cost-effective manner.  

The new research takes advantage of enhanced mobility in multi-legged robots, mechanical intelligence (passive flexible legs and tail), and simple cooperative effect.  Individualrobots perform simple or small tasks, but if the task is beyond the capability of the one unit, a team of robots physically connect to each other and form a larger multi-legged system to collectively overcome issues.

Additionally, the team’s use of widely available technologies – like 3D printers – could lead to cost-effective and rapid development of terrestrial robotic teams that can collaboratively move heavy or dangerous objects. They could also be used for search-and-rescue operations, environmental monitoring, or even space exploration. 

Ozkan-Aydin sees the work as a starting point in the development of land-based robot swarms with the ability to climb hills, overcome obstacles, and move on rough terrain by maintaining stability in a truly autonomous fashion.

“The development of physical connection between individual robot units can improve the mobility of an entire terrestrial collective system, and help prevent failures when attempting a task,” said Ozkan-Aydin. “Furthermore, the minimalist and modular robotic approach taken in this study can provide a low-cost platform for testing or generating new hypotheses for biological research.”

“Self-reconfigurable multilegged robot swarms collectively accomplish challenging terradynamic tasks”, Ozkan-Aydin and Daniel I. Goldman, Science Robotics; 28 Jul 2021: Vol. 6, Issue 56, eabf1628, DOI: 10.1126/scirobotics.abf1628

***

The Georgia Institute of Technology, or Georgia Tech, is a top 10 public research university developing leaders who advance technology and improve the human condition. The Institute offers business, computing, design, engineering, liberal arts, and sciences degrees. Its nearly 40,000 students representing 50 states and 149 countries, study at the main campus in Atlanta, at campuses in France and China, and through distance and online learning. As a leading technological university, Georgia Tech is an engine of economic development for Georgia, the Southeast, and the nation, conducting more than $1 billion in research annually for government, industry, and society.

VIDEO

See the robot in action here

Eric Schumacher, professor in the School of Psychology, taught a course this summer on stress and happiness. In his class he discusses how students can learn better study habits, learn to overcome disappointment, and improve their general well-being. They also learn about the science of the stress response, what it’s good for, and the negative effects of chronic stress.

He teaches that, with intentional practice, people can improve their happiness level regardless of the circumstances and their individual predisposition.

“In this course, especially given what has happened over the last year, I was interested in discussing the science behind the physiological stress system and then what can we do beyond that to increase our happiness,” he said. “We can work to reduce our stressors, and then can we do more to improve our happiness.” The course is not a substitute for seeing a therapist or taking prescribed medication. 

“We often think that happiness is largely determined by external forces,” he said. “Some of us might be stressed about how to pay the rent or mortgage this month or how to pay for school or a trip. So people think, ‘If I just had more money I would be happier.’ But the research shows that for most people who end up with a change in their financial status, it produces only a short-term increase in their level of happiness.”

Schumacher said there are techniques to help adjust how you frame the way you think about stress. That’s why Madeline Berns, a third-year neuroscience major, took the class.

“I’ve struggled with depression and anxiety for a long time and thought the class could teach me new outlooks and skills for handling stress,” Berns said. “I learned that stress is a very physical problem. Even when it’s not a life-or-death situation, your body is acting like it is; it’s trying to protect you via fight, flight, or freeze. So, stress is the body trying to help you out, and sometimes you can trick it into calming down through physical activity.”

Berns believes the class was particularly meaningful in teaching long-lasting strategies for viewing and treating stress.

“It didn’t just focus on one happiness-inducing activity,” she said. “Instead, it actually taught us meaningful activities like paced breathing, forgiveness prompts, mindfulness and meditation, and others that we can use over and over again, often with little to no effort at all — but a large payoff.”

Traffic and wind regularly cause low frequency vibrations to ripple through bridge building materials such as steel and concrete. This energy would normally travel away from its source before dissipating — but academics at Heriot-Watt University in Edinburgh alongside colleagues from Georgia State University and Georgia Tech in the US have recognized an opportunity. They intend to capture and recycle this untapped source by using the principles of physics.

They have received £340,000 (about $463,000) from the Engineering and Physical Sciences Research Council (EPSRC), part of UK Research and Innovation, and $443,000 from the National Science Foundation (NSF) to research and develop a revolutionary vibro-impact energy harvesting device.

Daniil Yurchenko, Ph.D., from Heriot-Watt University, has created a prototype called a ‘vibrant pack energy harvester’ that can be fitted at multiple locations on a bridge.

These autonomous devices, measuring around 5 – 10cm in length, do not require wiring to an electrical power source and are relatively cheap to manufacture. They work by holding a small ball housed within a tube that rolls back and forth as the device absorbs low frequency vibrations. As the ball moves, it impacts on non-conductive materials, known as dielectric membranes, located at either end of the tube. When the membrane is stretched, a brief electrical charge is applied but once it returns to its undeformed state, the generated excessive electrical charge can be harvested.

This electrical energy is stored in a battery and used to power a sensor capable of monitoring the structural integrity of a bridge. Engineers can then record multiple measurements, such as vibrations, traffic load, wind and temperature, all at the same time but without the need for specialist infrastructure to be installed at significant cost.

Yurchenko, from the School of Engineering and Physical Sciences at Heriot-Watt University, explains that while dielectric elastomer technology has been tried in wave energy, nothing has been done on this centimetre scale before.

“What we are doing is creating a more efficient and cost-effective solution by harvesting energy that would otherwise be lost,” he said.

“It’s something that has never been done before in this way.

“It’s a technology that can be used on any bridge anywhere in the world. There are plenty of places where these devices can be fitted to a bridge structure such as on cables, on the pillars, other side of the bridge deck, there really aren’t any limits.

“The biggest problem in energy harvesting is that the absolute amount of energy produced by a typical device is very small due to the low available level of vibrations. In fact, for the past 100 years scientists have been fighting adverse vibrations to ensure that bridges are safe. So, through this work we will try to optimise the performance of our vibro impact energy harvesting device tuning it to the bridge application.”

The team is working alongside Wenzel Consult, an independent company that specialises in bridge sensor technology in Austria and Turkey.

As the project advances, the scientists say they intend to carry our real-life testing of their prototype on a 32-meter long highway bridge in northern Austria.

The multidisciplinary project, entitled, Stochastic Nonsmooth Analysis For Energy Harvesting, is due to complete in 2024.

Rachel Kuske, professor and chair of the School of Mathematics at Georgia Tech, said: “While the device has nonlinear behaviour, which is beneficial in generating more energy than is used to power the device, the same nonlinearity can result in a range of complex responses to the vibrations.  

“We will use dynamical analyses to predict the different types of responses, as well as to select design choices for responses that optimise energy output. As the bridge vibrations are also inherently noisy, the analysis will also identify how to leverage noise sources that are beneficial and mitigate effects from detrimental noise sources.”

Professor Igor Belykh, co-investigator from Georgia State University, adds: “This project seeks to provide guidelines for designing power supplies that can harvest energy from bridge oscillations. These energy harvesters can be used in bridge damage sensors thereby minimising sensor maintenance/battery replacement and decreasing the associated risks to service personnel on high suspension bridges. Moreover, this project is synergistically connected to another project supported by NSF grant (2019-2022) ‘Modern approaches to modelling and predicting bridge instabilities’ that will inform the design of energy harvesters by offering a dynamical characterisation of bridge oscillations and external perturbations to be harvested.”

The scientists say that in the future the same technology could be adapted and used to harvest energy from other vibrating man-made structures and machines.
 

Related news coverage: Edinburgh Evening News, Scottish Construction Now, FutureScot, The Herald Scotland, Digit

The grant will create the Integrative and Quantitative Biosciences Accelerated Training Environment (InQuBATE) Predoctoral Training Program at Georgia Tech. InQuBATE is designed to train a new generation of biomedical researchers and thought leaders to harness the data revolution.

“We want to improve and enhance the training of students to focus on biological questions while leveraging modern tools, and in some cases developing new tools, to address foundational challenges at scales from molecules to systems,” said Joshua Weitz, professor and Tom and Marie Patton Chair in the School of Biological Sciences. Weitz is co-leading the program with Peng Qiu, associate professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University.

Biology is undergoing a transformation, according to Weitz and Qiu, requiring a new educational paradigm that integrates quantitative approaches like computational modeling and data analytics into the experimental study of living systems.

“Our intention is to develop a training environment that instills a quantitative, data-driven mindset, integrating quantitative and data science methods into all aspects of the life science training pipeline,” added Weitz, founding director of Tech’s Interdisciplinary Graduate Program in Quantitative Biosciences (QBioS).

The roots of InQuBATE go back to the fall of 2016, shortly after QBioS was launched. Weitz saw an opportunity to augment what he was teaching in his cornerstone course, Foundations of Quantitative Biosciences, in which students model living systems from the molecular level up through cells, organisms, populations, and ecosystems. In doing so, students “got a brief introduction to implementing high-dimensional data analytics, visual analytics, clustering, and modern machine learning methods. But we couldn’t cover allthose topics in detail,” Weitz said.

So, he reached out to Qiu, who was teaching data analytic methods in his Machine Learning in Biosciences course: “Instead of us developing that class, we started strongly encouraging QBioS students to take Peng’s class,” Weitz said.

“For me, this was a great opportunity to work with students from the biology side who had real interests in learning data mining and machine learning, as well as students from the engineering side,” said Qiu, principal investigator in the Machine Learning and Bioinformatics Lab in Coulter BME. “We could see that it was a great learning environment and the QBioS students really excelled in the class. That gave us confidence. Now we’re building this [InQuBATE] training program, and hope it will foster even greater cross pollination.”

The training program is designed to do exactly that, bringing together students and faculty from three Georgia Tech colleges: computing, engineering, and sciences. That combination of expertise is reflected in the leadership team. In addition to principal investigators Weitz (College of Sciences) and Qiu (College of Engineering), the faculty leadership team includes Elizabeth Cherry (School of Computational Science and Engineering, College of Computing), Eva Dyer (Coulter BME, College of Engineering and Emory School of Medicine), and Marvin Whiteley (School of Biological Sciences, College of Sciences).

The InQuBATE program will ultimately support 15 Ph.D. students over five years. The first cohort — prioritizing second-year Ph.D. students — will be selected in August. Next spring, the program will begin soliciting applications from first-year Ph.D. students.

“The program will extend the breadth of student training without adding time to the Ph.D.,” Weitz said. “For students on the engineering or computing side, InQuBATE will augment their living systems research experience. For students on the living systems side, the program will augment their training in modeling and data analytics.”

Weitz, Qiu, and their collaborators also are developing a series of semester-long and short-form (a week or less) courses that will be available to other graduate students, in addition to the InQuBATE cohorts.

“We intend to make programmatic offerings available to a broader community,” Weitz said. “In the long term, we hope InQuBATE takes on a central role in shaping the culture of integrative approaches in the study of living systems at Georgia Tech.”

So the Oak Ridge National Laboratory (ORNL) partnered with the USDA Forest Service to develop a one-of-its-kind field lab in the Marcel Experimental Forest, where below and above ground heating elements are gradually warming the bog in greenhouse-like enclosures big enough to include trees. The enclosures are roofless so that rain and snow can get in.

It’s called the SPRUCE (Spruce and Peatland Responses Under Changing Environments) experiment, and it was designed as a window into what would happen to peat bogs in a warmer world. A recent study, headed by Georgia Institute of Technology microbiologist Joel Kostka and published June 14 in the journal PNAS, provides a sobering outlook.

“The real concern and one of the major conclusions of this paper is that the ecosystem we’re studying is becoming more methanogenic,” said Kostka, professor and associate chair of research in the School of Biological Sciences, who holds a joint appointment in the School of Earth and Atmospheric Sciences and focuses on microbial ecology. “In other words, the warmed bog is enhancing the rate of methane production faster than that for carbon dioxide. This is what we think is going to happen in a warming world, based on our results.”

Testy Little Process

Methanogens are microbes that produce methane, a harmful greenhouse gas that traps up to 30 times more heat than carbon dioxide. Warming the peatland, the researchers found, basically creates a methane production line.

“This occurs because the plant community changes in response to warmer temperatures – mosses decrease and vascular plants increase,” said the paper’s lead author, Rachel Wilson, a researcher with Florida State University’s Department of Earth, Ocean, and Atmospheric Science, where she works in the lab of professor Jeff Chanton, co-author and co-principal investigator of the study.

The process forms a complete cycle: Vascular plants – shrubs and grass-like plants – produce more simple sugars, which are broken down by fermentative bacteria, and the breakdown products then fuel methane-producing microbes use to produce more methane.

While peatlands comprise just 3 percent of the Earth’s landmass, they store about one-third of the planet’s soil carbon. The thinking goes, as global temperatures rise, microbes could break into the carbon bank and the resulting decomposition of the ancient, combustible plant biomass would lead to increased levels of carbon dioxide and methane being released into the atmosphere, accelerating climate change.

“Methane is a stronger greenhouse gas than carbon dioxide,” said Wilson. “Warming the climate stimulates methane production, which will contribute to more warming in a positive feedback loop.”

It’s a scenario that Chanton called, “a critical ecosystem shift. Peat soils that have been stable for thousands of years are giving up the ghost, so to speak. It’s a testy little process.”

Delayed Response

That unpleasant outcome is being delayed somewhat by the extreme conditions found in many peat bogs around the world, including at the SPRUCE experiment site.

“Although most peatlands are in northern regions undergoing some of the most rapid warming on the planet, we’re talking about generally cold, acidic soils where there’s no oxygen,” Kostka noted. “Methanogens grow really slowly under these extreme conditions. We do see their activity increasing with warming, but they’re not yet growing that fast.”

He has a good idea of what could happen, though. Several years ago, Kostka took soil samples from the Minnesota site and tested them in his lab at Georgia Tech, exaggerating the temperature to a much greater degree than would be possible in a large-scale experiment like SPRUCE.

Raising the temperature by 20 degrees Celsius, about twice the temperature range used in the field experiment, “we saw huge increases in methane and large changes in the microbes that break down soil carbon into greenhouse gases,” he said.

It's a sped-up version of what they’re seeing in the field where the research team, Kostka explained, “and it is just beginning to scratch the surface of the changes we’re seeing in this ecosystem.”

Next Chapter

The SPRUCE site experiment involves two kinds of treatment, warming and also elevated carbon dioxide. The warming treatment started in 2014. All of the data sets for the PNAS paper are from 2016. The elevated carbon dioxide treatment began in the final days of data collection, so it wasn’t particularly relevant for this study. “Going forward, we’re thinking the effects of elevated carbon dioxide will be one potential future story to tell,” Kostka said. “This is a long-term experiment and many of these large scale climate change field experiments do not observe substantial changes to microbial communities until 10 years after they start.”

Ultimately, SPRUCE experimental activity is designed and intended to develop a quantitative mechanistic understanding of carbon cycling processes, according to Paul Hanson, the Oak Ridge National Laboratory scientist leading the long-range project as principal investigator.

“SPRUCE provides experimental insights for a broad range of plausible future warming conditions for an established peatland ecosystem, combined with or without elevated carbon dioxide,” Hanson said.

So far, the evidence is pointing to a grim possibility: Warming enhances the production of carbon substrates from plants, stimulating microbial activity and greenhouse gas production, possibly leading to amplified climate-peatland feedbacks. Think, gasoline on a fire.

“That would be the worst case scenario,” Kostka said. “We don’t really know yet how plants and microbes will exchange carbon and nutrients in a warmer world. Will that carbon be locked up by the plants and stored in the soil? Will it be respired by microbes and released as a gas?

 We are just beginning to see major changes in the microbes and plants at the SPRUCE peatland.  Although the first few years of the experiment indicate that a lot more methane will be released to the atmosphere, we will be looking to see if these changes are sustained over the long term.”

CITATIONS:  Rachel M. Wilson, Malak M. Tfaily, Max Kolton, Eric Johnston, Caitlin Petro, Cassandra A. Zalman, Paul J. Hanson, Heino M. Heyman, Jennifer E. Kyle, David W. Hoyt, Elizabeth K. Eder, Samuel O. Purvine, Randy K. Kolka, Stephen D. Sebestyen, Natalie A. Griffiths, Christopher W. Schadt, Jason K. Keller, Scott D. Bridgham, and Jeffrey P. Chanton, and Joel E. Kostka.  “Soil metabolome response to whole ecosystem warming at the Spruce and Peatland Responses Under Changing Environments experiment” (PNAS, June 2021) https://doi.org/10.1073/pnas.2004192118

AERIAL PHOTO: Hanson, P.J., M.B. Krassovski, and L.A. Hook. 2020. SPRUCE S1 Bog and SPRUCE Experiment Aerial Photographs. Oak Ridge National Laboratory, TES SFA, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A. https://doi.org/10.3334/CDIAC/spruce.012 (UAV image number 0050 collected on October 4, 2020).

RELATED LINKS:

“Soil metabolome response to whole ecosystem warming at the Spruce and Peatland Responses Under Changing Environments experiment” 

Joel Kostka – Microbial Ecology

SPRUCE Experiment

“Shaking a Sleeping Bog Monster” (Research Horizons)

NSF Supports Research on the Microbes in Peat Moss

ScienceMatters Podcast: Digging Up Climate Clues in Peat Moss

We’ve seen robots take to the air, dive beneath the waves and perform all sorts of maneuvers on land. Now, researchers at UC Santa Barbara and Georgia Institute of Technology are exploring a new frontier: the ground beneath our feet. Taking their cues from plants and animals that have evolved to navigate subterranean spaces, they’ve developed a fast, controllable soft robot that can burrow through sand. The technology not only enables new applications for fast, precise and minimally invasive movement underground, but also lays mechanical foundations for new types of robots.

“The biggest challenges with moving through the ground are simply the forces involved,” said Nicholas Naclerio, a graduate student researcher in the lab of UC Santa Barbara mechanical engineering professor Elliot Hawkes and lead author of a paper on the cover of the journal Science Robotics. Whereas air and water offer little resistance to objects moving through them, he explained, the subterranean world is another story.

“If you’re trying to move through the ground, you have to push the soil, sand or other medium out of the way,” Naclerio said.

Fortunately, the natural world provides numerous examples of underground navigation in the form of plants and fungi that build underground networks and animals that have mastered the ability to tunnel directly through granular media. Gaining a mechanical understanding of how plants and animals have mastered subterranean navigation opens up many possibilities for science and technology, according to Daniel Goldman, Dunn Family Professor of Physics at Georgia Tech.

“Discovery of principles by which diverse organisms successfully swim and dig within granular media can lead to development of new kinds of mechanisms and robots that can take advantage of such principles,” he said. “And reciprocally, development of a robot with such capabilities can inspire new animal studies as well as point to new phenomena in the physics of granular substrates.”

The researchers had a good head start with a vine-like soft robot designed in the Hawkes Lab that mimics plants and the way they navigate by growing from their tips, while the rest of the body remains stationary. In the subterranean setting, tip extension, according to the researchers, keeps resisting forces low and localized only to the growing end; if the whole body moved as it grew, friction over the entire surface would increase as more of the robot entered the sand until the robot could no longer move.

Burrowing animals, meanwhile, serve as inspiration for an additional strategy called granular fluidization, which suspends the particles in a fluid-like state and allows the animal to overcome the high level of resistance presented by sand or loose soil. The southern sand octopus, for instance, expels a jet of water into the ground, and uses its arms to pull itself into the temporarily loosened sand. That ability made its way onto the researchers’ robot in the form of a tip-based flow device that shoots air into the region just ahead of the growing end, enabling it to move into that area.

“The biggest challenge we found and what took the longest to solve was when we switched to horizontal burrowing, our robots would always surface,” Naclerio said. Whereas gases or liquids evenly flow over and under a traveling symmetric object, he explained, in fluidized sand, the distribution of forces is not as balanced, and creates a significant lift force for the horizontally travelling robot. “It’s much easier to push the sand up and out of the way than it is to compact it down.”

To understand the robot’s behavior and the largely unexplored  physics of air-aided intrusions, the team took drag and lift measurements as a result of different angles of airflow into from the tip of a solid rod shoved horizontally into sand.

“Frictional force response in granular materials greatly differs from that of Newtonian fluids, as intruding into sand can compact and stress large swaths of terrain in the direction of motion due to high friction,” said Andras Karsai, a graduate student researcher in Goldman’s lab. “To mitigate this, a low-density fluid that lifts and pushes grains away from an intruder will often reduce the net frictional stress it has to overcome.”

Unlike with gas or liquid, where a downward fluid jet would create lift for the travelling object, in sand the downward air flow reduced the lift forces and excavated the sand below the robot’s growing tip. This, combined with inspiration from the sandfish lizard, whose wedge-shaped head favors downward movement, allowed the researchers to modulate the resisting forces and keep the robot moving horizontally without rising out of the sand.

A small, exploratory, soft robot such as this has a variety of applications where shallow burrowing through dry granular media is needed, such as soil sampling, underground installation of utilities and erosion control. Tip extension enables changes in direction, while also allowing the body of the robot to modulate how firmly anchored it is in the medium — control that could become useful for exploration in low gravity environments. In fact, the team is working on a project with NASA to develop burrowing for the moon or even more distant bodies, like Enceladus, a moon of Jupiter.

“We believe burrowing has the potential to open new avenues and enable new capabilities for extraterrestrial robotics,” Hawkes said.

