May 21, 2018

For the foreseeable future, the only real tool to find life on potentially habitable planets that are light years away from Earth is to probe their atmospheres for biological fingerprints of life, called biosignatures.

This approach has two drawbacks, according to School of Earth and Atmospheric Sciences Assistant Professor Christopher Reinhard. “Some biosignatures can be made by abiotic processes, leading to false positives. Others can be masked by processes that consume biosignatures, leading to false negatives.”

To overcome these problems, Reinhard and colleagues in the NASA Astrobiology Institute Alternative Earths and Virtual Planetary Laboratory Teams are proposing use of dynamic biosignatures based on seasonal changes in Earth’s atmosphere. The approach – described recently in Astrophysical Journal Letters – uses the seasonal variation of biologically important gases as a way to deal with false positives and false negatives, Reinhard says.

Seasonality of Atmospheric Gases

As Earth orbits the sun, its tilted axis means different regions receive more rays at different times of the year. The most visible signs of this phenomenon are changes in the weather and length of the days, but atmospheric composition is also affected. For example, in the Northern Hemisphere, which contains most the world’s vegetation, plant growth in summer results in noticeably lower levels of carbon dioxide in the atmosphere. The reverse is true for oxygen.

“Atmospheric seasonality is a promising biosignature because it is biologically modulated on Earth and is likely to occur on other inhabited worlds,” says lead author Stephanie Olson, a graduate student in the Department of Earth Sciences of the University of California, Riverside (UCR). “Inferring life based on seasonality wouldn’t require a detailed understanding of alien biochemistry because it arises as a biological response to seasonal changes in the environment, rather than as a consequence of a specific biological activity that might be unique to Earth.”

In the study – funded by the NASA Astrobiology Institute and the National Science Foundation Frontiers in Earth System Dynamics – the researchers identify the opportunities and pitfalls in monitoring the seasonal ebbs and flows of oxygen, carbon dioxide, methane, and ozone. They also modeled fluctuations of atmospheric oxygen on a life-bearing planet with low oxygen content, just as Earth was billions of years ago. “Based on these evaluations,” Reinhard says, “seasonal variations in ozone could be a sensitive biosignature on planets with undetectable levels of oxygen in their atmospheres.”

Ozone as Indicator of Life

At Georgia Tech, the Reinhard research group develops comprehensive models for the production and maintenance of robust atmospheric biosignatures on habitable planets, and it played a key role in developing the concept of ozone seasonality as a fingerprint for life on low-oxygen planets. The idea emerged in part as an answer to the “biosignature blind spot” problem Reinhard and colleagues posed in the 2017 Astrobiology paper “False Negatives for Remote Life Detection on Ocean-Bearing Planets: Lessons from Early Earth.” 

“We are particularly excited about the prospect of characterizing oxygen fluctuations at the low levels we would expect to find on an early version of Earth,” says Timothy Lyons, a professor of biogeochemistry in UCR’s Department of Earth Science and director of the Alternative Earths Astrobiology Center. “Seasonal variations as revealed by ozone would be most readily detectable on a planet like Earth was billions of years ago, when most life was still microscopic and ocean dwelling.”

“Although we think the conceptual framework for this approach is robust,” Reinhard says, “observing and quantifying seasonality represents a daunting challenge. Research will need to take into account modulation of seasonal signals by the angle at which we observe a planet and the shape of its orbit, among other factors. Nevertheless, seasonality represents a potentially powerful approach toward finding life beyond our solar system.”

May 22, 2018

Most of what we know today about deadly bacteria such as Pseudomonas aeruginosa was obtained from studies done in laboratory settings. Research reported May 14 in the journal Proceedings of the National Academy of Sciences shows that this laboratory-based information may have important limits for predicting how these bugs behave once they’ve invaded humans.

Among the differences are increased expression of genes responsible for antibiotic resistance, the bane of drugs currently used to treat a wide range of infections. The new research could help scientists understand how to draw more accurate conclusions from their laboratory work – and provide doctors with better information on treating bacterial infections.

“Bacteria in human infections are often tolerant of antibiotics, but when we culture them outside the human they are highly susceptible,” said Marvin Whiteley, a professor in the School of Biological Sciences at the Georgia Institute of Technology and co-director of the Emory-Children’s Cystic Fibrosis Center. “In this paper, we show that several genes important for antibiotic tolerance are highly induced in humans compared to our laboratory and mouse modeling systems. There appears to be something unique in the human that is promoting resistance.”