Research for this paper was conducted also by Mason Murray-Cooper, Yasemin Ozkan-Aydin and Enes Aydin at Georgia Institute of Technology.

Funding: This work is supported by the NSF (grant nos. 1637446, 1915445, 1915355, and 1935548), the Army Research Office (grant no. GR10005043), the Packard Foundation, and by an Early Career Faculty grant from NASA’s Space Technology Research Grants Program. The work of Nicholas D. Naclerio is supported by a NASA Space Technology Research Fellowship. Competing interests: Nicholas D. Naclerio and Elliot W. Hawkes are authors of international patent application WO2020060858A1, related to this work. All other authors declare that they have no competing interests. https://doi.org/10.1126/scirobotics.abe2922

David Hu, professor of fluid mechanics in the George W. Woodruff School of Mechanical Engineering, holds a joint appointment in the School of Biological Sciences at Georgia Tech.

New research from the Georgia Institute of Technology finds that elephants dilate their nostrils in order to create more space in their trunks, allowing them to store up to 5.5 liters of water. They can also suck up three liters per second — a speed 30 times faster than a human sneeze (150 meters per second/330 mph).

The Georgia Tech College of Engineering study sought to better understand the physics of how elephants use their trunks to move and manipulate air, water, food and other objects. They also sought to learn if the mechanics could inspire the creation of more efficient robots that use air motion to hold and move things.

While octopus use jets of water to move and archer fish shoot water above the surface to catch insects, the Georgia Tech researchers found that elephants are the only animals able to use suction on land and underwater.

The paper, “Suction feeding by elephants,” is published in the Journal of the Royal Society Interface.

“An elephant eats about 400 pounds of food a day, but very little is known about how they use their trunks to pick up lightweight food and water for 18 hours, every day,” said Georgia Tech mechanical engineering Ph.D. student Andrew Schulz, who led the study. “It turns out their trunks act like suitcases, capable of expanding when necessary.”

Schulz and the Georgia Tech team worked with veterinarians at Zoo Atlanta, studying elephants as they ate various foods. For large rutabaga cubes, for example, the animal grabbed and collected them. It sucked up smaller cubes and made a loud vacuuming sound, or the sound of a person slurping noodles, before transferring the vegetables to its mouth.

To learn more about suction, the researchers gave elephants a tortilla chip and measured the applied force. Sometimes the animal pressed down on the chip and breathed in, suspending the chip on the tip of trunk without breaking it. It was similar to a person inhaling a piece of paper onto their mouth. Other times the elephant applied suction from a distance, drawing the chip to the edge of its trunk.

“An elephant uses its trunk like a Swiss Army Knife,” said David Hu, Schulz’s advisor and a professor in Georgia Tech’s George W. Woodruff School of Mechanical Engineering. “It can detect scents and grab things. Other times it blows objects away like a leaf blower or sniffs them in like a vacuum.”

By watching elephants inhale liquid from an aquarium, the team was able to time the durations and measure volume. In just 1.5 seconds, the trunk sucked up 3.7 liters, the equivalent of 20 toilets flushing simultaneously.

An ultrasonic probe was used to take trunk wall measurements and see how the trunk’s inner muscles work. By contracting those muscles, the animal dilates its nostrils up to 30 percent. This decreases the thickness of the walls and expands nasal volume by 64 percent.

“At first it didn’t make sense: an elephant’s nasal passage is relatively small and it was inhaling more water than it should,” said Schulz. “It wasn’t until we saw the ultrasonographic images and watched the nostrils expand that we realized how they did it. Air makes the walls open, and the animal can store far more water than we originally estimated.”

Based on the pressures applied, Schulz and the team suggest that elephants inhale at speeds that are comparable to Japan’s 300-mph bullet trains.

Schulz said these unique characteristics have applications in soft robotics and conservation efforts.

“By investigating the mechanics and physics behind trunk muscle movements, we can apply the physical mechanisms — combinations of suction and grasping — to find new ways to build robots,” Schulz said. “In the meantime, the African elephant is now listed as endangered because of poaching and loss of habitat. Its trunk makes it a unique species to study. By learning more about them, we can learn how to better conserve elephants in the wild.”

The work was supported by the US Army Research Laboratory and the US Army Research Office 294 Mechanical Sciences Division, Complex Dynamics and Systems Program, under contract number 295 W911NF-12-R-0011. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the view of the sponsoring agency.

Two School of Biological Sciences researchers have joined the effort to find answers to the crisis. Jeffrey Skolnick, Regents’ Professor, Mary and Maisie Gibson Chair, and GRA Eminent Scholar in Computational Systems Biology; and Hongyi Zhou, Senior Research Scientist in the school, are on a team that recently captured top honors in a recent National Institutes of Health-sponsored competition to find novel, outside-the-box approaches to the opioid problem. 

Their plan, “Development of a Comprehensive Integrated Platform for Translational Innovation in Pain, Opioid Abuse Disorder and Overdose” — which will use artificial intelligence, data and molecular analysis, cloud computing, and predictive algorithms in the search for new drugs — was one of five winning applications in a November 2020 competition. The results were announced April 26.

Skolnick and Zhou have now won two stages of the National Center for Advancing Translational Sciences (NCATS) ASPIRE Challenge, part of the NIH’s HEAL (Helping to End Addiction Long-Term) program. (ASPIRE stands for A Specialized Platform for Innovative Research Exploration.) 

Skolnick’s group includes Andre Ghetti with ANABIOS Corporation, and Nicole Jung with Karlsruhe Institute of Technology in Germany. 

“We’re extremely grateful,” Skolnick says. “We’re very excited about this. The problem of opioid addiction and chronic pain is a real plague in America and for most of the world, and there aren’t a lot of real, good answers, so this is motivating us to get people to think of novel solutions. We really appreciate the chance to put this team together.”

Rapidly translating scientific advances into immediate help for patients

NCATS defines translational science as “the process of turning observations in the laboratory, clinic, and community, into interventions that improve the health of individuals and the public — from diagnostics and therapeutics, to medical procedures and behavioral changes.” 

The 2018 NCATS ASPIRE Challenge involved design competition in four component areas: integrated chemistry database, electronic synthetic chemistry portal; predictive algorithms, and biological assays (strength/potency tests.) Skolnick and Zhou were also part of a winning team in that stage.

Skolnick calls his group’s predictive algorithms “our unfair competitive advantage” — data programs that can predict in advance the probability of a drug’s success. “In principle you could screen every molecule under the sun if you had infinite resources. You could test everything, but that’s very expensive and time-consuming. We can go through this list and prioritize them and say, this one has an 80 percent probability it will work.”

Skolnick’s group added Ghetti and June for the 2020 ASPIRE Reduction-to-Practice Challenge. “The goal of this Challenge is to combine the best solutions and develop a working platform that integrates the four component areas. The Reduction-to-Practice Challenge consists of three stages: planning; prototype development and milestone delivery; and prototype delivery, independent validation, and testing,” notes the NCATS website.

Skolnick says his team’s application is designed to be accessed digitally as part of a cloud service. It will use artificial intelligence and machine learning to investigate molecules that could be turned into new drugs, as well as explore undiscovered uses for existing drugs. 

“Andre’s company is going to do the testing of the molecules, and Nicole Jung will organize all the data and store it so we can have a platform that is used not just by us, but by the (scientific) community,” Skolnick explains. “We’re looking for novel mechanisms for drugs that relieve pain and treat addiction. The goal is to do this at high throughput, rather than one at a time. This is really designed to test the ideas at scale. You can get it to people a lot quicker.”

Skolnick hopes to have a robust working platform built within a year. Given the extent of the opioid crisis in the U.S. alone, the faster new non-addictive pain management drugs can be found and tested, the better, he adds.

“The need is critical. It’s one of these horrible societal problems that really require novel solutions, which means you want to understand all the mechanisms of pain, but do we understand the gears you want to turn to alleviate it?”

That theory, the “Oxygen Control Hypothesis,” suggests that the size of these early multicellular organisms was limited by the depth to which oxygen could diffuse into their bodies. The hypothesis makes a simple prediction that has been highly influential within both evolutionary biology and geosciences: Greater atmospheric oxygen should always increase the size to which multicellular organisms can grow. 

It’s a hypothesis that’s proven difficult to test in a lab. Yet a team of Georgia Tech researchers found a way — using directed evolution, synthetic biology, and mathematical modeling — all brought to bear on a simple multicellular lifeform called a ‘snowflake yeast’. The results? Significant new information on the correlations between oxygenation of the early Earth and the rise of large multicellular organisms — and it’s all about exactly how much O₂ was available to some of our earliest multicellular ancestors. 

“The positive effect of oxygen on the evolution of multicellularity is entirely dose-dependent — our planet's first oxygenation would have strongly constrained, not promoted, the evolution of multicellular life,” explains G. Ozan Bozdag, research scientist in the School of Biological Sciences and the study’s lead author. “The positive effect of oxygen on multicellular size may only be realized when it reaches high levels.”

“Oxygen suppression of macroscopic multicellularity” is published in the May 14, 2021 edition of the journal Nature Communications. Bozdag’s co-authors on the paper include Georgia Tech researchers Will Ratcliff, associate professor in the School of Biological Sciences; Chris Reinhard, associate professor in the School of Earth and Atmospheric Sciences; Rozenn Pineau, Ph.D. student in the School of Biological Sciences and the Interdisciplinary Graduate Program in Quantitative Biosciences (QBioS); along with Eric Libby, assistant professor at Umea University in Sweden and the Santa Fe Institute in New Mexico.

Directing yeast to evolve in record time 

“We show that the effect of oxygen is more complex than previously imagined. The early rise in global oxygen should in fact strongly constrain the evolution of macroscopic multicellularity, rather than selecting for larger and more complex organisms,” notes Ratcliff. 

“People have long believed that the oxygenation of Earth's surface was helpful — some going so far as to say it is a precondition — for the evolution of large, complex multicellular organisms,” he adds. “But nobody has ever tested this directly, because we haven't had a model system that is both able to undergo lots of generations of evolution quickly, and able to grow over the full range of oxygen conditions,” from anaerobic conditions up to modern levels.  

The researchers were able to do that, however, with snowflake yeast, simple multicellular organisms capable of rapid evolutionary change. By varying their growth environment, they evolved snowflake yeast for over 800 generations in the lab with selection for larger size. 

The results surprised Bozdag. “I was astonished to see that multicellular yeast doubled their size very rapidly when they could not use oxygen, while populations that evolved in the moderately oxygenated environment showed no size increase at all,” he says. “This effect is robust — even over much longer timescales.” 

Size — and oxygen levels — matter for multicellular growth 

In the team’s research, “large size easily evolved either when our yeast had no oxygen or plenty of it, but not when oxygen was present at low levels,” Ratcliff says. “We did a lot more work to show that this is actually a totally predictable and understandable outcome of the fact that oxygen, when limiting, acts as a resource — if cells can access it, they get a big metabolic benefit. When oxygen is scarce, it can't diffuse very far into organisms, so there is an evolutionary incentive for multicellular organisms to be small — allowing most of their cells access to oxygen — a constraint that is not there when oxygen simply isn't present, or when there's enough of it around to diffuse more deeply into tissues.”

Ratcliff says not only does his group’s work challenge the Oxygen Control Hypothesis, it also helps science understand why so little apparent evolutionary innovation was happening in the world of multicellular organisms in the billion years after the Great Oxygenation Event. Ratcliff explains that geologists call this period the “Boring Billion” in Earth’s history — also known as the Dullest Time in Earth's History, and Earth's Middle Ages — a period when oxygen was present in the atmosphere, but at low levels, and multicellular organisms stayed relatively small and simple.

Bozdag adds another insight into the unique nature of the study. “Previous work examined the interplay between oxygen and multicellular size mainly through the physical principles of gas diffusion,” he says. “While that reasoning is essential, we also need an inclusive consideration of principles of Darwinian evolution when studying the origin of complex multicellular life on our planet.” Finally being able to advance organisms through many generations of evolution helped the researchers accomplish just that, Bozdag adds.

This work was supported by National Science Foundation grant no. DEB-1845363 to W.C.R, NSF grant no. IOS-1656549 to W.C.R., NSF grant no. IOS-1656849 to E.L., and a Packard Foundation Fellowship for Science and Engineering to W.C.R. C.T.R. and W.C.R. acknowledge funding from the NASA Astrobiology Institute.

A team of researchers led by Dana Randall, ADVANCE Professor of Computing and Daniel Goldman, Dunn Family Professor of Physics, sought to show that even the simplest of robots can still accomplish tasks well beyond the capabilities of one, or even a few, of them. The goal of accomplishing these tasks with what the team dubbed "dumb robots" (essentially mobile granular particles) exceeded their expectations, and the researchers report being able to remove all sensors, communication, memory and computation — and instead accomplishing a set of tasks through leveraging the robots' physical characteristics, a trait that the team terms "task embodiment."

The team's simple BOBbots, or "behaving, organizing, buzzing bots" were named for granular physics pioneer Bob Behringer," explains Randall. "Their cylindrical chassis have vibrating brushes underneath and loose magnets on their periphery, causing them to spend more time at locations with more neighbors." The experimental platform was supplemented by precise computer simulations led by Georgia Tech physics student Shengkai Li, as a way to study aspects of the system inconvenient to study in the lab.

Despite the simplicity of the BOBbots, the researchers discovered that, as the robots move and bump into each other, "compact aggregates form that are capable of collectively clearing debris that is too heavy for one alone to move," according to Goldman. "While most people build increasingly complex and expensive robots to guarantee coordination, we wanted to see what complex tasks could be accomplished with very simple robots."

Their work, as reported April 23, 2021 in the journal Science Advances, was inspired by a theoretical model of particles moving around on a chessboard. A theoretical abstraction known as a self-organizing particle system was developed to rigorously study a mathematical model of the BOBbots. Using ideas from probability theory, statistical physics and stochastic algorithms, the researchers were able to prove that the theoretical model undergoes a phase change as the magnetic interactions increase — abruptly changing from dispersed to aggregating in large, compact clusters, similar to phase changes we see in common everyday systems, like water and ice.

"The rigorous analysis not only showed us how to build the BOBbots, but also revealed an inherent robustness of our algorithm that allowed some of the robots to be faulty or unpredictable," notes Randall, who also serves as a professor of computer science and adjunct professor of mathematics at Georgia Tech.

The collaboration is based on experiments and simulations also designed by Bahnisikha Dutta, Ram Avinery and Enes Aydin from Georgia Tech, as well as on theoretical work by Andrea Richa and Joshua Daymude from Arizona State University, and Sarah Cannon from Claremont McKenna College, who is a recent Georgia Tech graduate.

This work is part of a Multidisciplinary University Research Initiative (MURI) funded by the Army Research Office (ARO) to study the foundations of emergent computation and collective intelligence.

Funding: This work was supported by the Department of Defense under MURI award no. W911NF-19-1-0233 and by NSF awards DMS-1803325 (S.C.); CCF-1422603, CCF-1637393, and CCF-1733680 (A.W.R.); CCF-1637031 and CCF-1733812 (D.R. and D.I.G.); and CCF-1526900 (D.R.).

This story was first published on EurekAlert! by Georgia Tech. 

But experts have long run into choppy waters when trying to precisely define these ecoregions and how they relate to each other. A lack of data for regions that are not adjacent to coastal areas exacerbates the issue, along with the large-scale dispersal potential of ocean currents, which can impact factors like species migration from one region to the next. Ocean currents and water characteristics also change in space and time on scales of just a few months, and tens of kilometers — and biological communities can respond to these changes in similar scales of time and space. 

Now, a study by School of Earth and Atmospheric Sciences researchers, published this month in the journal NatureScientific Reports, is charting a new path to help scientists create tools to locate ecoregions and predict community susceptibility to those changes.

“Uncovering marine connectivity through sea surface temperature” suggests a new way to find these ecoregions and then connect them, thanks to recent advances in more than 40 years of satellite data that tracks surface temperatures that are indirectly related to ocean currents — as well as progress with computer science algorithms. 

“We are now poised to define ecoregions that meaningfully delimit marine biological communities based on their connectivity, and to follow their evolution through time,” write the co-authors: professor Annalisa Bracco, graduate student Fabrizio Falasca, and one of Bracco’s visiting students, Ljuba Novi from the Institute of Geosciences and Earth Resources (part of the National Research Council in Pisa, Italy). 
 

Through a time-dependent complex network framework applied to a 30-year dataset of sea surface temperatures in the Mediterranean Sea, Bracco says she and her team provide compelling evidence that ocean “ecoregionalization” based on connectivity can be achieved at space and time scales relevant to conservation management and planning. 


The researchers note that that’s particularly important for any future sustainable uses of oceans, since their resources require protection, conservation, and restoration of marine species biodiversity. 

“To achieve this goal, the identification of ecoregions and their connectivity in time and space is a key first step to developing effective strategies for targeted management — for example, figuring out where to implement marine protected areas,” Bracco explains. “The potential of a marine protected area to retain biodiversity and restock species abundance beyond its border is inherently linked to some form of regional discretization and population connectivity, such as larval and juvenile dispersal, or seeding across ecoregions.”  

At the same time, the framework the study proposes allows for looking at ecoregions across time. “We can easily figure out if changes in currents are affecting regions where there is a high biodiversity, or check quickly how currents help or block invasive species.” Bracco’s team found that in the Mediterranean Sea, the invasion of the lionfish was halted by the fragmentation of the ecoregions in the late 1990s and early 2000s, and that it has also been helped by ocean currents since 2011. 

Bracco and her researchers discovered the lionfish data thanks to new and higher resolution sea surface temperature data products that were previously unavailable to scientists. 

For the analysis and the identification of ecoregions and their links, Bracco’s team also adapted a complex network methodology developed at Georgia Tech by a group led by Constantine Dovrolis, who serves as a professor in the School of Computer Science within the College of Computing.

The authors write that future studies of ecoregionalization should be an interdisciplinary approach involving physical, biological, and ecological oceanographers, since “ecoregions are essential units of comparative analysis in the assessment, management and solution of ecosystems problems.”

A Georgia Tech Faculty Development Grant assisted with funding for this research (Novi, L., Bracco, A. & Falasca, F. Uncovering marine connectivity through sea surface temperature. Sci Rep 11, 8839 (2021). https://doi.org/10.1038/s41598-021-87711-z)

Stony Coral Tissue Loss Disease “is spreading really, really fast,” says Neha Garg, assistant professor in the School of Chemistry and Biochemistry. “Florida has 45 species of corals and more than 20 have already been impacted” by the disease. “It started in Florida, and the next we heard it had spread to the U.S. Virgin Island and other islands in the Caribbean — and the latest I heard is it has spread to the Cayman Islands.”

The cause is not known. “We know we can treat it with antibiotics, so bacteria does play a role,” Garg says, “and it can be transmitted by physical and water contact, which also tells us an infectious agent is likely at play.” Despite rising ocean temperatures, scientists don’t believe that’s the culprit behind Stony Coral Tissue Loss Disease, or SCTLD.

It’s an all hands on deck situation for marine biologists and the science community as they work to contain the spread and try to rejuvenate infected reefs. 

And now, Garg’s research to date into SCTLD has earned her a 2021 National Science Foundation Faculty Early Career Development Program (NSF CAREER) Award for her project to study the disease currently roaring through the reefs off Florida’s west coast. 

The disease adds another threat to beleaguered coral reefs around the globe. Climate change-related warming has already led to bleaching of reefs, chasing away organisms that use them for shelter and food. “Coral reefs generate carbon sources to support 20 percent of life in the oceans,” Garg says. “Then there’s the economic impact on coastal areas, with recreation, fishing. It can impact the livelihoods of coastal populations. If we lose them, it can cause imbalance in various ocean ecosystems.”

In early 2020, Garg and Georgia Tech received an Environmental Protection Agency grant to study biomarkers of coral reef disease. Her NSF CAREER award project will allow her to continue examining the changing chemical and microbial makeup of coral reefs experiencing outbreaks of SCTLD. 

As Garg shares in the project’s abstract, despite the disease’s rapid spread, “the understanding of chemical changes that accompany the onset of disease, the changes in bacterial inhabitants, and the disruption of the coral-algal symbiosis remain poorly known. Elucidating chemical changes and their symbiotic or pathogenic contributors is challenging and necessitates the use of state-of-the art multiomic and data analytic strategies.” (Multiomics combines data from several “omic” strategies including genomics, proteomics, transcriptomics, epigenomics, and microbiomics) 

She adds that “through the use of advanced multiomic approaches, knowledge gained from this research will provide understanding of the chemical and organismal signatures that define health or disease status of coral holobionts,” referring to an ecological symbiosis created by a host — in this case a coral — and the organisms that live in and around it. “Holobionts represent the multipartite symbiosis between the coral animal, the endosymbiotic dinoflagellate, resident microbiota (bacteria and archaea), as well as the fungal, protistan, and viral associates,” she explains.

A key component of any NSF CAREER Award is how it can enhance educational opportunities for high school and college students. Garg’s proposal will include teaching modules to train K-12 teachers through Georgia Tech’s Georgia Intern Fellowship for Teachers (GIFT) program. She says introducing high school students to the effects of climate change on coral reefs and the role of STEM in understanding disease mechanisms will enhance student participation in STEM fields. “Their participation in environmental science through training in biology and chemistry will serve as a strong scientific foundation for these students, and foster a future generation that cares for the environment and understands the role of science in creating a healthy future,” writes Garg.

The educational portion of her CAREER project will also involve the Georgia Aquarium. Garg reached out to researchers there, knowing that many aquariums in the U.S. maintain samples of corals behind the scenes for restoration purposes. “They are keeping an inventory of these corals so, in the future, we can go back to the ocean and replant them.” Students can take coral tissue samples in non-destructive ways to get them started on research methods, she adds.

“That’s one way we are thinking we can motivate high school students from low-income families to pursue and promote higher education in STEM fields,” Garg says. “We’ll be participating in the GIFT program to get high school students to spend the summer in our lab.”

Garg’s lab has already bought two tanks to serve as salt water aquariums, so students can isolate coral reef bacteria in the lab. She has also partnered with Valerie Paul, Smithsonian researcher and head scientist of the National Museum of History, for samples of corals with SCTLD. “We’ll run some phenotypic tests, and teach the students metabolomics.”  

“I am very pleased to announce Julia Kubanek as the next vice president for Interdisciplinary Research,” said Chaouki T. Abdallah, executive vice president for Research at Georgia Tech. “In her long and lauded career at Tech, she has proven herself an exemplary educator and leader who is committed to excellence in scholarship, and to building partnerships that grow collaborative research across the Institute.”

Kubanek joined Georgia Tech as an assistant professor in the School of Biology and the School of Chemistry and Biochemistry in 2001. She was named an associate professor in 2006, and professor in 2011. In that time, she also served as the associate chair of the School of Biology from 2009 to 2011. Kubanek has served as the associate dean for Research in the College of Sciences since 2014.

In her role as associate dean for Research, Kubanek was part of the leadership team that helped shepherd substantial research growth in the College of Sciences, including the enhancement of research opportunities and infrastructure for faculty and students. Kubanek supported the collaborative interests of faculty and students by organizing and hosting cross-disciplinary workshops, including with the Oak Ridge National Lab. Her work also included career development workshops for early career academic and research faculty; guidance to faculty looking to launch new collaborative projects; and one-on-one mentoring of faculty, postdoctoral researchers, and graduate students.

“With 20 years at Tech, I know this institution is filled with faculty, staff, and students who want to drive life-changing research in ways they cannot achieve alone,” Kubanek said. “In a supportive, collaborative, and interdisciplinary environment, I believe the creative, promising research visions of our Georgia Tech researchers can grow to international prominence and improve people’s lives and the health of our planet.”

The VPIR is responsible for ensuring the effective and strategic administration of interdisciplinary research and activities, including the Interdisciplinary Research Institutes, the Interdisciplinary Research Centers, the Pediatric Technology Center, the Georgia Center for Medical Innovation, and the Novelis Innovation Hub. The role has been filled on an interim basis since February by Devesh Ranjan, associate chair for Research, Ring Family Chair, and professor in the George W. Woodruff School of Mechanical Engineering.

“I’d like to extend my heartfelt thanks to Devesh Ranjan, who has expertly served in the role of interim VPIR and will continue to do so until June 30, providing critical continuity and leadership,” Abdallah said. “Thank you, too, to our search chair Rob Butera, professor of electrical and computer engineering and biomedical engineering, and vice president for Research Development and Operations, and the search committee who reviewed an exceptional field of candidates.”

Kubanek’s publications and grants have been supported by the National Science Foundation, the National Institutes of Health, industry, and national labs, as well as state agencies and foundations. Her educational and scientific contributions have seen her recognized for teaching excellence and mentoring by her students and colleagues, as well as accolades from national boards and associations. She is an elected fellow of the American Association for the Advancement of Science, and a recipient of the Presidential Early Career Award for Scientists and Engineers, as well as the National Science Foundation CAREER award, among many others.

Kubanek’s research focus has included aquatic chemical ecology, chemical signaling, chemical communication, chemoreception, chemical biology, marine natural products chemistry, secondary metabolism, drug discovery, and metabolomics. She has mentored and advised more than 90 students and postdocs and has published more than 100 papers in journals and conferences. Kubanek received a B.Sc. in chemistry from Queen's University and a Ph.D. in organic chemistry from the University of British Columbia.

A School of Biological Sciences professor who specializes in molecular and genomic evolution has uncovered some new information about how DNA methylation evolved in the human brain — and how that compares to brains of some of our primate relatives. She and a global team of researchers have published their findings, “Evolution of DNA methylation in the human brain” in Nature Communications. 

“The large and complex brain is a distinguishing trait of the human lineage,” explains Soojin Yi, who directs the Yi Lab of Comparative Genomics and Epigenomics at Georgia Tech. “Scientists have been very interested in finding genetic and gene expression changes that are associated with the evolution of human brains.”

DNA methylation is a biological process by which methyl groups — organic compounds made up of three hydrogen atoms and a carbon atom — are added to DNA, which in turn sets off molecular processes to help regulate gene expression and other genetic factors that are necessary in healthy brains and nervous systems. When something goes wrong with DNA methylation, it can lead to certain diseases, including cancer and neuropsychiatric conditions such as schizophrenia.

“To understand the contribution of DNA methylation to human brain-specific gene regulation and disease susceptibility, it is necessary to extend our knowledge of evolutionary changes in DNA methylation during human brain evolution,” Yi says. 

Science has long known about the DNA methylation connection to certain conditions, but the evolutionary aspect has so far been largely unexplored. “Previous studies used bulk tissues, while DNA methylation is known to vary substantially between cell types,” Yi shares, so her team, including the paper’s co-corresponding author Genevieve Konopka’s lab at UT Southwestern Medical Center, focused on the search for cell-type-specific epigenetic (gene-activity-changing) marks, including DNA methylation and histone (basic protein) modifications. Those are implicated in cell-type-specific gene expression and disease susceptibility in humans. 

“Data from bulk tissues can be biased toward specific cell types and consequently, underpowered to detect cell-type-specific evolutionary changes,” Yi explains. “Therefore, to fully understand the role of DNA methylation in human brain evolution, it is necessary to study cell-type-specific changes of DNA methylation.”

Yi and her team found suitable samples for chimpanzees and macaques in the specimen archives of the Yerkes National Primate Research Center at Emory University. “We also separated neurons and oligodendrocytes (which forms the protective sheaths for neural transmission) from bulk brain samples, so that we can study cell-type specific patterns of DNA methylation,” Yi says.

“We found that the human brains are particularly heavily methylated compared to chimpanzee and rhesus macaque brains — both in neurons and oligodendrocytes.” 

Yi and her team found that some positions that have unique patterns of DNA methylation in human brains were previously implicated in neuropsychiatric diseases including schizophrenia.

“Our work extends the knowledge of the unique roles of . . . methylation in human brain evolution, and offers a new framework for investigating the role of the epigenome evolution in connecting the genome to brain development, function, and diseases.” 

Yi’s research team included colleagues from the Yerkes National Primate Research Center, and the Department of Pathology, at Emory University; the Center for Cooperative Research in Biosciences, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Spain; The Department of Neuroscience at UT Southwestern Medical Center;  the Center for Medical Research and Education, Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Japan; the Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Metropolitan Institute of Medical Science, Japan; and the College of Nursing, The Research Institute of Nursing Science, Seoul National University, South Korea.

For human samples, UT Southwestern Medical Center Institutional Review Board (IRB) has determined that as this research was conducted using post-mortem specimens, the project does not meet the definition of human subjects research and does not require IRB approval and oversight. Non-human primate samples were obtained from archival, post-mortem brain tissue opportunistically collected from subjects that died from natural causes, and following procedures approved by the Emory Institutional Animal Care and Use Committee and in accordance with federal and institutional guidelines for the humane care and use of experimental animals. No living great apes were used in this study. 

In celebration of Women's History Month, Georgia Tech highlights the onward and upward trajectory of nine women across campus who are shattering the traditional "glass ceiling" — carving a path for others and for equitable recognition, respect, and inclusion. Included in the feature are professor Audrey Duarte and alumna Valerie Montgomery Rice:

“Alligator hearts don’t fibrillate – no matter what we do. They’re very resilient,” said Flavio Fenton, a professor in the School of Physics at the Georgia Institute of Technology, researcher in the Petit Institute for Bioengineering and Bioscience, and the report’s corresponding author. Fibrillation is one of the most dangerous arrhythmias, leading to blood clots and stroke when occurring in the atria and to death within minutes when it happens in the ventricles.  

The study looked at the action potential wavelengths of rabbit and young alligator hearts. Both species have four-chambered hearts of similar size (about  3 cm); however, while rabbits maintain a constant heart temperature of 38 degrees Celsius, the body temperature of active, wild alligators ranges from 10 to 37 degrees Celsius. Heart pumping is controlled by an electrical wave that tells the muscle cells to contract. An electrical signal drives this wave, which must occur in the same pattern to keep blood pumping normally. In a deadly arrhythmia, this electrical signal is no longer coherent.

“An arrhythmia can happen for many reasons, including temperature dropping. For example, if someone falls into cold water and gets hypothermia, very often this person will develop an arrythmia and then drown,” Fenton said.

During the study, the researchers recorded changes in the heart wave patterns at 38 C and 23 C. “The excitation wave in the rabbit heart reduced by more than half during temperature extremes while the alligator heart showed changes of only about 10% at most,” said Conner Herndon, a co-author and a graduate research assistant in the School of Physics. “We found that when the spatial wavelength reaches the size of the heart, the rabbit can undergo spontaneous fibrillation, but the alligator would always maintain this wavelength within a safe regime,” he added.

While alligators can function over a large temperature range without risk of heart trauma, their built-in safeguard has a drawback: it limits their maximum heart rate, making them unable to expend extra energy in an emergency. Rabbits and other warm-blooded mammals, on the other hand, can accommodate higher heart rates necessary to sustain an active, endothermic metabolism but they face increased risk of cardiac arrhythmia and critical vulnerability to temperature changes. 

The physicists from Georgia Tech collaborated with two biologists on the study, including former Georgia Tech postdoctoral fellow Henry Astley, now assistant professor in the Biomimicry Research and Innovation Center at the University of Akron’s Department of Biology.   

“I was a little surprised by how massive the difference was – the sheer resilience of the crocodilian heart and the fragility of the rabbit heart. I had not expected the rabbit heart to come apart at the seams as easily as it did,” noted Astley. 

Lower temperatures are one cause of cardiac electrophysiological arrhythmias, where fast-rotating electrical waves can cause the heart to beat faster and faster, leading to compromised cardiac function and potentially sudden cardiac death. Lowering  the temperature of the body – frequently done for patients before certain surgeries – also can induce an arrhythmia. 

The researchers agree that this study could help better understand how the heart works and what can cause a deadly arrhythmia – which fundamentally happens when the heart doesn’t pump blood correctly any longer.  

The authors also consider the research a promising step toward better understanding of heart electrophysiology and how to help minimize fibrillation risk. Until December 2020, when Covid-19 took the top spot, heart disease was the leading cause of death in the United States and in most industrialized countries, with more people dying of heart disease than the next two causes of death combined.

Astley said the research provides a deeper understanding of the natural world and insight into the different coping mechanisms of cold- and warm-blooded animals. 

Co-author Tomasz Owerkowicz, associate  professor in the Department of Biology at California State University, San Bernardino, considers the findings “another piece of the puzzle that helps us realize how really cool non-human animals are and how many different tricks they have up their sleeves.”

He expressed hope that more researchers will follow their example and use a non-traditional animal model in future research.

“Everyone studies mammals, fruit flies, and zebrafish. There's such a huge wealth of resources among the wild animals that have not been brought to the laboratory setting that have such neat physiologies, that are waiting to be uncovered. All we have to do is look,” he said.

CITATION: C. Herndon, et al., “Defibrillate you Later, Alligator; Q10 Scaling and Refractoriness Keeps Alligators from Fibrillation.” (Integrative Organismal Biology, 2021)  https://academic.oup.com/iob/advance-article/doi/10.1093/iob/obaa047/6120966?login=true.

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Writer: Anne Wainscott-Sargent

While other organisms form collective flocks, schools, or swarms for such purposes as mating, predation, and protection, the Lumbriculus variegatus worms are unusual in their ability to braid themselves together to accomplish tasks that unconnected individuals cannot. A new study reported by researchers at the Georgia Institute of Technology describes how the worms self-organize to act as entangled “active matter,” creating surprising collective behaviors whose principles have been applied to help blobs of simple robots evolve their own locomotion.

The research, supported by the National Science Foundation and the Army Research Office, was reported Feb. 5 in the journal Proceedings of the National Academy of Sciences. Findings from the work could help developers of swarm robots understand how emergent behavior of entangled active matter can produce unexpected, complex, and potentially useful mechanically driven behaviors.

Collective Behavior in Worms

The spark for the research came several years ago in California, where Saad Bhamla was intrigued by blobs of the worms he saw in a backyard pond.

“We were curious about why these worms would form these living blobs,” said Bhamla, an assistant professor in Georgia Tech’s School of Chemical and Biomolecular Engineering. “We have now shown through mathematical models and biological experiments that forming the blobs confers a kind of collective decision-making that enables worms in a larger blob to survive longer against desiccation. We also showed that they can move together, a collective behavior that’s not done by any other organisms we know of at the macro scale.”

Such collective behavior in living systems is of interest to researchers exploring ways to apply the principles of living systems to human-designed systems such as swarm robots, in which individuals must also work together to create complex behaviors.

“The worm blob collective turns out to have capabilities that are more than what the individuals have, a wonderful example of biological emergence,” said Daniel Goldman, a Dunn Family Professor in Georgia Tech’s School of Physics, who studies the physics of living systems.

Why the Worms Form Blobs

The worm blob system was studied extensively by Yasemin Ozkan-Aydin, a research associate in Goldman’s lab. Using bundles of worms she originally ordered from a California aquarium supply company – and now raises in Georgia Tech labs – Ozkan-Aydin put the worms through several experiments. Those included development of a “worm gymnasium” that allowed her to measure the strength of individual worms, knowledge important to understanding how small numbers of the creatures can move an entire blob.

She started by taking the aquatic worms out of the water and watching their behavior. First, they individually began searching for water. When that search failed, they formed a ball-shaped blob in which individuals took turns on the outer surface exposed to the air where evaporation was taking place – behavior she theorized would reduce the effect of evaporation on the collective. By studying the blobs, she learned that worms in a blob could survive out of water 10 times longer than individual worms could.

“They would certainly want to reduce desiccation, but the way in which they would do this is not obvious and points to a kind of collective intelligence in the system,” said Goldman. “They are not just surface-minimizing machines. They are looking to exploit good conditions and resources.”

Using Blobs to Escape Threats

Ozkan-Aydin also studied how worm blobs responded to both temperature gradients and intense light. The worms need a specific range of temperatures to survive and dislike intense light. When a blob was placed on a heated plate, it slowly moved away from the hotter portion of the plate to the cooler portion and under intense light formed tightly entangled blobs. The worms appeared to divide responsibilities for the movement, with some individuals pulling the blob while others helped lift the aggregation to reduce friction.

As with evaporation, the collective activity improves the chances of survival for the entire group, which can range from 10 worms up to as many as 50,000.

“For an individual worm going from hot to cold, survival depends on chance,” said Bhamla. “When they move as a blob, they move more slowly because they have to coordinate the mechanics. But if they move as a blob, 95% of them get to the cold side, so being part of the blob confers many survival advantages.”

A Worm Gymnasium

The researchers noted that only two or three “puller” worms were needed to drag a 15-worm blob. That led them to wonder just how strong the creatures were, so Ozkan-Aydin created a series of poles and cantilevers in which she could measure the forces exerted by individual worms. This “worm gymnasium” allowed her to appreciate how the pullers managed to do their jobs.

“When the worms are happy and cool, they stretch out and grab onto one of the poles with their heads and they pull onto it,” Bhamla said. “When they are pulling, you can see the deflection of the cantilever to which their tails were attached. Yasemin was able to use known weights to calibrate the forces the worms create. The force measurement shows the individual worms are packing a lot of power.”

Some worms were stronger than others, and as the temperature increased, their willingness to work out at the gym declined.

Applying Worm Principles to Robots

Ozkan-Aydin also applied the principles observed in the worms to small robotic blobs composed of “smart active particles,” six 3D-printed robots with two arms and two sensors allowing them to sense light. She added a mesh enclosure and pins to arms that allowed these “smarticles” to be entangled like the worms and tested a variety of gaits and movements that could be programmed into them.

“Depending on the intensity, the robots try to move away from the light,” Ozkan-Aydin said. “They generate emergent behavior that is similar to what we saw in the worms.”

She noted that there was no communication among the robots. “Each robot is doing its own thing in a decentralized way,” she said. “Using just the mechanical interaction and the attraction each robot had for light intensity, we could control the robot blob.”

By measuring the energy consumption of an individual robot when it performed different gaits (wiggle and crawl), she determined that the wiggle gait uses less power than the crawl gait. The researchers anticipate that by exploiting gait differentiation, future entangled robotic swarms could improve their energy efficiency. 

Expanding What Robot Swarms Can Do

The researchers hope to continue their study of the collective dynamics of the worm blobs and apply what they learn to swarm robots, which must work together with little communication to accomplish tasks that they could not do alone. But those systems must be able to work in the real world.

“Often people want to make robot swarms do specific things, but they tend to be operating in pristine environments with simple situations,” said Goldman. “With these blobs, the whole point is that they work only because of physical interaction among the individuals. That’s an interesting factor to bring into robotics.”

Among the challenges ahead are recruiting graduate students willing to work with the worm blobs, which have the consistency of bread dough. 

“The worms are very nice to work with,” said Ozkan-Aydin. “We can play with them and they are very friendly. But it takes a person who is very comfortable working with living systems.”

The project shows how the biological world can provide insights beneficial to the field of robotics, said Kathryn Dickson, program director of the Physiological Mechanisms and Biomechanics Program at the National Science Foundation.

“This discovery shows that observations of animal behavior in natural settings, along with biological experiments and modeling, can offer new insights, and how new knowledge gained from interdisciplinary research can help humans, for example, in the robotic control applications arising from this work,” she said.

This research was supported by the National Science Foundation (NSF) under grants CAREER 1941933 and 1817334 and the Army Research Office under grant W911NF-11-1-0514. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the sponsoring agencies.

CITATION: Yasemin Ozkan-Aydin, Daniel I. Goldman, and M. Saad Bhamla, “Collective dynamics in entangled worm and robot blobs. (Proceedings of the National Academy of Sciences, 2021). https://doi.org/10.1073/pnas.2010542118

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Fenton is a professor in the School of Physics. He once wanted to be a particle physicist, with hopes of working on the Higgs boson while working at the Superconducting Super Collider. Instead, he’s spent the last three decades learning and sharing everything he can about cardiac electrical signals. Why?

It’s because the heart “is a fascinating system that involves a lot of physics,” Fenton shares. “When you think about the physics of a heart, the first thing that comes to mind is the pumping action and the forcing of fluids. But the reason it contracts is an electrical signal. There’s a lot of physiology and biology behind the function of the heart, but underneath it all, there’s so many areas of physics you can apply to it to understand how it works — and how it fails to work, like in the case of arrhythmias,” which happen when a heart beats in an abnormal rhythm, beating too slow or too fast and often irregularly. 

Yes, the story of the heart is one of fluids and mechanics, staples of basic physics. But it also involves the chaos of electrical storms within cardiac tissue that cause those arrhythmias. Fenton’s ability to find the physics and mathematics in those cardiac rhythms has resulted in research that’s helped to create 3D images of arrhythmias, studies that put the latest technologies of computer simulations into consumer electronics so more scientists can have access to them, and work that’s helped us better understand how certain Covid-19 treatments can negatively impact patients’ hearts.

How Fenton came to focus on the heart is also the story of how science, and life, can force adaptations to long-range plans. 

An early career decision: follow the heart

The massive Super Collider project where Fenton hoped to conduct particle physics research in Texas in the 1990s was halfway dug out of the ground when Congress decided to cut its funding. Fenton shares that he didn’t want to compete with a number of suddenly unemployed high energy physicists, so he changed his academic plans and pursued a different scientific mystery.

“At the time it was being discovered that electrical spiral waves in the heart drove certain kinds of arrhythmias. My advisor and I decided to investigate how anatomical features of the heart destabilized spiral waves, leading to deadly arrhythmias.” 

That would necessitate learning physiology and biology, while filling in other gaps in his education so he could pivot to cardiac studies—after he already had spent several years working in particle physics. “In the end, my Ph.D. took ten years,” he recalls. Then, he wanted to apply his nascent theories about cardiac spiral waves and how they propagate within heart tissue. “As a postdoc, I worked for a few years in hospitals so I could learn from a cardiologist, Dr. Steve Evans, about arrhythmias in the clinic.”

Deciding he needed more background in performing experiments, he then went to Cornell to work with Robert Gilmour, a professor “doing cool experiments” with cardiac signals. “Even though I was not trained as an experimentalist, I was allowed a great deal of freedom in the lab, and I learned a lot even when experiments did not always go according to plan in the beginning,” he says with a laugh. 

He was also building his fascination with cardiac electrical signals that would result in published research, grants from the National Science Foundation and National Institutes of Health, and breakthroughs involving how science can image, and possibly treat, the electrical storms that plague unstable hearts. 