What might be causing that difference remains a mystery, though bacteria are known to be affected by their environment. Understanding how bacterial genes and their expression levels differ in humans could allow researchers to search for laboratory conditions that better mimic the human conditions – and provide better guidance for the use of antibiotics.

“Understanding which antibiotic resistance genes are highly expressed in humans may inform our therapeutic decisions on antibiotic usage,” said Whiteley, who holds the Bennie H. & Nelson D. Abell Chair in Molecular and Cellular Biology at Georgia Tech and is a Georgia Research Alliance Eminent Scholar. “For instance, one might predict antibiotic resistance of an infecting community from gene expression data without the need for culturing microbes in the clinical lab.”

The study was supported by the National Institutes of Health, the Cystic Fibrosis Foundation, and the Lundbeck Foundation. In addition to the Georgia Tech researchers, the research team included scientists at the Texas Tech University Health Sciences Center, the University of Mississippi Medical Center, the University of California, and several clinical and research organizations in Denmark.

Pseudomonas aeruginosa is an important pathogen that threatens immunocompromised people, including those with cystic fibrosis, diabetes and obesity. It is a major hospital-acquired infection, and the Centers for Disease Control and Prevention characterizes multi-drug resistant strains of the bacteria as a serious threat.

In their research, the scientists analyzed RNA sequencing data from both human clinical infections and laboratory experiments. The human samples were obtained from collaborating clinicians, who took the samples directly from patients and put them into a chemical that preserved their RNA for later processing. The laboratory experiments studied different strains of the bacterium under a variety of growth conditions, from antibiotic treatment to competition with other bacteria.

The researchers also included previously published in vitro and mouse experiment data from the Whiteley laboratory and other research teams. Data analysis techniques included a machine learning approach known as Support Vector Machines, which was used to distinguish between gene expression profiles of samples taken from human and in vitro sources.

“We saw high expression in several genes notorious for antibiotic resistance, including genes that encode efflux pumps that extrude antibiotics from the cell as well as an enzyme that degrades certain antibiotics, such as ampicillin,” said Daniel Cornforth, a research scientist in Whiteley’s laboratory and the paper’s first author. “There were also less studied antibiotic resistance genes, including three related to zinc transport that our previous work has identified as critical antibiotic resistance determinants that were also highly expressed in the human patients.”

Though the research focused only on a single troublesome pathogen, Whiteley believes the results could have broader implications. “We actually know very little about bacteria behaviors during human infection and most model systems cannot replicate most aspects of human infection. I expect that this work would be generalizable to other bacteria.”

By identifying how bacteria behave differently in humans compared to standard laboratory settings, the work could provide a foundation for additional study with more samples and different types of infection.

“The key takeaway from this work is that now microbiologists can perform transcriptomics on bacterial populations in a range of human infections, so we can better understand what bacteria are actually doing in these clinical infections,” said Cornforth. “We can also determine where our laboratory models succeed and where they fail in mimicking these infection environments.”

This study was funded by National Institutes of Health Grant R01GM116547-01A1, a Human Frontiers Science grant, Cystic Fibrosis Foundation Grant WHITEL16G0, Lundbeck Foundation Grant R204-2015-4205 and Lundbeck Foundation Grant R105-A9791, and by Cystic Fibrosis postdoctoral Fellowships CORNFO15F0 and IBBERS16F0.

CITATION: Daniel Cornforth, et al., “Pseudomonas aeruginosa transcriptome during human infection,” (Proceedings of the National Academy of Sciences, 2018). https://doi.org/10.1073/pnas.1717525115

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May 25, 2018

A new national project, which includes the Georgia Institute of Technology, aims to convey the benefits of physics’ age-old intertwining with math upon biology, a science historically less connected with it. The National Science Foundation and the Simons Foundation have launched four centers to do this, funded with $40 million, one of which is headquartered at Georgia Tech and will receive a fourth of the funding.

For centuries, together mathematics and physics have shifted paradigms in science and rattled human perception by predicting planetary orbits, theorizing relativity or explaining how one particle can be in two places at the same time. Can theoretical math and biosystems team up to similarly shake the foundations of knowledge?

“We certainly think it’s possible,” said Christine Heitsch, a professor in Georgia Tech’s School of Mathematics who leads the new regional center. “But our immediate goals are more realistic,” she said. “Our first step is getting more mathematicians and bioscience researchers working together in research collaborations."