A colorful and scary view of heart arrhythmias

Fenton’s fascination with heart rhythms collided with the Covid-19 pandemic in May 2020, when he and colleagues at Georgia Tech, Emory University, and Johns Hopkins University published a paper in the journal Heart Rhythm on the anti-malaria drug hydroxychloroquine. At the time, the drug was touted as a potential treatment for those with Covid-19, but the team’s study showed how hydroxychloroquine at the higher proposed doses triggered abnormal heart activity.

“We have illustrated experimentally how the drug actually changes the electrical waves in the heart, and how that can initiate an arrhythmia,” Fenton told Georgia Tech’s Research Horizons. “We used optical mapping, which allows us to see exactly how the waveforms in the heart were changed and why that is dangerous.”

The scientists used a powerful LED-based optical mapping system, along with fluorescent dyes to make visible the movement of the electrical waves. A video produced by Georgia Tech shows sections of a heart lighting up with colors illustrating electrical activity in regions of the organ. Waveform graphics show how a so-called “T-wave” in the heartbeat grows longer with the introduction of hydroxychloroquine. Fenton says that can create problems with succeeding waves.

“The wavelength becomes less homogeneous and that produces sections of the heart where the waves do not propagate well,” he said. “In the worst case, there are multiple waves going in different directions. Sections of the heart are contracting at different times, so the heart is just quivering. At that point, it can no longer pump blood throughout the body.”

The picture of a heart in distress

Two years before the pandemic hit, optical mapping technology had also figured into a 2018 research paper published by Fenton and colleagues. The idea was to find a way to provide more visual, detailed three-dimensional evidence of what goes on throughout the heart during cardiac arrest, something that up until then had largely evaded science.

The kinds of spiral-like waves seen in heart fibrillation (where the cardiac rhythms are dangerously out of sync, and the upper or lower chambers of your heart experience chaotic electrical signals) needed to be visualized in order to see what effects they were having inside cardiac muscle. “However, visualization of the 3D wave phenomena that occur within the cardiac muscle has remained a major scientific challenge. Despite substantial progress in the development of tomographic optical techniques, the measurement of transient electrical scroll waves inside cardiac tissue has so far been impossible,” the authors stated.

Fenton, School of Physics postdoctoral fellow Ilija Uzelac, and colleagues from Germany’s Max Planck Institute for Dynamics and Self-organization and University of California San Diego came up with a mix of panoramic optical mapping and high-resolution four-dimensional ultrasound imaging. “Until now, only surface recording of complex fibrillation was possible,” Fenton said at the time.

The team’s new imaging technique could help lead to earlier identification of heart rhythm disorders and development of better treatments. Thanks to the group’s research, a more complete picture of what exactly happens to a human heart while in distress is also coming into view.

Dialing up heart rhythms on a smartphone 

In 2019, Fenton and researchers had been able to take technologies that allowed them to simulate the spiral waves of heart rhythms by solving mathematical equations using supercomputers, and apply them to widely available consumer electronics like smartphones and laptop computers. 

That research, co-authored by Fenton, School of Physics research scientist Abouzar Kaboudian, and School of Computational Science and Engineering associate professor Elizabeth M. Cherry (then at Rochester Institute of Technology) was published in the journal Science Advances. 

While heart rhythm studies in general required powerful computers — sometimes supercomputers — the march of digital technology’s progress has resulted in scientists being able to use the same computer chips used in high-end gaming applications and commercial software found in web browsers to expand the reach of 3D modeling. 

“Models that might have been accessible to only a handful of researchers in the world will now be available to many more groups,” Fenton shares. “This also opens the door to many other areas of research where people have equations that can be solved in parallel. Anybody can have access to these programs, which run simulations as much as thousands of times faster than standard CPUs (central processing units).”

Sounding out future cardiac research       

Fenton says he has never looked back at the decision he made to forgo particle physics so he could work on cardiac electrical signals. 

“It showed me that even though you think you want something, you have to be open to new things,” he says. “You may find those other things are more interesting. I’m having so much fun in doing this. I’m so glad I changed to this area.”

And as to what’s next? Fenton’s current projects involve possible advances in the amount of voltage used to treat fibrillations, and new knowledge about where in the heart to apply that voltage. He maintains collaborations with agencies like the Food and Drug Administration and a wide array of researchers and clinicians, with hopes that hospitals will eventually be able to directly apply what he has studied over the years to assist in better patient care and health outcomes. 

“The heart has been a really fun system to study, there’s so much that we still don’t know,” he adds, “but on top of that, it has a main application of directly saving lives, if we can find better and safer ways to prevent and terminate arrhythmias.”

A new study from the School of Psychology points to evidence that in the midst of the brain’s electrically induced chaos of firing neurons and snapping synapses, encoding and recalling memories seems to follow a pattern, regardless of age. Further studies of this process could someday help lead to earlier diagnosis of neurological diseases like Alzheimer’s.

“When we are experiencing visual events like we do on a daily basis, our brain will first perceive and encode into memory the simple features that are in color before the complex features like the scene, the room that we are in,” says Audrey Duarte, co-author of the study and principal investigator in Georgia Tech’s Memory and Aging Lab. Duarte is also a professor in the School of Psychology. 

“When we bring that event back, it’s the opposite temporal order. First the scene, then the color.”

A key factor in that process? Just like your teachers told you — it’s all about paying attention. 

Those are the main takeaways from the study, published January 15 in eNeuro, the journal of the Society for Neuroscience, under the title, “Context Memory Encoding and Retrieval Temporal Dynamics Are Modulated by Attention across the Adult Lifespan.” The lead author is Soroush Mirjalili, a research assistant and grad student of Duarte’s. 

Mirjalili described the study’s findings in a way that might resonate with those dealing with pandemic restrictions. Imagine viewing a talk in a virtual conference. “Your brain would be processing the simple features like colors on the slides before it would process the spatial layout of the presentation or perhaps the layout of the room in which you are viewing it,” Mirjalili says. “But later if you are remembering this experience, it is these more complex spatial details like those of the room you are sitting in that are likely brought back to mind first before the simpler features like the colors.

“Now imagine that a colleague later asks you about your experience at this conference and whether you tuned in from home or work. Your brain would be able to retrieve information about the spatial context of wherever you are right now even faster than if they didn't prompt you with that question about the location.”

Georgia Tech researchers Jonathan Strunk, Taylor James, and Patrick Powell are also co-authors of the paper, which was presented at a January 15, 2021 virtual news conference. 

How Memories Get Filed Away 

The study’s primary focus is episodic memory, or a category of long-term memory that involves the recollection of personally experienced specific events, situations, and experiences. It has both simple and complex features, and it becomes less reliable with age.

As the authors state in the abstract of the research paper, “How we successfully encode and recover these features in time, whether these temporal dynamics are preserved across age, even under conditions of reduced memory performance, and the role of attention on these temporal dynamics, is unknown.”

Duarte and her students started to dig at those unknowns with the help of 58 study volunteers, ages ranging from 18 to 72, fitted with electroencephalography (EEG) skullcaps recording activity in their brains. Survey participants studied pictures of black and white objects presented with both color (representing low-level or simple features) and scenes (high-level or complex features), and subsequently made context memory decisions for both features. “Attentional demands were manipulated by having participants attend to the relationship between the object and either the color or scene while ignoring the other context feature,” the authors say.

Duarte’s team started with existing research about the brain, particularly how it deals with perception. “Both in humans and animals, studies have shown that the brain can tell different colors apart before it can tell different scene features apart,” Duarte says. “That’s just because of the way the brain is organized. Those areas that are sensitive to color are just earlier in the stream of visual processing. Then there are those regions that are more sensitive to more complex, spatial details.”

Duarte and her team hypothesized that memory might happen the same way that perception does. “My brain can tell red from green earlier than whether it’s an indoor or outdoor scene,” she says. “But we didn’t know about memories. Maybe they’re encoded in the same order.”

It turns out, according to the team’s data, that it does encode the memory in the same order — but not when it comes to remembering. That’s where attention comes in.

“That was a novel aspect of our study,” Duarte says. “We hypothesized that what people are attending to is going to make a difference there.”

The results? Color is encoded into memory earlier than scene, and attention enhances this difference. The order in which color and scene are retrieved from memory is reversed, and attention enhances this reversal.

“The temporal order in which we learn and remember is dependent on these hardwired visual pathways in the brain, but it’s also dependent on what we’re paying attention to,” Duarte says.

An earlier diagnosis for Alzheimer’s?

Learning as much as possible about how memories are stored and retrieved is helpful on a basic science level, but several other studies conducted in Duarte’s Memory and Aging Lab deal with the impact of neurological diseases like Alzheimer’s. 

Duarte says the regions of the brain discussed in the study — the visual pathway, regions sensitive to color and scenes — don’t change a lot with normal aging. “But in pathology, which can occur even in a person’s 20s, with genetic predisposition, you can see this pathology in the brain but only with invasive methods,” she says. “If you see that pathology in those people in the same regions, they may not have amnesia yet but they might have a different temporal disorder. Perhaps early on in this disease, you can measure the timeline of memory recovery to see if there’s something else going on.” 

Even for those who might not develop Alzheimer’s in 30 or 40 years, who may not yet have any detectable impairment, “it could be there’s something different in the temporal order of their memory, what’s recovered before what,” Duarte adds. “That might be an application for this kind of work, which isn’t invasive.”

Scientists had already described the microstructure of the skin on the ventral, or belly, surface of snakes. Many of the snakes studied, including all viper species, had distinctive rearward facing “microspicules” (micron-sized protrusions on scales) that had been interpreted in the context of reducing friction in the forward direction—the direction the crawling snake—and increasing friction in the backward direction to reduce slip. 

Considered through the lens of a sidewinder’s peculiar form of locomotion, however, it seemed that these microspicules would not function in the same manner. But no one had examined the microstructure of sidewinders, nor of a handful of unrelated African vipers that also sidewind.

Working with naturally-shed skins collected from snakes in zoos, researchers used atomic force microscopy to visualize and measure the microstructures of these scale protrusions in three species of sidewinding vipers as well as many other viper species for comparison. The results of the research, published this week in the journal Proceedings of the National Academy of Sciences, found that indeed the sidewinders have a unique structure distinct from other snakes. 

The microspicules were absent in the African sidewinding species and reduced to tiny nubbins in the North American sidewinder. All three snakes also had distinctive crater-like micro-depressions producing a distinctive texture not seen in other snakes. 

Daniel Goldman, Dunn Family Professor of Physics at the Georgia Institute of Technology, and Jennifer Rieser, working as a postdoctoral researcher in Goldman’s group and currently an assistant professor in the Department of Physics at Emory University, developed mathematical models to test how both the typical texture of rearward-directed microspicules and spicule-less cratered texture function as snakes interact with the ground. The models revealed that the microspicules would actually impede sidewinding, explaining their evolutionary loss in these species. 

The models also revealed an unexpected result that microspicules function to improve performance of snakes that use lateral undulation to move. Lateral undulation is the typical side-to-side mode locomotion used by the majority of snake species. “This discovery adds a new dimension to our knowledge of the functionality of these structures, that is more complex than the previous ideas,” said Joseph Mendelson, director of research at Zoo Atlanta and adjunct associate professor in the Georgia Tech School of Biological Sciences.

The models indicate that the microspicules act a bit like corduroy fabric. “Friction is low when you run your finger along the length of the furrowed fabric—consistent with previous work—but the furrows produce significant friction when you move your finger sideways across the fabric texture,” said Goldman. The functionality of the distinct craters remains a mystery.

The findings could be important to the development of future generations of robots able to move across challenging surfaces such as loose sand. “Understanding how and why this example of convergent evolution works may allow us to adapt it for our own needs, such as building robots that can move in challenging environments,” Rieser said.

In terms of anatomy, this was a classic example of convergent evolution between a pair of snake species in Africa and a very distantly related snake in North America, Mendelson noted. Biogeographic reconstructions conducted by Jessica Tingle, a doctoral student at University of California Riverside, indicated that the African snakes are evolutionarily much older than the North American sidewinder, suggesting that the sidewinders represented an earlier phase in adaptation for sidewinding.

Tai-De Li, then at Georgia Tech in the lab of Prof Elisa Riedo and now at the City University of New York, did the AFM measurements. 

Drawing from the fields of evolutionary biology, living systems physics, and mathematical modelling, the team produced a study that explains some aspects of what these microstructures on the bellies of snakes do and how they evolved in snakes. 

“Our results highlight how an integrated approach can provide quantitative predictions for structure-function relationships and insights into behavioral and evolutionary adaptions in biological systems,” the authors wrote. 

This research was supported by the Georgia Tech Elizabeth Smithgall Watts Fund; National Science Foundation Physics of Living Systems Grants PHY-1205878 and PHY-1150760; and Army Research Office Grant W911NF-11-1-0514. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the sponsoring agencies.

CITATION: Jennifer M. Rieser, Tai-De Li, Jessica L. Tingle, Daniel I. Goldman, and Joseph R. Mendelson III, “Functional consequences of convergently evolved microscopic skin features on snake locomotion.” (Proceedings of the National Academy of Sciences, 2021)

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This annual symposium, in its 29^th year, provides a forum for researchers to share the latest research in bioengineering and bioscience. Each year the symposium topic changes and is held to celebrate the life and contributions of F.L. “Bud” Suddath, a Georgia Tech professor who excelled at research, teaching, and in administrative roles.

The 2021 symposium “Origins and Early Evolution of Life” was co-chaired by Nicholas Hud and Loren Williams. Nicholas Hud, Ph.D., is a Regents’ professor in the School of Chemistry and Biochemistry, director of the NSF/NASA Center for Chemical Evolution, and associate director of the Petit Institute. Loren Williams, Ph.D., is a professor in the School of Chemistry and Biochemistry at Georgia Tech, director of the Georgia Tech Center for the Origin of Life, and researcher at the Petit Institute.

“This year's Suddath Symposium was the perfect opportunity for us to share our latest research on the origins of life and to celebrate 10 years of the Center for Chemical Evolution, said Nicholas Hud. “Our center has been focused on a grand challenge… to discover plausible prebiotic syntheses for the polymers of life or their predecessors. Now that our center has completed 10 years, the maximum number of years that can be supported by NSF, we have a cadre of early career scientists ready to take the reins on future research efforts. It’s exciting to see the impact we have made on the field, and to share these accomplishments through the Suddath Symposium with the broader scientific community.”

The 2021 Suddath Symposium was the first in this 29 year series of symposia to go virtual with 251 attendees from 18 countries around the world.

Each year, the symposium kicks off with a presentation from a Georgia Tech Ph.D. candidate who has won the annual Suddath Memorial Award, which was established by the family, friends, and colleagues of Bud Suddath. This year’s 2021 award went to Cristian Crisan, a doctoral candidate advised by Brian Hammer, Ph.D., associate professor in the school of biological sciences at Georgia Tech.

Crisan’s presentation, “Antimicrobial Competition Dynamics of the Vibrio cholerae Type VI Secretion System,” began at 11 a.m. EST on Thursday, January 28^th, and was followed by the 1 p.m. start of the 2021 Suddath Symposium on “Origins and Early Evolution of Life.”

VIEW PRESENTATION RECORDINGS

The lineup of “Origins and Early Evolution of Life” speakers included:

• Keynote presentation by Nobel laureate Jack Szostak, Ph.D. – Harvard Medical School, Harvard University, Massachusetts General Hospital
• Donna Blackmond, Ph.D. – Scripps Research Institute
• Facundo Fernandez, Ph.D. – Georgia Tech
• Vicki Grassian, Ph.D. – University of California, San Diego
• Martha Grover, Ph.D. – Georgia Tech
• Nicholas Hud, Ph.D. – Georgia Tech
• Ramanarayanan Krishnamurthy, Ph.D. – Scripps Research Institute
• Antonio Lazcano, Ph.D. – National Autonomous University of Mexico, Mexico City
• Luke Leman, Ph.D. – Scripps Research Institute
• Thomas Orlando, Ph.D. – Georgia Tech
• Greg Springsteen, Ph.D. – Furman University
• Loren Williams, Ph.D. – Georgia Tech

Even though much has been studied about the sunlight-powered process that provides Earth with oxygen, Barry knew that there was still a lot to uncover about photosynthesis for the good of humankind. “You could work with it to make crops more productive,” Barry said in 2018. With an eye on climate change’s impact on nature, she added, “We may have to repair and adapt the photosynthesis process someday, too.”

Professor Barry, a renowned professor of biochemistry and biophysics in the School of Chemistry and Biochemistry, and a member of the Parker H. Petit Institute for Bioengineering and Bioscience, died January 20, 2021. She was 63. According to a memorial written by her family, her death comes after several years of bravely battling a severe autoimmune disease and the side effects of treatment.

Professor Barry’s husband, Peter Dardi, and her family have shared details here for a virtual memorial service which may be viewed by all on Saturday, January 30, 2021 at 11 a.m. ET.

All are additionally invited to share thoughts and remembrances on this memorial page, which has been kindly organized by the School of Chemistry and Biochemistry. Joining our six schools and the Institute, the College sends heartfelt condolences to all of Professor Barry’s family, colleagues, students, and friends. She will be missed.

Professor Barry was director of Georgia Tech’s Molecular Biophysics Training Program, and of the Barry Group Laboratory. Her Institute biography said of her research interests, “Research in my group is focused on how the dynamic and responsive protein matrix facilitates biological catalysis. We use a wide range of high resolution spectroscopic, biochemical, and structural techniques to describe the reaction coordinate, which reveals the motion of the protein in space and time. We test the design principles, which we uncover, by building biomimetic models.”

She received an A.B. in Chemistry with High Honors from Oberlin College in 1978, and a Ph.D. in Chemistry from the University of California, Berkeley, where she met her husband, in 1984. After earning her Ph.D., she completed post-doctoral training at Michigan State University before starting as an assistant professor at the University of Minnesota.

Professor Barry received tenure and advanced to full professorship at the University of Minnesota before moving to Georgia Tech in 2003. She also made a significant impact through training and mentoring students and faculty alike, and in 2012 received Georgia Tech's Faculty Mentoring Award.

She held the Graduate Opportunity Fellowship at the University of California, Berkeley (1982-1983), a McKnight Postdoctoral Fellowship at Michigan State University (1985), a Public Health Service Award at the National Institutes of Health (1985-1988), Faculty Summer Research Fellowship at the University of Minnesota (1989), fellowship at the American Association for the Advancement of Science (2009), and fellowship in the American Chemical Society (2010). She participated in the Bush Foundation Faculty Development Program (1992-1993) and received the Bush Sabbatical Award from the University of Minnesota in 1997. During that same year, Barry also received the Career Advancement Award from the National Science Foundation. She is a national honorary member of Iota Sigma Pi.

School of Chemistry and Biochemistry Chair and Professor M.G. Finn recently noted, “Bridgette influenced everyone who knew her with equal measures of scientific passion, dedication to quality, kindness, and consideration. I have always admired her papers — clear, insightful, frequently breathtaking — as wonderful examples of how we figure out how the world works. And I came to admire at least as much her quiet courage in these past years, dealing with her health challenges while maintaining the highest professional standards. When Bridgette spoke, everyone listened. We'll miss her greatly.”

Professor Barry is survived by her husband of 36 years, Peter Dardi; a brother and sister-in-law, Michael and Jen Barry; and several nieces and nephews. In lieu of flowers, her family asks that contributions may be made to your local food bank.

Several of Professor Barry’s colleagues and friends are in the process of gathering and sharing memories and tributes to her life and research, which can be found on this aforementioned memorial page. These thoughts and remembrances will be shared with Professor Barry’s family.

Assistant professor Jenny McGuire and former postdoc Silvia Pineda-Munoz, of the Spatial Ecology and Paleontology Lab in the Schools of Biological Sciences and Earth and Atmospheric Sciences at Georgia Tech, sought to find out in their latest research. They analyzed fossils spanning 11,700 years to investigate how different animal species have changed their habitats as a result of human activity.

“Humans have expanded, but they haven’t expanded homogenously across North America – we are where it’s nicer to live,” explains Pineda-Munoz, who is currently a post-doctoral fellow at Indiana University. “So, it got me thinking about this habitat selection from a human perspective. Knowing that we’re really displacing animals, plants, and all sorts of organisms from their habitats, have their habitat selections changed and can we actually compute that?”

To compute potential changes in habitat selections, Pineda-Munoz and colleagues studied the fossil records of 46 species, representing roughly one quarter of the mammals present in the lower 48 states. These fossil records spanned from the end of the ice age to present day, covering events like the agricultural expansion of Native Americans, the arrival of European settlers, and the Industrial Revolution.

With these records, Pineda-Munoz, McGuire, and their colleagues were able to calculate how human activity has shifted the habitat selection of different mammals. As was expected, they found that most of the studied species – roughly 74% – changed their habitat after the start of the Industrial Revolution. Unexpectedly, however, not all mammals were affected equally.

“I was really surprised by what we found,” says McGuire. According to their results, the mammals’ diet and body size were big predictors of whether they were facilitated or deterred by human activity. “I was expecting that most species would have been excluded from the climates that they normally would have liked to live in, and we did find that especially for the larger species. But what I wasn't expecting was all these small mammal species to be living outside of their historic climate range, and to have been facilitated so much by human impacts and anthropogenic change.” While larger species like bison and cougars were pushed out of their preferred climates, smaller mammals expanded into regions with human settlements. “That was very surprising, I think that's a really interesting result that we ended up with.”

Why are smaller mammals thriving within the expanding footprint of humans? There are several theories. “We haven't specifically tested this,” says Pineda-Munoz, “but I think it also has to do with the fact that we are losing some competitive interactions between mammals or other organisms.” McGuire has another theory, explaining that “we're creating this increasing dimensionality of the landscape.” By building cities and plowing fields, we’ve created plenty of nooks and crannies for small mammals to live. But, as McGuire points out, “for the large species, they can't hide. They can't fit into the little nooks and crannies and cohabitate with us.”

This has marked impacts on animal conservation, particularly for large species. “Just looking at the climates in which species live in today is not sufficient to understand where they can and should be living,” explains McGuire. To understand how best to protect larger species from human activity and the threat of climate change, we should use data from the past. “You can learn a lot from near short-term studies, like how is something responding over the last five years? But you can't really fully understand how something is going to respond to the magnitude and the rate of change that's going on right now with things like climate change and the expansion of human footprints, unless you really get a long term, deeper time perspective on that.”

In the 19th century, scientists and engineers developed the discipline of statistical mechanics, which predicts how groups of simple particles transition between order and disorder, as when a collection of randomly colliding atoms freezes to form a uniform crystal lattice.

More challenging to predict are the collective behaviors that can be achieved when the particles become more complicated, such that they can move under their own power. This type of system — observed in bird flocks, bacterial colonies, and robot swarms — goes by the name "active matter.”

As reported in the January 1, 2021 issue of the journal Science, a team of physicists and engineers have proposed a new principle by which active matter systems can spontaneously order, without need for higher level instructions or even programmed interaction among the agents. And they have demonstrated this principle in a variety of systems, including groups of periodically shape-changing robots called "smarticles" — smart, active particles.

The theory, developed by Postdoctoral Researcher Pavel Chvykov at the Massachusetts Institute of Technology while a student of Prof. Jeremy England, who is now a researcher in the School of Physics at Georgia Institute of Technology, posits that certain types of active matter with sufficiently messy dynamics will spontaneously find what the researchers refer to as "low rattling" states.

“Rattling is when matter takes energy flowing into it and turns it into random motion,” England said. “Rattling can be greater either when the motion is more violent, or more random. Conversely, low rattling is either very slight or highly organized — or both. So, the idea is that if your matter and energy source allow for the possibility of a low rattling state, the system will randomly rearrange until it finds that state and then gets stuck there. If you supply energy through forces with a particular pattern, this means the selected state will discover a way for the matter to move that finely matches that pattern.”

To develop their theory, England and Chvykov took inspiration from a phenomenon — dubbed thermophoresis — discovered by the Swiss physicist Charles Soret in the late 19th century. In Soret's experiments, he discovered that subjecting an initially uniform salt solution in a tube to a difference in temperature would spontaneously lead to an increase in salt concentration in the colder region — which corresponds to an increase in order of the solution. 

Chvykov and England developed numerous mathematical models to demonstrate the low rattling principle, but it wasn't until they connected with Daniel Goldman, Dunn Family Professor of Physics at the Georgia Institute of Technology, that they were able to test their predictions. 

Said Goldman, "A few years back, I saw England give a seminar and thought that some of our smarticle robots might prove valuable to test this theory." Working with Chvykov, who visited Goldman's lab, Ph.D. students William Savoie and Akash Vardhan used three flapping smarticles enclosed in a ring to compare experiments to theory. The students observed that instead of displaying complicated dynamics and exploring the container completely, the robots would spontaneously self-organize into a few dances — for example, one dance consists of three robots slapping each other's arms in sequence. These dances could persist for hundreds of flaps, but suddenly lose stability and be replaced by a dance of a different pattern.

After first demonstrating that these simple dances were indeed low rattling states, Chvykov worked with engineers at Northwestern University, Prof. Todd Murphey and Ph.D. student Thomas Berrueta, who developed more refined and better controlled smarticles. The improved smarticles allowed the researchers to test the limits of the theory, including how the types and number of dances varied for different arm flapping patterns, as well as how these dances could be controlled. "By controlling sequences of low rattling states, we were able to make the system reach configurations that do useful work," Berrueta said. The Northwestern University researchers say that these findings may have broad practical implications for micro-robotic swarms, active matter, and metamaterials.

As England noted: “For robot swarms, it’s about getting many adaptive and smart group behaviors that you can design to be realized in a single swarm, even though the individual robots are relatively cheap and computationally simple. For living cells and novel materials, it might be about understanding what the ‘swarm’ of atoms or proteins can get you, as far as new material or computational properties.”

The study’s Georgia Tech-based team includes Jeremy L. England, a Physics of Living Systems scientist who researches with the School of Physics; Dunn Family Professor Daniel Goldman; professor Kurt Wiesenfeld, and graduate students Akash Vardhan (Quantitative Biosciences) and William Savoie (School of Physics). They join Pavel Chvykov (Massachusetts Institute of Technology), along with professor Todd D. Murphey and graduate students Thomas A. Berrueta and Alexander Samland of Northwestern University.

This material is based on work supported by the Army Research Office under awards from ARO W911NF-18-1-0101, ARO MURI Award W911NF-19-1-0233, ARO W911NF-13-1-0347, by the National Science Foundation under grants PoLS-0957659, PHY-1205878, PHY-1205878, PHY-1205878, and DMR-1551095, NSF CBET-1637764, by the James S. McDonnell Foundation Scholar Grant 220020476, and the Georgia Institute of Technology Dunn Family Professorship. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the sponsoring agencies.

CITATION: Chvykov & Berrueta, et al., “Low rattling: A predictive principle for self-organization in active collectives,” (Science 2021). https://science.sciencemag.org/content/371/6524/90/tab-pdf

Reinhard’s latest research successes keep him on both of those tracks.

In November, Reinhard, an associate professor in the School of Earth and Atmospheric Sciences (EAS), found out that NASA will fund Georgia Tech to be part of its new Interdisciplinary Consortia on Astrobiology Research (ICAR) organizational structure, which will replace its NASA Astrobiology Institutes (NAIs). (Georgia Tech has hosted an NAI since 2015.)  Reinhard and other EAS scientists join an ICAR team based at the University of California, Riverside that will study “Alternative Earths – How to Build and Sustain a Detectable Biosphere.”

Meanwhile, Reinhard and a postdoctoral researcher in his group,  Mojtaba Fakhraee, published a study in November in Nature Geosciences about the Earth’s so-called “biological pump,” the process that sends carbon dioxide from the atmosphere deep into the ocean, where it mixes with biomass and sediment, thereby helping to regulate the planet’s carbon cycle, atmospheric composition, and climate. A new model developed by Fakhraee, the lead author for the paper, shows that environmental factors like temperature have played “an important and underappreciated role” in the evolution of the Earth’s carbon cycle. 

NASA’s search for life in the cosmos — and its origins on Earth

NASA began its NAI program in 1998 as a way to partner with institutions of higher learning and other research centers, to unlock more secrets about potential life in the cosmos, as well as its origins on Earth. Georgia Tech was funded as a principal "node" of the NASA Astrobiology Institute team called Alternative Earths, initially funded in 2015. The new ICAR team has the same name and shares a number of overarching goals, and involves a number of researchers at Georgia Tech, including Reinhard and EAS colleagues Jennifer Glass, Britney Schmidt, Taka Ito, and Sean Crowe (adjunct EAS appointee.) Most of Reinhard’s lab group, Earth System Science@Georgia Tech, is also aboard the ICAR team. 

The new NASA astrobiology research system, as explained in an early November press release announcing the agency’s eight new ICAR teams, “has developed over time to meet the needs of a rapidly-evolving field with an expanded scope and emergent questions driven by two decades of research and discovery in astrobiology.”

The main goals from the 2015 NASA Astrobiology Initiative remain in place:

• Identifying abiotic (non-living) sources of organic compounds
• Synthesis and function of macromolecules in the origin of life
• Early life and increasing complexity
• Co-evolution of life and the physical environment
• Identifying, exploring, and characterizing environments for habitability and biosignatures
• Constructing habitable worlds

NASA says the NAIs and Research Coordination Networks — which provide interdisciplinary and community support to scientists — helped establish those common goals for the astrobiology community, and now the ICARs will take advantage of next-generation tools, techniques, and resources to keep pursuing them. 

“A key component of our pitch is to leverage some existing tools that haven’t been used much in this space,” Reinhard says. “For example, 3D ocean biogeochemistry models have existed for a while, and have been used for recent and future projections of the carbon cycle and climate change. These are potentially powerful tools for for studying exoplanets, so we’re trying to pursue that kind of model development and application in a big way.”

New computational models that will take advantage of high-performance computing capabilities at Georgia Tech’s Coda and PACE facilities, and elsewhere in the U.S., should also help with Reinhard’s ICAR team research. “There’s quite a bit of uncertainty on how these models work, and how they can be applied outside of standard Earth boundary conditions. And of course any habitable planet, like Earth, will be an incredibly complex system with numerous interacting components. The challenge is to represent this in a way that doesn’t require six months of computing time to run a single model.”

The ICAR Alternate Earths team will use data from the forthcoming James Webb Space Telescope (JWST), set to launch in 2021. They’ll also help NASA design what the generation of observational instruments beyond JWST should look for when it comes to biosignatures on exoplanets. Many of those instruments are now in design stages, Reinhard says. 

“What particular signals do we predict as being the most likely, the most robust, to look for?” he says, referring to chemicals such as oxygen and ozone. “What kind of recommendations can we make about wavelength ranges? What kind of spectral resolutions do we need? What are the signs of life in an atmosphere that totally lacks oxygen — and how might geological processes mislead you?”

From exoplanets to Earth’s “biological pump”

One of Reinhard’s co-authors on the Nature Geoscience paper, Noah Planavsky, assistant professor of Earth and Planetary Sciences at Yale University, is also on the UC-Riverside Alternate Earths ICAR team. Reinhard notes that it’s another connection between research involving our Earth, and the search for habitable exoplanets. 

“A key aspect of trying to use the Earth to learn what these other planets may be like is better understanding how the Earth behaves over time,” Reinhard says. 

For the Nature Geoscience study, Fakhraee had to come up with a new mechanistic model that takes into account the amount of marine organisms, like algae and phytoplankton, that also help absorb sequestered carbon. 

“The model we used simulates the formation of marine particles,” Fakhraee says. “The faster the particles reach the seafloor, the more carbon would escape from the water column to be stored in the sediment. So the model tries to find out how change in temperature and biology of the ocean could have impacted the speed of those marine particles, whereby influencing the strength of carbon sequestration in the ocean.”

Previously, scientists thought that as algae evolved with bigger cell sizes, along with other ocean biological structure changes, it would speed up the descent of marine particles in the ocean and help keep carbon sequestered. “But our results indicate that such increase in speed of marine particles caused by evolution of bigger-sized algae is not substantial when compared to the impact that change in average global temperature could have had on the ocean carbon sequestration.”

That’s important, he adds, not only for understanding the biological carbon pump in the ocean, but “for understanding how climate change could impact the strength of the carbon sequestration in the ocean.”

“The added dimension that we think is cool is the impact of oxygen,” Reinhard adds. “How have changes in ocean oxygen abundance and distribution combined with changes in temperature to impact the strength and dynamics of the biological pump?”

The tension between awareness and fatigue can lead to case-count plateaus, shoulder-like dynamics, and oscillations as rising numbers of deaths cause people to become more cautious before they let down their guard to engage once again in behaviors that increase risk for transmission, which, in turn, leads to rising death counts — and renewed awareness.

“Epidemics don’t necessarily have a single peak after which the risk subsides,” said Joshua Weitz, Patton Distinguished Professor of Biological Sciences and founding director of the Interdisciplinary Ph.D. in Quantitative Biosciences at the Georgia Institute of Technology. “People’s behaviors are both influenced by and influence epidemic dynamics, potentially driving plateaus, and oscillations in incidence.”

A paper describing the connection between human behavior and viral spread was published this month in the journal Proceedings of the National Academy of Sciences. It was authored by researchers at Georgia Tech, McMaster University, Princeton University, and Texas A&M.

In the early days of the pandemic, many scientists turned to traditional epidemiological studies, which showed epidemic cases could rise to a peak and then fall smoothly as immunity to the infection reached high levels in a population in the absence of large-scale interventions. Public health messages urged the population to “flatten the curve” to prevent disease from overwhelming hospitals.

“We were concerned that a focus on ‘the peak’ was potentially misguided because it implied that the shape was a feature of the disease alone without considering the consequence of behavior,” Weitz said. “In reality, there does not have to be a single peak during an epidemic.”

“If people are aware of the severity of the epidemic, they may change their behavior, and if they change their behavior, there will be fewer severe outcomes,” Weitz said. “But if awareness is short-term, individuals may tire of public health regulations and the virus will come roaring back. Instead of a single peak in cases, there can be plateaus or oscillations balanced between cautious behavior and relaxation.”

The research team analyzed data from the early phase of the epidemic and found evidence that the decrease in fatalities after a peak was slower than the rise toward it. However, in contrast to simple models of awareness-driven behavior, the research team also found evidence that individuals tended to increase their activity — as measured by mobility indicators — before epidemic severity waned. This means that individuals may have grown fatigued, worsening the epidemic severity. The study also found that other preventive measures, like mask wearing, have the potential to avert worst-case outcomes in disease transmission even as mobility increases in light of fatigue.

“This study underlines the importance of human behavior in driving epidemic outcomes,” said Jonathan Dushoff from the Department of Biology at McMaster University. “To make good predictions beyond the short term, we need to understand all of the factors driving human responses to the virus — fear, fatigue, information, misinformation, and so forth. We have a long way to go.” 

Weitz and Dushoff share optimism as well as concerns on the potential effects of anticipation of imminent vaccine distribution on behavior associated with transmission.

“It’s hard to be sure what impacts vaccine distribution will have on behavior,” Dushoff said. “There is concern in public health circles that people who think the vaccine is just around the corner could relax their guard. Human behavior is complicated.”

Lessons for future public health responses may help focus on the role of human behavior as well as communications that make disease impacts personal, fostering long-term awareness and changes in behavior that can reduce collective transmission.

Weitz and Dushoff coauthored the study with Sang Woo Park from the Department of Ecology and Evolutionary Biology at Princeton University and Professor Ceyhun Eksin from the Department of Industrial and Systems Engineering at Texas A&M.

This research was supported by the Simons Foundation (SCOPE Award ID 329108), the Army Research Office (W911NF1910384), National Institutes of Health (1R01AI46592-01), and National Science Foundation (1806606 and 1829636). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the funding agencies.

CITATION: Joshua S. Weitz, Sang Woo Park, Ceyhun Eksin, and Jonathan Dushoff, “Awareness-driven Behavior Changes Can Shift the Shape of Epidemics Away from Peaks and Towards Plateaus, Shoulders and Oscillations.” (Proceedings of the National Academy of Sciences, 2020) https://doi.org/10.1073/pnas.2009911117

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The work, published this month in the journal eLife, references “division of labor,” “trade,” “productivity” and “return on investment,” (ROI) to describe those cellular activities. If that sounds like a paper destined for a business magazine instead of a peer-reviewed journal on biological sciences research, there’s a good reason. 

As the study, led by assistant professor Peter Yunker and associate professor Will Ratcliff, notes in the abstract, “A large body of work from evolutionary biology, economics, and ecology has shown that specialization is beneficial when further division of labor produces an accelerating increase in absolute productivity.” In other words, the prevailing theories state that specialization pays off only when it increases total productivity – whether it’s multicellular organism or widgets streaming out of a factory. 

What Yunker, from the School of Physics and the Parker H. Petit Institute for Bioengineering and Bioscience, and Ratcliff, from the School of Biological Sciences and co-director of the Interdisciplinary Ph.D. in Quantitative Biosciences (QBioS) have found is that the conditions for the evolution of specialized cells were actually much broader than previously thought. Absolute productivity be darned, the cells seem to say; specialization appeared to be a winning strategy, even under conditions that should favor cellular self-sufficiency. 

Why? It has to do with the topology of the network of cells within the organism – what Ratcliff calls a branchy structure. That topology determines that the division of labor can be favored, even if productivity suffers. 

“Topological constraints in early multicellularity favor reproductive division of labor” is the title of the team’s paper. Yunker and Ratcliff collaborated with several other Georgia Tech faculty and graduate students on the research: Joshua S. Weitz, Patton Distinguished Professor in the School of Biological Sciences and co-director of QBioS; School of Physics graduate students David Yanni and Shane Jacobeen; and School of Biological Sciences graduate student Pedro Marquez-Zacarias. All are members of Georgia Tech’s Center for Microbial Dynamics and Infection.

Multicellular multitasking

As cells get more complex, they begin to specialize. Some cells are dedicated to reproduction, while others are devoted to other general tasks such as making and maintaining the organism’s body. “In this paper, what we’re trying to figure out is, when is it a good idea to specialize and have that pay off, and when it is a good idea for your cells to remain generalists?” Ratcliff says. “Under what conditions does evolution favor specialization, and in what conditions do simple multicellular organisms keep every cell a generalist?”

For centuries, scientists have known that specialization is very important for multicellularity. “Once we had microscopes, we were off to the races learning about specialization,” Ratcliff says. 

The thinking for the last few decades has been that more specialized cells evolve when specialization results in increasingly higher productivity. “That will push things to complete specialization because there’s more to be gained by specializing than not specializing.” 

Yet what if those cells are not interacting randomly with a lot of other cells, but only with a few cells over and over again? “This is actually the case for a little branchy structure that contains mom and all her kids. The only cells you are attached to are the ones that gave rise to you, and the ones that arise from you,” he says. Those “branchy structures” offer the topological constraints mentioned in the title of the research study. 

Branch banking of cellular products

Yunker explains that those tree-branchy structures can be thought of as similar to fractals, in which math functions are repeated again and again and are depicted as jagged borders stretching into infinity. 

“Mandelbrot sets and the broader study of fractals have been an inspiration for a lot of this,” Yunker says. “After the concepts behind fractals were identified, people eventually started to see them everywhere. Instead of some unique esoteric thing, it was pervasive. In a similar vein, the structures that we find make evolving division of labor easier, these sparse filaments and branched topologies, are common in nature,” including so-called snowflake yeast and some forms of algae.

Yunker agrees that it may seem counter-intuitive, but as you restrict cellular interactions, like swapping of products that can enhance reproduction or specialization, that specialization actually becomes easier according to his team’s mathematical models. 

Cells that produce the same products won’t interact or 'trade' with each other, since that would be a waste of energy and efficiency. “A redundancy comes into play here,” Yunker says. “If you have a lot of similar cells trading, that increased productivity doesn’t do you a lot of good. Whereas if you have dissimilar or opposites trading, even with lower productivity, they’re able to direct those resources in a more efficient manner.”

What can economists and cancer researchers learn from these cells?

Since economics has already figured into the study of how multicellular organisms evolved, with all of that labor and trade and ROI, could that discipline have something to learn from Yunker and Ratcliff’s new theory — could the lessons mean a more efficient way to make all kinds of products?

“Could this apply in economics? Could it apply elsewhere?” Yunker echoes. “This is something we would love to pursue going forward.”

Ratcliff notes the multidisciplinary approach his biophysics and biosciences team took to approaching the study, which also involved mathematical models developed by Weitz. “We were really motivated by understanding both how life got to be complex, and the rules for why it did,” he says. “This paper follows into the ‘why’ category. Fundamental mathematics tells you about the rules evolution plays by, and there are a lot of downstream applications, like cancer research, agriculture, and infectious disease. You never really can predict how someone will leverage basic insight.”

Only two faculty members from each of the 26 University System of Georgia institutions are invited to participate in the Governor’s Teaching Fellows Program each academic school year. Anna Holcomb, a lecturer in the School of Electrical and Computer Engineering (ECE) and assistant director of the Undergraduate Professional Communication Program (UPCP), is also a 2020-2021 Fellow.

The Governor's Teaching Fellows Program was established in 1995 by former Governor Zell Miller to provide Georgia's higher education faculty with expanded opportunities for developing important teaching skills. Participants are selected “on the basis of their teaching experience, their interest in continuing instructional and professional development, their ability to make a positive impact on their own campus, and a strong commitment by their home institution for release time and other forms of support for the duration of their participation in the program.”  

“Being a Governor’s Teaching Fellow is a great honor for me,” Fenton says. “Not only is it allowing me to further my teaching skills, but also it is making me transform how I approach teaching. This year-long program allows me to spend three days a month interacting closely with enthusiastic and thoughtful educators from other colleges and universities of Georgia and learning about several instructional techniques that have been new to me. The diverse composition in teaching fields of the Teaching Fellows cohort has opened me to new ways of thinking that will have an impact on how I select and organize course content and delivery in all my future courses.”

Fellows must work on a project during their appointed one-year term that will benefit both the faculty member and their school. Fenton is creating a large database of physics demonstrations to be used in Georgia Tech’s Physics I course, taken by nearly 2,000 students each year.

“The idea is to have at least two real-life demos for each class given in the semester to help exemplify the physics concept introduced in the class, which will be over 80 experimental demonstrations,” Fenton says. “The demos can help students stay focused and motivated and provide new opportunities for students to engage with the material as they connect theory with reality in an interactive way. The demos will also be recorded while being demonstrated, so that they can be used by instructors in other institutions if they do not have direct access to the equipment.”

Fenton came to Georgia Tech in 2012 as an associate professor, and was made a full professor in 2018. He received his B.S. in Physics from Universidad Nacional Autonoma de Mexico in Mexico City, and a M.S. and Ph.D. in Physics from Northeastern University in Boston, MA.