Bio-math synergy

On an everyday basis, that means the Southeast Center for Mathematics and Biology (SCMB) headquartered at Georgia Tech will tackle open questions in biology using novel math.

“Math can potentially change the way we do our experiments,” said Hang Lu, a professor in Georgia Tech’s School of Chemical and Biomolecular Engineering who co-leads of the center. “If you model your data with topology (a field of mathematics) you see that your data can have a shape,” Lu said. “And that can make you go look for different kinds of data.”

“It will be a two-way street,” Heitsch said. “Math always benefits when it’s challenged by reality.”

Over time, the math-bio spiral could lead to eureka moments.

“Biological systems can look overwhelmingly complex, and that just means we haven’t found the right way of looking at them yet,” Heitsch said.

NSF vision

The SCMB is one of three NSF-Simons Research Centers for Mathematics of Complex Biological Systems. The other two are based at Harvard University and at the University of California, Irvine. Together, they will not only advance the math-biosciences synergy but also spread their knowledge to hundreds of undergraduate and K-12 students throughout the region through educational outreaches.

The SCMB comprises 14 researchers, including collaborators throughout the Southeastern United States. Tulane University, the University of Florida, the University of South Florida, Clemson University, and the Oak Ridge National Laboratory are each contributing a mathematician, and one bioscientist is based at Duke University.

“This project has visionary potential to shake up the way we view biological systems, and also expand mathematics,” said Julia Kubanek, Associate Dean of Research in Georgia Tech’s College of Sciences. “The National Science Foundation and the Simons Foundation have shown tremendous foresight in creating these three centers, and I think headquartering one at Georgia Tech is a great fit because cross-connecting research disciplines is already one of our core missions.”

Biosciences enigmas

To understand the particular value of combining math with biosciences, it’s important to not conflate the latter with physics.

A graphic depiction of canalization. The path of the ball represents the development toward a phenotype, which may start with varying genetic foundations but roll out to secure phenotypical outcomes. But canalization can also lead to more than one possible phenotypical outcome from one set of genes.

For example, in relativity, near-light speeds change an object’s mass, its length, and its passage through time. Those warped phenomena and their equations aren’t so applicable in the world of experimental biosciences, which live in a more Newtonian reality, but one with intricate enigmas for math to demystify.

Take the phenomenon called canalization, which saves living things from the little genetic snafus inside of us all by making sure that proper physical traits usually get produced in spite of mutations.

Clone contradictions

Canalization shatters a stubborn popular notion that genes determine how an organism is built.

“Genes are not deterministic,” said Lu, who is Love Family Professor. She studies the intricate pathways that lead from genetic foundations to measurable physical or behavioral traits, or phenotypes, in C. elegans roundworms. “You often have two individuals with identical genotypes (specific sets of genes) that have different sets of phenotypes.”

That means that canalization may not offer just one but two options -- or more -- to form a trait based on a single set of genes. “What fascinates me is that you can have (C. elegans) clones that are genetically identical but exhibit different behavior,” Heitsch said.

Canalization is not new; it dates to 1942. But its labyrinthine mechanisms and how they “chose” one phenotypical pathway over the other still contain many mysteries. “Maybe math can help us find answers,” Lu said.

Labyrinthine intricacies

Algebra has already taken up canalization but at the SCMB, more maths will join in. Topology, computation, stochastics (principles of randomness), and geometry may enlighten canalization’s myriad interworkings of DNA, RNA, enzymes, protein folding, and just plain randomness.

Other questions SCMB bioscientists and mathematicians are pursuing:

How do stem cells know whether to become a neuron or a skin cell?

How does one cell transport molecules to others?

What exactly does RNA do to help repair DNA damage?

Heitsch, for example, specializes in a field of mathematics called combinatorics, and she applies it to the way molecules of RNA fold.

Historical divergence

Biology is no stranger to stochastics or computation in the analysis of its data, but it has been much less connected than other sciences to the aerial acrobatics of theoretical mathematics.

“There is enormous unrealized potential in applying more theoretical areas of math like algebra, topology, and geometry,” Heitsch said. “That’s new territory, which also means new risks. But we’ve hedged our bets with mathematics already more used in biology to get guaranteed returns.”

Biology and theoretical math have not interfaced much in the past for a couple of reasons.

The endless intricacies of biology, from hundreds of thousands of species to countless biomolecular structures, has made it a gathering and cataloging science for centuries with data that is tough to unify. Also, much data has had to wait for technology to be invented to collect it.