Fenton and School of Physics colleague Carlos Silva were elected in 2019 to the American Physics Society Fellows program. Fenton has also won the 2017 Junior Faculty Outstanding Undergraduate Research Mentor Award, the 2017 Geoffrey B. Eichholz Faculty Teaching Award, and the 2018 Faculty Award for Academic Outreach.

The warning comes from a study of 14,189 fossil pollen samples taken from 358 locations across the continent. Researchers at the Georgia Institute of Technology used data from the samples to determine landscape resilience, including how long specific landscapes such as forests and grasslands existed – a factor known as residence time — and how well they rebounded following perturbations such as forest fires — a factor termed recovery.

“Our work indicates that landscapes today are once again exhibiting low resilience, foreboding potential extinctions to come,” wrote authors Yue Wang, Benjamin Shipley, Daniel Lauer, Roseann Pineau, and Jenny McGuire. “Conservation strategies focused on improving both landscape and ecosystem resilience by increasing local connectivity and targeting regions with high richness and diverse landforms can mitigate these extinction risks.”

The research, supported by the National Science Foundation, is believed to be the first to quantify biome residence and recovery time over an extended period. The researchers studied 12 major plant biomes in North America over the past 20,000 years using pollen data from the Neotoma Paleoecology Database.

“We find that the retreat of North American glaciers destabilized ecosystems, causing large herbivores — including mammoths, horses, and camels — to struggle for food supplies,” said McGuire, an assistant professor in Georgia Tech’s School of Biological Sciences and School of Earth and Atmospheric Sciences. “That destabilization combined with the arrival of humans in North America to land a one-two punch that resulted in the extinction of large terrestrial mammals on the continent.”

The researchers found that landscapes today are experiencing resilience lower than any seen since the end of the Pleistocene megafauna extinctions.

“Today, we see a similarly low landscape resilience, and we see a similar one-two punch: humans are expanding our footprint and climates are changing rapidly,” said Wang, a postdoctoral researcher who led the study. “Though we know that strategies exist to mitigate some of these effects, our findings serve as a dire warning about the vulnerability of natural systems to extinction.”

By studying the mix of plants represented by pollen samples, the researchers found that over the past 20,000 years, forests persisted for longer than grassland habitats — averaging 700 years versus about 360 years, though they also took much longer to reestablish after being perturbed — averaging 360 years versus 260 years. “These findings were somewhat surprising,” said McGuire. “We had expected biomes to persist much longer, perhaps for thousands of years rather than hundreds.”

The research also found that forests and grasslands transition quickly when temperatures are changing fast, and that they recover most rapidly if the ecosystem contains high plant biodiversity. Yet not all biomes recover; the study found that only 64% regain their original biome type through a process that can take up to three centuries. Arctic systems were least likely to recover, the study found.

Landscape resilience, the ability of habitats to persist or quickly rebound in response to disturbances, has helped maintain terrestrial biodiversity during periods of climatic and environmental changes, the researchers noted. 

“Identifying the tempo and mode of landscape transitions and the drivers of landscape resilience is critical to maintaining natural systems and preserving biodiversity given today's rapid climate and land use changes,” the authors wrote. “However, resilient landscapes are difficult to recognize on short time scales, as perturbations are challenging to quantify and ecosystem transitions are rare.”

Contrary to prevailing ecological theory, the researchers found that pollen richness — indicating diversity of species — did not necessarily correlate with residence time. Ecological theory suggests that biodiversity increases ecosystem resilience by improving "functional redundancy,” allowing a system to maintain stability even if a single or several species are lost. “But species richness does not necessarily reflect functional redundancy, and as a result may not be correlated with ecosystem stability,” the researchers wrote.

The study used pollen data from five forest types — forest-tundra, conifer/hardwood, boreal forest, deciduous forest, and coastal forest; five shrub/herb biome types — Arctic vegetation, desert, mountain vegetation, prairies, and Mediterranean vegetation; and two no-analog biome types — spruce parkland and mixed parkland.

The Neotoma Paleoecology Database contains fossil pollen and spores that are ubiquitous in lake and mire sediments. Collected through core sampling, the samples represent a wide diversity of plant taxa and cover an extended period of time.

Though the effects of climate change and human environmental impacts don’t bode well for the future of North American plant biomes, there are ways to address it, Wang said. “We know that strategies exist to mitigate some of these effects, such as prioritizing biodiverse regions that can rebound quickly and increasing the connectivity between natural habitats so that species can move in response to warming.”

This work was supported by the National Science Foundation (NSF) Grants DEB 1655898 and SGP 1945013. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the NSF.

CITATION: Yue Wang, Benjamin R. Shipley, Daniel A. Lauer, Rozenn M. Pineau, and Jenny L. McGuire, “Plant biomes demonstrate that landscape resilience today is the lowest it has been since end?Pleistocene megafaunal extinctions” (Global Change Biology, 2020). https://doi.org/10.1111/gcb.15299

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The research from assistant professor Taka Ito and professor Annalisa Bracco is one of nine projects that will share $7 million in DOE funding. The goal of the studies, according to a recent press release, is “improving DOE’s Energy Exascale Earth System Model (E3SM), the first comprehensive model of the Earth system to take full advantage of the world-leading supercomputing capabilities at DOE's national laboratories.”

The nine studies “will focus on a range of different topics, from improved representation of ecological systems and cloud-aerosol interactions in predictive models, to quantifying uncertainties across a range of processes, scales, time horizons, and regional impacts.” 

Bracco and Ito are the two principal investigators of their research study, with colleagues from the DOE’s Los Alamos National Laboratory in New Mexico collaborating on the project. 

A quick primer on earth system models 

“Ocean physical-biogeochemical interactions in the CMIP6 and E3SM Earth System Models” is the official title for Ito and Bracco’s forthcoming research, and it refers to two climate models among a suite available to climate scientists: the World Climate Research Programme’s Coupled Model Intercomparison Project Phase 6 (CMIP6) and the DOE’s model. 

Earth system models (ESMs) are computer and math-based tools that can help explain the global carbon cycle that is integral to the Earth system. The models represent “the atmosphere, ocean, land surface, chemical, and some biological processes in the Earth system,” he says. “This a huge code that kind of encapsulates what we think is going on process-wise. We describe them in the mathematical and computer languages, and then we simulate the computer code and we simulate the systems and how they interact.”

Ito adds that to date, those models haven’t kept up with rapid advances in observational and analytical data concerning the global carbon cycle. 

Giving earth system models a makeover

Ito and Bracco explain in an informal abstract for their project that Earth’s three major reservoirs — land, atmosphere, and oceans — exchange carbon for the planet. They note an estimate that the ocean now holds the vast majority — more than 90 percent — of carbon. They also explain that, during the past two centuries, humans tapping into fossil fuels have dramatically altered that cycle, with the ocean now becoming a significant carbon sink. 

“The excess anthropogenic carbon that has been accumulating in the ocean is altering its chemistry and the marine ecosystems,” Ito and Bracco share. “At the same time, climate change is modifying the ocean physics, with consequences for the transport of carbon into the ocean. Changing ocean circulation is similarly important for the global oxygen cycling. Approximately half of oxygen production occurs in the ocean, but changes in ocean transport, mixing, and biological production are changing oxygen production and cycling.” 

This is where ESMs can be a valuable tool for understanding these changes, but “unfortunately, these models underestimate the amplitude of the changes in ocean carbon uptake and dissolved oxygen content on the timescales of tens of years,” Ito says. “Additionally, they disagree over the sign of predicted changes in dissolved oxygen in the tropical oceans under global warming scenarios.”

In other words, climate change is happening so rapidly, some of the leading climate models aren’t keeping up.

“We think those are major regions of uncertainty, and we want to understand what causes those differences,” Ito says. “For the case of carbon dioxide uptake, what are the key differences between models and observation? Hopefully, that information will help us improve the next generation of ESMs. We want to eventually contribute to the better model performance and projections.”

Bringing big data, machine learning into the mix 

The project is an extension of the research that Annalisa Bracco started in 2018 for a separate DOE grant involving climate science. The methodology she developed there relied more on data mining and machine learning to take all climate factors – aerosols, winds, clouds, and other data – into account without overwhelming individuals having to manage and interpret the data. Bracco’s methodology enabled software and computers to do the work that humans had to do before, and further allows for faster input of the latest climate data into the models. 

“With this project we hope to identify and contribute to correct some of the major biases that models have in representing the ocean carbon cycle, which is fundamental in the anthropogenic (human-caused) carbon dioxide uptake,” Bracco says. “Working with DOE scientists who develop the model will make our results all the more relevant, because they can be 'turned' into model improvements right away.”

Bracco and a graduate student in her lab group, Fabrizio Falasca, 
have continued to build on her 2018 work, “developing more tools to complete a framework to investigate climate variability and change. The possibility to collaborate and learn from scientists in the College of Computing has been invaluable, of course,” Bracco notes. 

Bracco and Ito add that any analysis tools that arise from their project will be shared in the public domain. 

Soon, that research will focus on another aspect of daily — and nightly — life that changes as people grow older, in an area that often impacts their memory: sleep. 

“When you start thinking about what is underlying memory changes and aging, and individual differences in memory ability, there are certain factors that you can look at that are malleable – health-related factors, and sleep is a huge one,” Duarte says. 

The problem with gathering data from sleeping subjects is that many times, the devices that individuals have to wear can be cumbersome and make it difficult to attain a good night’s sleep. That can impact the quality of the data. That’s why Duarte is collaborating with assistant professor W. Hong Yeo, who researches micro and nano engineering in the George W. Woodruff School of Mechanical Engineering. Together, the team is creating a much smaller, wearable electronics device that can read brain waves while allowing the wearer to easily drift off into the various stages of sleep. That device may be ready for home testing soon, Yeo says.

Currently, Duarte and Yeo are working on two projects. One is supported by a National Institutes of Health grant, which aims to develop an at-home sleep monitoring system that measures brain signals on the forehead. This single device platform will be used to find neural signatures related to early detection of Alzheimer’s disease. The other project is supported by Huxley Medical Inc., a company Yeo founded, to build a low-cost, wireless, polysomnography system. Polysomnography describes a certain kind of sleep study that involves measuring brain waves, heart rates, and other vital signs to help health professionals understand sleep disorders. 

Nanotechnology to the rescue 

Making this new device affordable, easy to manufacture on a wide scale, and above all, wireless would allow patients to place the device on their foreheads, in the comfort of their own homes versus a visit to an in-person sleep lab. 

Yeo says that nanotechnology helped him dream up a way to make the device small and unobtrusive enough that test subjects can forget they’re wearing a monitor.

“Basically, we will develop a new nanomanufacturing method that can print multiple nanomaterials to fabricate an integrated wireless sensor system,” Yeo says. “Overall, this device will have an exceptionally small form factor,” with a thickness less than five millimeters that weighs less than eight grams. “The device size is similar to or smaller than a credit card.”

The soft electronics, mounted on a patient’s forehead, will include multiple sensors to measure brain signals, as well as a Bluetooth circuit. “It's basically offering the similar wireless functionality as an Apple watch, such that this device can be connected with any smartphone or tablet to record brain signals up to 20 meters away from the device,” Yeo says. 

Waking up to a new way to monitor sleep 

The team’s project started in 2019 when Yeo contacted Duarte about his need to access a lab that measures electroencephalograms (EEGs), which show the electrical activity in the brain. Yeo wanted to check a different device he was working on, and Duarte says the connection led to thinking about other possible collaborations.

“I saw the potential right away,” she says, sharing that Yeo’s previous nanotechnology work grabbed her attention. “We just started talking when I saw what he was building.” 

Yeo focuses on “soft, wearable electronics for health monitoring and human-computer interfaces,” according to his research website. He has previously designed biomimetic materials, or “skin-like electronics.” One of his device proposals, placed under the chins of those with dysphagia, or difficulty swallowing, would read electronic impulses to the throat, and is designed to help patients learn how to swallow again. Another project uses ultra-thin membrane biosensors that could help patients wirelessly control robotic wheelchairs. 

“His devices, you forget they’re on,” Duarte says of the designs. And “they really send out high quality signals that you can record.”

She adds that while devices that monitor movements during sleep currently exist, “and you can learn things about sleep-wake cycles — it’s objective data, but it’s not brain activity. There were all of these reasons why I wanted to get to brain activity.”

The sleep-memory-health connection

Duarte explains that science has long known about the connection between memory and sleep. “Looking at brain activity when people are sleeping, you can see patterns of activities related to memory. Events we experience during the day are replaying during sleep, and memories can be strengthened.”

Consistent nights of good sleep can translate into health benefits like stronger immune systems and better cardiovascular health, along with improved memory, Duarte adds. 

She shares that Alzheimer’s patients are the subject of an unrelated sleep study. “There could be some things in sleep brain activities that serve as biomarkers of Alzheimer’s pathology,” she says. If that can be verified, a smaller sleep monitoring device could keep patients from requiring more invasive procedures like spinal taps or brain scans. “They could just wear this device at home.”

Both Duarte and Yeo say the Covid-19 pandemic has rearranged their testing schedule for the device. Test subjects, including older people, can’t come in to labs to try out the device and have their data taken, but the researchers say they are getting ready to send them out for home testing. 

“Due to Covid-19, overall progress is slow,” Yeo says. “However, we’ve made progress in device design and fabrication. I believe that we can start using one or two devices with human subjects in late August.”

“After we’re sure we have a design that’s high fidelity and doesn’t break easily, we’re going to start mailing it out to volunteers of different ages,” Duarte says. And with video chat platforms like “Blue Jeans or Zoom, we can answer questions as they’re placing it on their heads.”

Yeo is founder and shareholder of Huxley Medical, the company sponsoring this research. He is also an inventor of technologies that include wearable electronics for health monitoring, which Huxley licensed for commercialization. The outcome of this research could impact his personal financial interests. His financial conflicts of interest have been disclosed to and are managed by the Georgia Institute of Technology Office of Research Integrity Assurance.

They’re friends because clathrate-trapped natural gas could be another source of energy for the oil and gas industry. Yet clathrates are also foes if they heat up too fast inside offshore wells. They can rapidly expand with dangerous results, as was suggested in the 2010 Deepwater Horizon oil spill. Clathrates buried deep within the Arctic permafrost can also trap methane, which is a major greenhouse gas, and rising global temperatures could unlock those chilly 'crystal cages' and add to climate change concerns. 

If science can figure out a safe, eco-friendly way to manipulate clathrates, then a wide range of disciplines and industries could benefit from the applications. A unique interdisciplinary team of Georgia Tech researchers may have found a way to accomplish that goal, using proteins embedded in bacteria from deep below the Earth’s surface to bind to clathrates and change them. 

“Mainly on the Plane: Deep Subsurface Bacterial Proteins Bind and Alter Clathrate Structure”, published July 23 in Crystal Growth & Design (an American Chemical Society publication) is the result of a 2018 grant from the NASA Exobiology program. The researchers are Abigail Johnson and Jennifer Glass from the School of Earth and Atmospheric Sciences, Dustin Huard and Raquel Lieberman from the School of Chemistry and Biochemistry, Priyam Raut from the School of Biological Sciences, and Sheng Dai and Jongchan Kim from the School of Civil and Environmental Engineering.

The petroleum industry currently tries to slow and cool off clathrates in pipelines and wells with synthetic compounds, but “there is a strong need for alternative, ‘green,’ antifreeze materials” to lower the temperature at which hydrates (clathrates) will form, says Lieberman, a professor in the School of Chemistry and Biochemistry. “While antifreeze proteins derived from cold water fish show some promise, our unique proteins come from those found in microbes that natively inhabit gas clathrates, and thus hold promise as more potent and tailored inhibitors of natural gas clathrate.”

Making protein magic in the lab

The researchers found that their cocktail of protein-embedded bacteria changed the structure of clathrate crystal lattices to “polycrystalline and plate-like, instead of forming single, octahedral crystals,” as the study’s abstract notes. 

“A big takeaway here is that this is one of the very first times that any group has created proteins in the lab using bacterial gene sequences from Earth’s deep biosphere,” says Glass, an associate professor in the School of Earth and Atmospheric Sciences. “Deep biosphere” refers to organic materials found beneath the Earth’s surface. “Due to the great difficulty of culturing and isolating microbes from the deep biosphere, we have taken the approach of expressing these novel proteins recombinantly, using workhorse bacteria like E. coli.” 

Glass says the study shows scientists can make these proteins in the lab and that they are stable enough to use in experiments. “This opens up huge possibilities for exploring functions of novel proteins from the deep biosphere in our laboratories. It’s possible these proteins could have use in biotechnology, medicine, industry, environmental remediation, and many other fields.”

Huard, a research scientist in the School of Chemistry and Biochemistry, marvels at how nature is capable of evolving simple yet elegant solutions to complex problems like figuring out clathrate structure. A simple amino acid sequence, when blended into proteins that bind to clathrates, “allows for organisms to thrive in extremely harsh, cold environments,” he says. 

Huard adds that clathrates are known to exist elsewhere in the solar system. “Our clathrate-binding proteins, produced by bacteria, could provide a clue as to how life might survive on other planetary bodies that have gas clathrates, such as Mars.”

Don’t forget about discoveries in the past few years about the role methane clathrates may play in maintaining subsurface liquid oceans on icy moons and planetary bodies in the outer solar system, adds Glass. “Gas clathrates are thought to be possible habitable zones for microbial life. I’m very excited to connect our research to results from future [NASA] missions.”

The full extent of the capabilities of clathrate-binding proteins is not yet known, Huard says. For example, the food industry could benefit if the proteins also inhibit ice growth, since antifreeze proteins are already found in many food products. 

The perfect mix of Georgia Tech researchers and disciplines 

Huard researches in Lieberman’s lab, which has produced studies of the protein structure found in certain forms of glaucoma. Lieberman and Huard ended up being part of a team that Glass says illustrates Georgia Tech’s interdisciplinary strengths.

“This project is a perfect example of the exciting results that emerge when fields that often don’t talk come together to try something new,” Glass says. “Our team at Georgia Tech is truly one of the only in the world, to my knowledge, that has the scientific and engineering expertise to do this work.” 

The clathrate project brought together marine microbiologists and geochemists from the Glass Lab, bioinformaticians from the Georgia Tech Bioinformatics Graduate Program, and geosystems engineers. It was catalyzed by the Ocean Science and Engineering program (OSE), in which doctoral candidate Johnson is an inaugural class member. “OSE uniquely encourages graduate projects on ocean-related research that bridge the disciplinary divides between marine science and engineering,” Glass says. 

The impact of clathrates on climate science 

For Johnson, the study afforded her an opportunity to offer a better understanding of clathrates, which have trapped methane under the ocean floor and deep in the Arctic permafrost.

Clathrates “basically occur anywhere there is low temperature, high pressure, water, and sufficient gas concentrations,” Johnson says. “Gigatons of methane, a known potent greenhouse gas, are stored in gas clathrates. A warming global climate could cause clathrate dissociation, potentially leading to a disastrous snowball effect. This is why it’s so critical that we have a firm understanding on the forces controlling clathrate stability.”

Johnson says the role microbiology plays in that stability is important to consider but has not been well researched. “Our study elucidates a potential role that bacteria have in stabilizing gas clathrates by producing CBPs (clathrate binding proteins). We found that CBPs bind and significantly change the morphology of the clathrate structure, which hints at a potential role in stability. Our future research will help us determine if these CBPs work to inhibit or nucleate (crystallize) gas clathrate. We hypothesize that CBPs are secreted by bacteria into their fluid habitat within the clathrate, and then bind to the clathrate, thereby inhibiting further clathrate growth; this mechanism would allow the bacteria to maintain their fluid habitat."

The Weitz Group at Georgia Tech has created various models and figures to help explain the spread and epidemiology of Covid-19. Weitz has frequently shared his findings with local and national media outlets.

This year marked the fourth annual “Quantitative Biosciences Hands-On Modeling Workshop”. Due to Covid-19, the summer 2020 event was held virtually. Focused on the basics of epidemic modeling, the workshop was joined by more than 50 online attendees from around the globe. 

Weitz delivered two lectures on epidemic theory and the latest Covid-19 research. In addition, ten QBioS students, two post-doctoral scientists from the Weitz group (David Demory and Stephen Beckett), and one external post-doctoral scientist (Bradford Taylor) served as instructors for small group sessions, focusing on the hands-on experience of coding deterministic and stochastic models to predict the spread of epidemics.

The QBioS Ph.D. student organizers collected surveys following the event, which provided feedback on both the content and format of the workshop. Some examples:

“The flow of the workshop is great. Learning introductory concepts to start, the ability to apply some of them with hands-on, and then finishing with applications and extensions. Having many participants from many backgrounds adds a lot to the small group sessions as well.”

“I thought it was a great workshop to get core concepts across. I think the online format was done as best as possible and appreciated the thoughtful instructors.”

Weitz and Pablo Bravo, a second year QBioS Ph.D. student in Quantitative Biosciences, share thoughts on how they ran the virtual workshop — along with ideas and advice for those looking to host similar online workshops:

What were the biggest lessons learned from your summer workshop?

Weitz: The survey results communicated two important lessons. First, positive
responses to the workshop structure reinforce just how critical it is to contextualize modeling in terms of a key biological challenge. Providing a biological scaffold helps to focus student work and keep their interest and attention on the technical material. The second lesson is that there is an adaptation period to hands-on learning online. We intentionally spaced out the coding sessions with a mid-day break and most of the issues appeared in the morning as students and instructors adjusted to their group's dynamic, including debugging code while in different locations, and indeed, countries. 

Bravo: One aspect that made the workshop possible was the participation of many members in different roles: coordinators, advertising, lecturers, instructors, IT support.  Planning and working early as a team were essential.

What were the biggest challenges you had to overcome?

Bravo: There were two main problems that we had to solve. First, we offered support for three programming languages (MATLAB, Python, R), and given the high number of registrations, the first year QBioS cohort couldn't handle all of them. Members of the QBioS community, current and past members of the Weitz group stepped in and helped us in leading activity groups. It wouldn't have been possible without them!

Also, debugging was an issue. Debugging scripts over video calls was extremely difficult. Attendees were not keen on screen-sharing their code at the beginning, but as they got to know each other, this stopped being an issue. Delay between the video and audio feed remained an issue throughout the whole workshop.

What’s the one takeaway you want to stress to instructors looking to offer similar webinars and online workshops?

Weitz: Overall, we are optimistic about our ability to continue to develop and implement innovative teaching strategies in QBioS — but remain realistic that adjustment periods will be needed to foster an atmosphere conducive to small group learning when groups are dispersed.

Bravo: I think the biggest factor in the success of the workshop is that it was centered around interactive activity sessions, in which five students and an instructor would go through the material and write the scripts together. This promoted both active learning and discussion between the attendees, and also allowed attendees to follow up with questions and comments to their respective instructors ­­— even days after the workshop finalized.

For many researchers, the answer lies within the ‘RNA World,’ a widely-accepted hypothesis in which self-replicating RNA proliferated, serving a dual role as both genetic polymer and catalytic polymer, long before the evolution of DNA and protein.

The RNA World model is an attractive cradle-of-life premise, according to Georgia Institute of Technology researcher Moran Frenkel-Pinter, “because it avoids the extreme improbability of simultaneous independent origins of two different types of polymers. According to that theory, over time the RNA World incrementally invented the ribosome, giving rise to the current biological system comprised of RNA, DNA, and protein.”

She adds, “it’s kind of a parsimonious idea, basically saying that RNA made everything. But there is a much simpler solution.” Frenkel-Pinter and her research partners have offered an alternative – the concerted evolution of polymers – of nucleic acids and proteins. “A Ribonucleoprotein World,” quips Frenkel-Pinter, a research scientist and former NASA Postdoctoral Fellow who works in the labs of Nick Hud and Loren Williams at Georgia Tech, and is the lead author of a recently published paper that provides experimental support for this model.

The paper, “Mutually stabilizing interactions between proto-peptides and RNA,” in the journal Nature Communications, describes the chemical linkage that could have been at play during the origins of biopolymers. Their results suggest that neither nucleic acids or proteins came first, but that RNA and proteins were selected together through a process of co-evolution. In other words, it wasn’t a single selfish gene competing for survival that drove evolution; it was the rising tide of collaboration between molecules from the very beginning.

“People have wondered, ‘was it protein first, was it nucleic acid first?’ This work says is, they were connected from early on,” says co-author Hud, regents professor in the School of Chemistry and Biochemistry, director of the NSF/NASA Center for Chemical Evolution, and associate director of the Petit Institute for Bioengineering and Bioscience.

So, there was more interdependence than independence underlying the machinery of early life. Or as co-author and Petit Institute researcher Williams puts it, “it isn’t really an independent dog eat dog world. You have systems working together – birds that eat the bugs off zebras, microbes in our gut, plants that make the oxygen we breathe.”

The researchers hypothesized that positively-charged (cationic) proto-peptides might functionally interact with nucleic acids, and then experimentally prove it. The cationic proto-peptides (either produced as mixtures from plausibly prebiotic dry-down reactions or synthetically prepared) directly interact with RNA, resulting in mutual stabilization: The proto-peptides significantly increase the thermal stability of folded RNA structures, and in turn, RNA increases the lifetime of the proto-peptide.

“There are all kinds of mutualistic relationships in biology, and we’re saying that maybe molecules work this way, too – the origin of life was matter of molecules working together,” says Williams, professor in the School of Chemistry and Biochemistry and director of the NASA Center for the Origin of Life at Tech.

Ultimately, the research team determined that collaborative molecules are the molecules that survived.

“It’s like the difference between a jungle and a cornfield,” says Williams. “The RNA World model is kind of like a cornfield in Ohio. Under certain circumstances, it works well – for example, Ohio grows a lot of corn. We’re looking at the origin of life like it was a jungle – a jungle of molecules interacting, working together for mutual benefit.”

In addition to Frenkel-Pinter, Hud, and Williams, the other authors were: Jay Haynes (graduate researcher in Williams lab); Ahmad Mohyeldin (graduate researcher in Williams lab), Martin C (graduate researcher in Hud lab), Alyssa Sargon (undergraduate researcher in Hud lab), Anton Petrov (research scientist, School of Chemistry and Biochemistry), Ramanarayanan Krishnamurthy (associate professor, Scripps Research Institute), Luke Leman (assistant professor, Scripps Research Institute). The work was supported by the NSF and NASA Astrobiology Program under the Center for Chemical Evolution (based at Georgia Tech).

An interactive dashboard that estimates Covid-19 incidence at gatherings in the U.S. has added a new feature: the ability to calculate county-level risk of attending an event with someone actively infected with Coronavirus (Covid-19). Previously, the dashboard estimated exposure for different size events by state.

The new “Covid-19 Event Risk Assessment Planning Tool” is the work of Joshua Weitz, professor in the School of Biological Sciences and founding director of Georgia Tech’s Ph.D. in Quantitative Biosciences program, in collaboration with the lab of Clio Andris, an assistant professor in the School of City and Regional Planning with a joint appointment in the School of Interactive Computing at Georgia Tech, and with researchers from the Applied Bioinformatics Laboratory (a public/private partnership between Georgia Tech, IHRC Inc., and ASRT Inc.).

“We have developed an interactive county-level map of the risk that one or more individuals may have Covid-19 in events of different sizes,” Weitz says. “The issue of understanding risks associated with gatherings is even more relevant as many kinds of businesses, including sports and universities, are considering how to re-open safely.”

The dashboard accounts for widespread gaps in U.S. testing for the Coronavirus, which can silently spread through individuals who display mild or no symptoms of illness. “Precisely because of under-testing and the risk of exposure and infection, these risk calculations provide further support for the ongoing need for social distancing and protective measures. Such precautions are still needed even in small events, given the large number of circulating cases,” states the dashboard’s website.

For example: As of Monday, July 6, for an event with 100 attendees in Fulton County, Georgia, the estimated risk of someone in attendance being actively infected with Coronavirus is 76 percent. For that same day at an event with 1,000 attendees, the estimated risk in all but 16 of Georgia’s 159 counties exceeds 99 percent.

The dashboard’s technical development was made possible by contributions from Seolha Lee, a master’s student in Andris' group, and Aroon Chande, a Ph.D. candidate in Bioinformatics at Georgia Tech.

The dashboard’s website, which is updated daily, incorporates data from The New York Times case count and Covidtracking.com dashboard (a resource led by journalist Alexis Madrigal of The Atlantic). Both of these databases record confirmed case reports from state-level departments of public health.

“The Covid-19 Event Risk Assessment Planning Tool takes the number of cases reported in the past 14 days in each county, and multiplies these by an under-testing factor to estimate the number of circulating cases in a particular county,” Weitz explains. (In late June, Robert Redfield, director of the U.S. Centers for Disease Control and Prevention (CDC), stated on a press call that “now that serology tests are available, which test for antibodies, the estimates we have right now show about 10 times more people have antibodies in the jurisdictions tested than had documented infections.”)

Tracking tools developed earlier this year by Weitz and colleagues at Georgia Tech and other institutions are also factored into the team’s new county-level calculator. “The model is simple, intentionally so, and provided context for the rationale to halt large gatherings in early-mid March and newly relevant context for considering when and how to re-open,” states the dashboard website.

At this time of year, the Georgia Tech campus would typically be buzzing with the activity of students and Institute staff. However, the campus is currently closed to everyone apart from those involved in essential activities. This includes the activity of a group of astrobiologists who are hard at work on research efforts to help aid with Covid-19 response.

Over the years, the Astrobiology Program has supported a number of projects at Georgia Tech. This includes the Center for Chemical Evolution (CCE), a joint program between the National Science Foundation (NSF) and NASA Astrobiology, as well as a team of the former NASA Astrobiology Institute (NAI). Today, NASA Astrobiology continues to support many scientists at the Institute across a wide range of topics, including prebiotic chemistry and the origin of life, evolution and the early Earth environment, and studies on the potential habitability of icy moons. Each of these researchers is contributing to our knowledge of the origins of life and the potential for life in the Universe. In the past few months, they have used their expertise to aid in our country’s healthcare response here at home.

Alongside their work supported by the NASA Astrobiology Program, this team has expanded their laboratory efforts to include the production of biochemical components for Covid-19 test kits. The researchers are part of the State of Georgia Covid-19 Lab Surge Capacity Task Force, and they are collaborating with a number of other university labs across the state of Georgia. The work of these dedicated scientists is helping to address gaps in the supply of testing kits that provide a vital step in identifying people who are carriers of the virus and may need care, or individuals who may need to remain isolated from other people even though they are asymptomatic.

Astrobiology at Georgia Tech

Loren Williams (School of Chemistry and Biochemistry) is leading the Georgia Tech Test Kit Support Group. Williams is currently a Co-Lead of an Astrobiology Program Research Coordination Network (RCN) dubbed the Prebiotic Chemistry and Early Earth Environment Consortium (PCE₃). He also serves as Director of the NASA-funded Center for the Origin of Life (COOL). Additional principal investigators supported by the Astrobiology Program who are part of the initiative include Jennifer Glass (School of Earth and Atmospheric Sciences), who is also on the steering committee of the Network for Ocean Worlds RCN and a co-lead on the NASA-funded Oceans Across Space and Time, and Nicholas Hud (School of Chemistry and Biochemistry) a current PI with the Exobiology Program and steering committee member for the PCE₃ RCN.

“Research scientists, grad students, technicians, and postdocs in biochemistry labs at Georgia Tech have been working around the clock,” said Jennifer Glass. “They are the real heroes here. They include many astrobiologists from Loren Williams’ lab including Jessica Bowman, Anton Petrov, Brooke Rothschild-Mancinelli, Petar Penev, Rebecca Guth-Metzler, Kavita Matange, Santi Mestre-Fos, Sara Fakhretaha-Aval, and Moran Frenkel-Pinter, as well as Chiamaka Obianyor, a PhD candidate in Nick Hud and Martha Grover’s lab. Another is Justin Lawrence, an astrobiology PhD candidate in Britney Schmidt’s lab, who working on testing different disinfectants for masks.”

The work of Justin Lawrence and the team of scientists supported by the NASA Astrobiology program was also featured in a recent story from National Geographic.

The team at Georgia Tech is making components for test kits that work using a reaction called the ‘reverse transcription quantitative-polymerase chain reaction (RT-qPCR).’ This reaction is used to identify the presence of small amounts of viral RNA in samples from a patient by taking that RNA and converting it to DNA. The DNA is then amplified by PCR and tagged with fluorescent probes, making it easy to spot.

“Raquel Lieberman is a protein chemist at Georgia Tech who is also a Co-I on my current NASA Exobiology grant,” said Glass. “In addition to us writing an exciting manuscript on our NASA project, she’s also an integral member of the Georgia Tech Test Kit Support Group. Her lab members are making the essential enzyme and protein components for the kit: reverse transcriptase, DNA polymerase, and ribonuclease inhibitor.”

The reverse transcriptase enzyme that Lieberman makes is the RTX enzyme developed by Andrew Ellington and his team at the University of Texas at Austin. This enzyme was developed in 2016 and has unique properties that allow scientists to replicate DNA and RNA faster and more accurately in the lab than previously before. (Further information on the RTX enzyme can be found in the accompanying article: Astrobiologists Aid in Fighting Coronavirus.)

“So far, the team has successfully synthesized, purified, and quality controlled the primers and primer-probes used in the reactions,” explained Glass. “These are [components of] the most common [test kits] currently being used in the US, but other types of tests that can give results in less time are coming online, and we might switch to working on those methods in the future.”

From Astrobiology to Virology

In utilizing their astrobiology skills to focus on the global pandemic, the team at Georgia Tech has faced a number of logistical challenges. As researchers continue their work in the laboratory, care is taken to make sure safety procedures are in line with recommendations from the Centers for Disease Control and Prevention (CDC). The team has remained connected by video chat, with each member performing tasks in isolation. An electronic ‘buddy system’ has been implemented so that the scientists, while isolated, still have access to emergency help if necessary.

“Research scientists, grad students, technicians, and postdocs in biochemistry labs at Georgia Tech are the ones doing the bulk of the work,” said Glass. “But they are social distancing, and all of the meetings are virtual. I miss the days when we could all talk science together on campus.”

The efforts of the team have required researchers to quickly adapt and learn new skills, expanding their work to research beyond their typical fields of expertise.

The research, reported May 29 in the journal Heart Rhythm, found that the drug made it “surprisingly easy” to trigger worrisome arrhythmias in two types of animal hearts by altering the timing of the electrical waves that control heartbeat. While the findings of animal studies can’t necessarily be generalized to humans, the videos created by the research team clearly show how the drug can cause cardiac electrical signals to become dysfunctional.

“We have illustrated experimentally how the drug actually changes the waves in the heart, and how that can initiate an arrhythmia,” said Flavio Fenton, a professor in the School of Physics at the Georgia Institute of Technology and the paper’s corresponding author. “We have demonstrated that with optical mapping, which allows us to see exactly how the waveform is changing. This gives us a visual demonstration of how the drug can alter the wave propagation in the heart.”

What the team saw was an elongation of the T wave, a portion of the heart cycle during which voltages normally dissipate in preparation for the next beat. By extending the QT portion of one wave cycle, the drug sets the stage for disturbances in the next wave, potentially creating an arrhythmia. Such disturbances can transition to fibrillation that interferes with the heart’s ability to pump.

The ability to easily trigger disturbances known as “long QT” reinforces cautions about using hydroxychloroquine (HCQ) in humans – particularly in those who may have heart damage from Covid-19, cautioned Dr. Shahriar Iravanian, a co-author of the paper and a cardiologist in the Division of Cardiology, Section of Electrophysiology, at Emory University Hospital.

“The hearts used in the study are small and very resistant to this form of arrhythmia,” Iravanian said. “If we had not seen any HCQ-induced arrhythmias in this model, the results would not have been reassuring. However, in reality, we observed that HCQ readily induced arrhythmia in those hearts. This finding is very concerning and, in combination with the clinical reports of sudden death and arrhythmia in Covid-19 patients taking HCQ, suggests that the drug should be considered a potentially harmful medication and its use in Covid-19 patients be restricted to clinical trial settings.”

Georgia Tech postdoctoral fellow Ilija Uzelac administered HCQ to the animal hearts – one from a guinea pig and one from a rabbit – while quantifying wave patterns changing across the hearts using a high-powered, LED-based optical mapping system. Voltage-sensitive fluorescent dyes made the electrical waves visible as they moved across the surface of the hearts.

“The effect of the arrhythmia and the long QT was quite obvious,” said Uzelac. “HCQ shifts the wavelengths to larger values, and when we quantified the dispersion of the electrical current in portions of the heart, we saw the extension of the voltage across the tissue. The change was very dramatic comparing the waveforms in the heart with and without the HCQ.”

The drug concentration used in the study was at the high end of what’s being recommended for humans. HCQ normally takes a few days to accumulate in the body, so the researchers used a higher initial dose to simulate the drug’s effect over time.

In a normal heartbeat, an electrical wave is generated in specialized cells of a heart’s right atrium. The wave propagates through the entire atria and then to the ventricles. As the wave moves through the heart, the electrical potential created causes calcium ions to be released, which stimulates contraction of the heart muscle in a coordinated pattern.

Drugs such as HCQ modify the properties of these ion channels and inhibit the flow of potassium currents, which prolongs the length of the electrical waves and creates spatial variations in their properties. Ultimately, that can lead to the development of dangerously rapid and dysfunctional heart rhythms.

“The wavelength becomes less homogeneous and that affects the propagation of additional waves, producing sections of the heart where the waves do not propagate well,” Fenton said. “In the worst case, there are multiple waves going in different directions. Every section of the heart is contracting at a different time, so the heart is just quivering. At that point, it can no longer pump blood throughout the body.”

Patients taking HCQ for diseases such as lupus and rheumatoid arthritis rarely suffer from arrythmia because the doses they take are smaller than those being recommended for Covid-19 patients, Iravanian said.

“Covid-19 patients are different and are at a much higher risk of HCQ-induced arrhythmia,” he said. “Not only is the proposed dose of HCQ for Covid-19 patients two to three times the usual dose, but Covid-19 has effects on the heart and lowers potassium levels, further increasing the risk of arrythmias.”

Fenton and his colleagues have already begun a new study to evaluate the effects of HCQ with the antibiotic azithromycin, which has been suggested as a companion treatment. Azithromycin can also cause the long QT effect, potentially increasing the impact on Covid-19 patients.

The study, which was supported by grants from the National Institutes of Health and National Science Foundation, was also coauthored by Dr. Hiroshi Ashikaga from Johns Hopkins University School of Medicine; Dr. Neal Bathia from the Division of Cardiology, Section of Electrophysiology at Emory University Hospital; Conner Herndon, Abouzar Kaboudian, and James C. Gumbart from the Georgia Tech School of Physics, and Elizabeth Cherry from the Georgia Tech School of Computational Science and Engineering.

This research is supported by the National Institutes of Health under award number 1R01HL143450-01 and the National Science Foundation under grant 1446675. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or the National Science Foundation.

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As populations of P. aeruginosa swell, they often aggregate into slimy biofilms that stick to one another and to various surfaces, from medical equipment to airways in the lungs and onto other organs. Thriving in humid environments, the bacteria can create chronic infections that are notoriously resistant to antibiotic treatment.

The pathogen is especially dangerous for cystic fibrosis patients. This genetic disease leads to an overproduction of thick mucus, which provides good growth conditions for microbes like P. aeruginosa, which can then produce antibiotic-resistant biofilms — blankets of microorganisms that cover lung tissue and provide a host environment for more damaging pathogens.

A team of Georgia Tech researchers from the School of Biological Sciences has released a study that points to another problem with Pseudomonas aeruginosa: in a synthetic media that mimics cystic fibrosis sputum, populations of cells can quickly evolve to develop tolerance and resistance to certain antibiotics — despite having no previous exposure to them.

“We were surprised that the antibiotic tolerance increased so quickly in our experiment” says Sheyda Azimi, a Cystic Fibrosis Foundation Postdoctoral Fellow. “What our data tells us is that in a single species evolved population, with a mixture of diverse single isolates, becomes antibiotic tolerant even without the selective pressure of antibiotics.”

Azimi and four fellow School of Biological Sciences scientists – Steve Diggle (who served as Georgia Tech's lead in developing the project), Joshua Weitz, Samuel Brown, and graduate student Shengyun Peng, have published the results of their study, “Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations,” in The ISME Journal, the official journal of the International Society of Microbial Ecology. The team also includes two researchers from Swansea University Medical School and The University of Birmingham.

Azimi says the increase in tolerance to antibiotics is due to changes in the function of key genes that control social trait production in P. aeruginosa. “Simply put, the changes in population dynamics leads to the tolerance phenotype, so if the P. aeruginosa populations evolve in a chemical environment similar to lungs of individuals with cystic fibrosis, it can display the same phenotype of increased tolerance to certain antibiotics.” Those include beta-lactam antibiotics, one of the most commonly prescribed classes of clinical antibiotics, and the type researchers used in the study.

Even though P. aeruginosa is a well-studied microbe, fewer studies have explored its heterogeneity, or the diversity in its traits and characteristics, and how that diversity helps its cells communicate with one another. The team’s study sought to better understand these social behaviors and how they can influence the microbe’s development and evolution.

The team evolved P. aeruginosa in biofilms, growing the bacteria in a synthetic sputum medium, meant to mimic a mixture of saliva and mucus, for 50 days. “We measured social trait production and antibiotic tolerance, and used a metagenomic approach to analyze and assess genomic changes over the duration of the evolution experiment,” she writes in the article’s abstract (metagenomics is the study of genetic material recovered directly from environmental samples). The team found that evolutionary trajectories were reproducible in independently evolving populations, and that over 60% of that genomic diversity occurred within the first 10 days of selection.

The study showed emergent behavior and interesting interactions between different evolved isolates of P. aeruginosa — co-existing alongside each other and acting as one functional entity.  “You can imagine a team where each individual is equipped with particular skills,” says Azimi. “Not all members need to be the best at all functions. Some members of the team may produce lots of toxins, whereas some may be better at forming biofilms or resisting antibiotics. Put together they function more effectively as a unit.”

Azimi emphasizes that these interactions take place within a diverse population of the same species, a community that has evolved from a single ancestor. “The individuals are not teaching each other. I would call it more of ‘hand-waving’; they actually signal to and sense one another, and evolve in a certain way that appears to benefit the whole group.”

Learn more about Azimi’s work, sociomicrobiology, and The Diggle Lab at Georgia Tech.

The research team thanks the following funding sources: The Human Frontier Science Program (RGY0081/2012) and Georgia Institute of Technology, The Cystic Fibrosis Foundation (DIGGLE18I0) to SPD, Cystic Fibrosis Foundation for a Fellowship to SA (AZIMI18F0), and CF@latna for a Fellowship to SA (3206AXB). The team also thanks the National Heart Lung Blood Institute (R56HL142857) and The Simons Foundation (396001). 

Studying bacteria in a petri dish or test tube has yielded insights into how they function and, in some cases, contribute to disease. But this approach leaves out crucial details about how bacteria act in the real world.

Taking a translational approach, researchers at the University of Pennsylvania School of Dental Medicine and the Georgia Institute of Technology imaged the bacteria that cause tooth decay in three dimensions in their natural environment, the sticky biofilm known as dental plaque formed on toddlers’ teeth that were affected by cavities.

The work, published in the journal Proceedings of the National Academy of Sciences, found that Streptococcus mutans, a major bacterial species responsible for tooth decay, is encased in a protective multilayered community of other bacteria and polymers forming a unique spatial organization associated with the location of the disease onset.

“We started with these clinical samples, extracted teeth from children with severe tooth decay,” says Hyun (Michel) Koo of Penn Dental Medicine, a co-senior author on the work. “The question that popped in our minds was, how these bacteria are organized and whether their specific architecture can tell us about the disease they cause?”

To address this question, the researchers, including lead author Dongyeop Kim of Penn Dental Medicine and co-senior author Marvin Whiteley of Georgia Tech, used a combination of super-resolution confocal and scanning electron microscopy with computational analysis to dissect the arrangement of S. mutans and other microbes of the intact biofilm on the teeth. These techniques allowed the team to examine the biofilm layer by layer, gaining a three-dimensional picture of the specific architectures.

This approach, of understanding the locations and patterns of bacteria, is one that Whiteley has pursued in other diseases. 

“It’s clear that identifying the constituents of the human microbiome is not enough to understand their impact on human health,” Whiteley says. “We also have to know how they are spatially organized. This is largely under studied as obtaining intact samples that maintain spatial structure is difficult.”  

In the current work, the researchers discovered that S. mutans in dental plaque most often appeared in a particular fashion: arranged in a mound against the tooth’s surface. But it wasn’t alone. While S. mutans formed the inner core of the rotund architecture, other commensal bacteria, such as S. oralis, formed additional outer layers precisely arranged in a crownlike structure. Supporting and separating these layers was an extracellular scaffold made of sugars produced by S. mutans, effectively encasing and protecting the disease-causing bacteria.

“We found this highly ordered community with a dense accumulation of S. mutans in the middle surrounded by these ‘halos’ of different bacteria, and wondered how this could cause tooth decay,” Koo says. “

To learn more about how structure impacted the function of the biofilm, the research team attempted to recreate the natural plaque formations on a toothlike surface in the lab using S. mutans, S. oralis, and a sugar solution. They successfully grew the formations, with rotund-shaped architecture and crown-like structure, and then measured levels of acid and demineralization associated with them. 

“What we discovered, and what was exciting for us, is that the rotund areas perfectly matched with the demineralized and high acid levels on the enamel surface,” says Koo. “This mirrors what clinicians see when they find dental caries: punctuated areas of decalcification known as ‘white spots.’ The crown-like structure could explain how cavities get their start.” 

In a final set of experiments, the team put the community to the test, applying an antimicrobial treatment and observing how the bacteria fared. When the crown-like structures were intact, the S. mutans in the inner core largely avoided dying from the antimicrobial treatment. Only breaking up the scaffolding material holding the outer layers together enabled the antimicrobial to penetrate and effectively kill the cavity-causing bacteria.

The study’s findings may help researcher more effectively target the pathogenic core of dental biofilms but also have implications for other fields.

“It demonstrates that the spatial structure of the microbiome may mediate function and the disease outcome, which could be applicable to other medical fields dealing with polymicrobial infections,” says Koo. 

“It’s not just which pathogens are there but how they’re structured that tells you about the disease that they cause,” adds Whiteley. “Bacteria are highly social creatures and have friends and enemies that dictate their behaviors.” 

The field of microbial biogeography is young, the researchers say, but extending this demonstration that links community structure with disease onset opens up a vast array of possibilities for future medically relevant insights.

Dongyeop Kim was a research associate at Penn’s School of Dental Medicine’s Department of Orthodontics and is now an assistant professor at the Jeonbuk National University (Korea).

Hyun (Michel) Koo is a professor in Penn’s School of Dental Medicine’s Department of Orthodontics in the divisions of Community Oral Health and Pediatric Dentistry.

Marvin Whiteley is a professor of biological sciences, the Georgia Tech Bennie H. and Nelson D. Abell Chair in Molecular and Cellular Biology, and the Georgia Research Alliance Eminent Scholar co-director in Emory-Children’s CF Center at the Georgia Institute of Technology.

Koo, Kim, and Whiteley’s coauthors were Penn Dental Medicine’s Rodrigo A. Arthur, Yuan Liu, Elizabeth L. Scisci, and Evlambia Hajishengallis; Georgia Tech’s Juan P. Barraza; and Indiana University’s Anderson Hara and Karl Lewis.

The work was supported in part by the National Institute for Dental and Craniofacial Research (grants DE025220, DE018023, DE020100, and DE023193).

Built with wheeled appendages that can be lifted and wheels able to wiggle, a new robot known as the “Mini Rover” has developed and tested complex locomotion techniques robust enough to help it climb hills covered with such granular material – and avoid the risk of getting ignominiously stuck on some remote planet or moon. 

Using a complex move the researchers dubbed “rear rotator pedaling,” the robot can climb a slope by using its unique design to combine paddling, walking, and wheel spinning motions. The rover’s behaviors were modeled using a branch of physics known as terradynamics.

“When loose materials flow, that can create problems for robots moving across it,” said Dan Goldman, the Dunn Family Professor in the School of Physics at the Georgia Institute of Technology. “This rover has enough degrees of freedom that it can get out of jams pretty effectively. By avalanching materials from the front wheels, it creates a localized fluid hill for the back wheels that is not as steep as the real slope. The rover is always self-generating and self-organizing a good hill for itself.”

The research was reported on May 13 as the cover article in the journal Science Robotics. The work was supported by the NASA National Robotics Initiative and the Army Research Office.

A robot built by NASA’s Johnson Space Center pioneered the ability to spin its wheels, sweep the surface with those wheels and lift each of its wheeled appendages where necessary, creating a broad range of potential motions. Using in-house 3D printers, the Georgia Tech researchers collaborated with the Johnson Space Center to re-create those capabilities in a scaled-down vehicle with four wheeled appendages driven by 12 different motors.

“The rover was developed with a modular mechatronic architecture, commercially available components, and a minimal number of parts,” said Siddharth Shrivastava, an undergraduate student in Georgia Tech’s George W. Woodruff School of Mechanical Engineering. “This enabled our team to use our robot as a robust laboratory tool and focus our efforts on exploring creative and interesting experiments without worrying about damaging the rover, service downtime, or hitting performance limitations.” 

The rover’s broad range of movements gave the research team an opportunity to test many variations that were studied using granular drag force measurements and modified Resistive Force Theory. Shrivastava and School of Physics Ph.D. candidate Andras Karsai began with the gaits explored by the NASA RP15 robot, and were able to experiment with locomotion schemes that could not have been tested on a full-size rover.

The researchers also tested their experimental gaits on slopes designed to simulate planetary and lunar hills using a fluidized bed system known as SCATTER (Systematic Creation of Arbitrary Terrain and Testing of Exploratory Robots) that could be tilted to evaluate the role of controlling the granular substrate. Karsai and Shrivastava collaborated with Yasemin Ozkan-Aydin, a postdoctoral research fellow in Goldman’s lab, to study the rover motion in the SCATTER test facility. 

“By creating a small robot with capabilities similar to the RP15 rover, we could test the principles of locomoting with various gaits in a controlled laboratory environment,” Karsai said. “In our tests, we primarily varied the gait, the locomotion medium, and the slope the robot had to climb. We quickly iterated over many gait strategies and terrain conditions to examine the phenomena that emerged.”

In the paper, the authors describe a gait that allowed the rover to climb a steep slope with the front wheels stirring up the granular material – poppy seeds for the lab testing – and pushing them back toward the rear wheels. The rear wheels wiggled from side-to-side, lifting and spinning to create a motion that resembles paddling in water. The material pushed to the back wheels effectively changed the slope the rear wheels had to climb, allowing the rover to make steady progress up a hill that might have stopped a simple wheeled robot.

The experiments provided a variation on earlier robophysics work in Goldman’s group that involved moving with legs or flippers, which had emphasized disturbing the granular surfaces as little as possible to avoid getting the robot stuck.

“In our previous studies of pure legged robots, modeled on animals, we had kind of figured out that the secret was to not make a mess,” said Goldman. “If you end up making too much of a mess with most robots, you end up just paddling and digging into the granular material. If you want fast locomotion, we found that you should try to keep the material as solid as possible by tweaking the parameters of motion.”

But simple motions had proved problematic for Mars rovers, which got stuck in granular materials. Goldman says the gait discovered by Shrivastava, Karsai and Ozkan-Aydin might be able to help future rovers avoid that fate.

“This combination of lifting and wheeling and paddling, if used properly, provides the ability to maintain some forward progress even if it is slow,” Goldman said. “Through our laboratory experiments, we have shown principles that could lead to improved robustness in planetary exploration – and even in challenging surfaces on our own planet.”

The researchers hope next to scale up the unusual gaits to larger robots, and to explore the idea of studying robots and their localized environments together. “We’d like to think about the locomotor and its environment as a single entity,” Goldman said. “There are certainly some interesting granular and soft matter physics issues to explore.”

Though the Mini Rover was designed to study lunar and planetary exploration, the lessons learned could also be applicable to terrestrial locomotion – an area of interest to the Army Research Laboratory, one of the project’s sponsors.

"This basic research is revealing exciting new approaches for locomotion in complex terrain," said Dr. Samuel Stanton, program manager, Army Research Office, an element of the U.S. Army Combat Capabilities Development Command's Army Research Laboratory. "This could lead to platforms capable of intelligently transitioning between wheeled and legged modes of movement to maintain high operational tempo."

Beyond those already mentioned, the researchers worked with Robert Ambrose and William Bluethmann at NASA, and traveled to NASA JSC to study the full-size NASA RP15 rover.

This work was supported by the Army Research Office (W911NF-18-1-0120) and the NASA National Robotics Initiative (NNX15AR21G). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the sponsoring agencies.

CITATION: Siddharth Shrivastava, Andras Karsai, Yasemin Ozkan-Aydin, Ross Pettinger, William Bluethmann, Robert O. Ambrose, Daniel I. Goldman, “Material remodeling on granular terrain yields robustness benefits for a robophysical rover.” (Science Robotics, May 2020)

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Weitz, a professor in the School of Biological Sciences and Director of the Interdisciplinary Ph.D. in Quantitative Biosciences, was recognized for those efforts this spring with the Faculty of the Year Award from the Graduate Student Government Association (SGA).

The first student fees were $100 per semester. In Fall 2019, Weitz drafted and presented a resolution before the Faculty Senate detailing how the graduate student fee, now totaling $1,000 per fall and spring semester, was a major concern for the students. “While the faculty have been generally supportive of this cause, this was the first time that the Faculty Senate went on record to acknowledge the issue,” says Narayan Shirolkar, Graduate SGA president, in an email to School of Biological Sciences Chairman Todd Streelman announcing the award. “He (Weitz) has been ardent advocate for graduate students, raising this issue through social media, and has contributed to numerous public articles on this topic, including an op-ed in The Atlanta Journal Constitution in March 2019.”

“It is an honor to be recognized by the Georgia Tech community of graduate students,” Weitz says. “I am deeply grateful for the critical contributions that graduate students make to Georgia Tech's research, teaching, and entrepreneurship missions. I am also particularly proud of their collective service and action-taking in the past year, whether as members of the SGA, or as concerned students acting of their own accord, to raise awareness on the critical need to reduce fees and improve graduate student financial well-being. I remain optimistic that progress this past year will mark a change point towards long-term improvements to support graduate students at Georgia Tech in the broadest sense.”

Weitz’s research team, the Weitz Group @ Georgia Tech, studies theoretical ecology and quantitative biology. The group is working collaboratively with researchers at Tech and around the globe on several projects related to COVID-19 modeling and response efforts.

The presumed immunity of those who have recovered from the infection could allow them to safely substitute for susceptible people in certain high-contact occupations such as healthcare. Dubbed “shield immunity,” the anticipated protection against short-term reinfection could allow recovered patients to expand their interactions with infected and susceptible people, potentially reducing overall transmission rates when interactions are permitted to expand. 

New modeling of the virus’ behavior suggests that an intervention strategy based on shield immunity could reduce the risk of allowing the higher levels of human interaction needed to support expanded economic activity. The number of Americans infected by the novel coronavirus is likely much higher than what has been officially reported, and that could be good news for efforts to utilize their presumed immunity to protect the larger community.

However, there are two important caveats to the strategy. The first is that the duration of immunity to reinfection by SARS-CoV-2 remains unknown; however, individuals who survived infections by related viral infections, like SARS, had persistent antibodies for approximately two years – and those who survived infection to MERS had evidence of immunity for approximately three years. The second issue is that determining on a broad scale who has antibodies that may protect them from the coronavirus will require a level of reliable serological testing not yet available in the United States. 

“Our model describes ways in which serological tests used to identify individuals who have been infected by and recovered from COVID-19 could help both reduce future transmission and foster increased economic engagement,” said Joshua Weitz, professor in the School of Biological Sciences and founding director of the Interdisciplinary Ph.D. in Quantitative Biosciences at the Georgia Institute of Technology. “The idea is to think in advance about how identifying recovered individuals could help serve the collective good, using information collected on neutralizing antibodies in new ways.”

A paper describing the modeling behind the concept of shield immunity was published May 7 in the journal Nature Medicine by a team of researchers from Georgia Tech, Princeton University and McMaster University. The researchers studied the potential impacts of presumed immunity among recovered persons using a computational model of COVID-19 epidemiological dynamics, building upon a SEIR (susceptible-exposed-infectious-recovered) framework.

In a population of 10 million citizens, for example, the model predicts that in a worst-case transmission scenario, implementation of an intermediate shielding strategy could help reduce deaths from 71,000 to 58,000, while an enhanced shielding plan could cut deaths from 71,000 to 20,000. The model also suggests that shielding could enhance the effects of social distancing strategies that may remain in place once higher levels of economic activity resume.

Identification of individuals who have protective antibodies against the novel coronavirus has begun only recently. Antibody tests are not 100% specific, implying that tests can lead to false positives. However, targeted use of antibody testing in groups with elevated exposure will lead to increases in positive predictive value, even with imperfect tests. The serological antibody test differs from widespread polymerase chain reaction (PCR) testing being done to determine whether people are actively infected with the virus. 

Among healthcare professionals, serological testing could identify recovered individuals who might then be able to interact with patients with reduced concern for infection. Other recovered individuals could be used to help reduce transmission risk in nursing homes, the food service industry, emergency medical services, grocery stores, retailing and other essential operations. Across society, the relatively small number of individuals with immunity could substitute for people whose immunity status isn’t known; reducing transmission risk both for recovered individuals and those who remain immunologically naive. 

“We want to think about serology as an intervention,” Weitz said. “Finding out who is immune to the coronavirus could make a big difference in trying to reduce the risk to people who would be vulnerable by interacting with someone who could pass on the disease.”

Serological testing to identify those with immunity might begin with healthcare workers, who may be more likely to have been infected by the coronavirus because of their exposure to infected persons, Weitz said. Because so many infections do not produce the distinctive COVID-19 symptoms, it’s likely that many people have recovered from the illness without knowing they’ve had had it, potentially expanding the pool of recovered persons.

“There may be a deeper pool of individuals who can help within their own fields and other fields of specialization to reduce transmission,” Weitz said. “The reality is that people within high-contact jobs probably are likely to have a higher incidence of infection than other groups.”

But using antibody information about individuals would create potential privacy issues, and require that those individuals make informed decisions about accepting additional risks for the greater good of the community. 

“What this model says is that if we could identify individuals who are immune, there is a chance that some individuals would not have to reduce their level of interaction with others because that interaction would be less risky,” he added. “Rather than trying to keep reducing interactions, which is helpful for reducing transmission but bad for what it does for the economy, we might be able to maintain interactions while reducing the risk, combined with other mitigation approaches.”

Ultimately, addressing the pandemic will require development and mass production of a vaccine that could boost immunity levels beyond 60 percent in the general population. Until that is available, Weitz believes that shield immunity could become part of the approach to the challenge.

“We don’t have a silver bullet,” he said. “Until we have a vaccine, we will have to use a combination of strategies to control COVID-19, and shield immunity is potentially one of them.”

In addition to Weitz, co-authors of the paper included Dr. Stephen J. Beckett, Ashley R. Coenen, Dr. David Demory, Marian Dominguez-Mirazo, Dr. Chung-Yin Leung, Guanlin Li, Andreea Magalie, Rogelio Rodriguez-Gonzalez, Shashwat Shivam, and Conan Zhao, all from Georgia Tech; Prof. Jonathan Dushoff of McMaster University, and Sang Woo Park of Princeton University.

This research was supported by the Simons Foundation (SCOPE Award ID 329108), the Army Research Office (W911NF1910384), National Institutes of Health (1R01AI46592-01), and National Science Foundation (1806606 and 1829636). Any findings, conclusions, and recommendations are those of the authors and not necessarily of the sponsoring agencies.

CITATION: Joshua S. Weitz, et al., “Intervention Serology and Interaction Substitution: Modeling the Role of `Shield Immunity' in Reducing COVID-19 Epidemic Spread.” (Nature Medicine, 2020) http://dx.doi.org/10.1038/s41591-020-0895-3

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The goal is to supply a broad initiative by the governor’s office involving multiple universities and partners to rapidly produce and administer more tests. At least 35 volunteers at Georgia Tech, while adhering to social distancing, are reorienting labs normally used for scientific discovery to do larger-scale production of biochemical components.

“We are inventing new ways of doing things like an electronic buddy system so people can be alone – but not alone – while they work in the lab. The technical part is actually the easiest. The logistics of testing, data security, and regulatory considerations – those things are more challenging,” said Loren Williams, a professor in Georgia Tech’s School of Chemistry and Biochemistry.

Williams and the researchers are supporting Georgia Governor Brian Kemp’s COVID-19 State Lab Surge Capacity Task Force, which is a project managed through the Georgia Tech Research Institute (GTRI). GTRI is also leading the coordination and integration of data management across the lab surge effort.

“We are providing technical and project management of the effort which is focused on increasing the state’s ability to expand testing beyond current limitations,” said Mike Shannon, GTRI’s lead in the project and a principal research engineer at GTRI.

Exoplanets and coronavirus

The science behind coronavirus testing is complementary to the researchers’ usual work. That includes understanding proteins associated with glaucoma, figuring out how RNA and DNA evolved in the first place, or whether ribosomes – lumps of RNA and protein key to translating genetic code into life – may exist on exoplanets.

Williams’ research team studies the last topic, and some of their work is related to the core of coronavirus testing, a chemical reaction that amplifies the virus’ genetic fingerprint. It is called a reverse transcription polymerase chain reaction (RT-PCR), and it transcribes trace amounts of coronavirus’ RNA code into ample amounts of corresponding DNA in the lab for easy analysis.

“His lab members are very familiar with RT-PCR, and when the lack of tests became apparent, they swung into action. The group grew from there, based on the technical needs for the project,” said Raquel Lieberman, another leading scientist in the effort and also a professor in Georgia Tech’s School of Chemistry and Biochemistry.

“Every day, very talented, hardworking people with perfect skill sets come out of the woodwork and ask to help,” Williams said.

The group has teams that engineer the production of enzymes or other chemicals needed for RT-PCR to work: Two central enzymes are reverse transcriptase, which converts RNA to DNA and Taq polymerase, which rapidly replicates DNA. Another important component is ribonuclease inhibitor, which slows coronavirus RNA decay.

Global COVID allies

Other researchers develop processes for mass production or implementation of COVID-19 safety procedures; the list goes on. Some colleagues telework; others work in labs but spaced far from each other while they wear masks.

“The group is planning to produce enough enzyme components for hundreds of tests per day,” said Vinayah Agarwal, an assistant professor in Georgia Tech’s School of Chemistry and Biochemistry and School of Biological Sciences. “Using these components, we will also build cheaper and more robust testing kits going forward.”

Instructions already exist for some of the ingredients for the test, but they are not readily available because the rights to them are exclusive.

“Intellectual property and other proprietary issues hinder our effort,” Lieberman said. “But we have received help from scientists all over the world to piece together protocols on how to make what we need.”

The state wants to increase current testing capacities by 3,000 more tests per day. The task force also includes teams from Augusta University Health System, Georgia State University, Emory University, University of Georgia, and the Georgia Public Health Laboratory. The task force lead is Captain Kevin Caspary who is with the Georgia National Guard.

Raw footage and images as press handouts for journalists. (No commercial or personal use): 

https://www.dropbox.com/sh/f2wc2i74lz1lffl/AADLJ8dQnZMr4uEDxAiIMusoa?dl=0

Also read this: Interactive COVID-19 tool shows the importance of staying at home