“Biology hasn’t had the measurement tools until just recently, like mass spectrometry and high-end microscopy, to get the hard data needed for math to work with,” Lu said. “Now is a great time for biology and math to come together,” she said.

Cultural exchange

Also, history has separated the disciplines. For centuries, physicists were also mathematicians and vice versa. “And they were engineers,” Lu said. But biologists?

“Darwin was assuredly not a mathematician,” Heitsch said. “He said he didn’t understand as much math as he would have liked to.”

Not many mathematicians have been biologists either.

The NSF-Simons Foundation centers are building the bridge to join them, and the SCMB at Georgia Tech makes for a good pillar. Most of its bioscience researchers already know engineering or physics math, and its mathematicians are already delving into life sciences.

Editor's Note: This article is a slightly modified clone of the feature story by Ben Brumfield published on May 24, 2018 in Research Horizons online.

This article was corrected on May 30, 2018, to reflect corrections in the original story about the number of centers (four), total funding ($40 M), and the Georgia Tech's share (one-fourth).  

May 29, 2018

School of Chemistry and Biochemistry Assistant Professor Henry La Pierre has received a Beckman Young Investigator Award. He will use the award, from the Arnold and Mabel Beckman Foundation,  to pursue research that would establish the foundation for innovations in magnetic materials based on f-block elements.

The f-block elements are the lanthanides and actinides. They are characterized by partially filled f-orbitals. The property imparts unique magnetic properties, making the naturally occurring members commercially important.

According to La Pierre, f-block elements are in materials for energy production, conversion, and use. They are also driving advances in lighting, hard magnets, and electronics.

Because of strong demand, geopolitical factors, and limited availability, the U.S. Department of Energy has deemed five lanthanide elements to be in critical supply: praseodymium (Pr), neodymium (Nd), europium (Eu), terbium (Tb), and dysprosium (Dy).

La Pierre will use X-ray absorption spectroscopy to determine the fundamental basis of the magnetic exchange properties of f-block materials. “A primary goal of my group is to establish chemistry-based rules that will provide a new basis for innovation in controlling magnetic properties of f-block element materials,” La Pierre says.

The new understanding, he adds, “will be applied to the synthesis and characterization of materials that potentially can be exploited for a variety of applications, including high-temperature superconductivity and quantum information technologies.”    

La Pierre received a Bachelor of Arts degree from Harvard University and a Ph.D. from the University of California, Berkeley. After postdoctoral appointments in Friederich Alexander University, in Erlangen, Germany, and Los Alamos National Laboratory, he joined Georgia Tech in 2016.

La Pierre’s research program develops the molecular and solid-state coordination chemistry of the f-block elements for unique and scalable solutions to contemporary problems in energy use. He uses a broad range of physical methods – including single-crystal and powder X-ray diffraction, magnetometry, multinuclear magnetic resonance spectrometry, and X-ray absorption spectroscopy – to characterize new materials.

May 30, 2018

Mark Wheeler has been named interim chair of the School of Psychology, effective on July 1, 2018. Wheeler is currently the school’s associate chair with oversight of operations and graduate studies. 

Wheeler joined Georgia Tech in 2014. His lab investigates how cognitive abilities are affected by lifestyle factors such as sleep quality and physical activity, as well as how these abilities may change in healthy aging.

Wheeler specialized in functional brain imaging of human memory for his Ph.D. from Washington University in St. Louis.

After a postdoctoral stint at Washington University School of Medicine, he joined the University of Pittsburgh. There, he developed functional imaging techniques to study neural dynamics of the accumulation and representation of evidence during decision-making.

Wheeler takes over from Frank Durso, who has served as interim chair since July 1, 2017.

“It is a pleasure for me to thank Professor Frank Durso for his exemplary contributions during his service as interim chair of the school,” says College of Sciences Dean and Sutherland Chair Paul Goldbart. “Under Frank’s leadership, the school has developed relationships that will be of enduring value to the school, both across the campus and beyond.”

May 31, 2018

“A large part of my research is thinking about how bacteria communicate,” says Sophie Darch. The postdoctoral researcher works with School of Biological Sciences Professor Marvin Whiteley, studying the social lives of bacteria.

Darch observes the conversations of bacteria, which take place via molecules they release into the environment and are sensed by other bacteria. In Darch’s experiments, completed messages are marked by the red-to-green change in the color of the bacterium sensing the molecule.

By sending and receiving extracellular signals, bacteria sense their neighbors. When enough bacteria are in the conversation, things happen. Sometimes it leads to changes in virulence or ability to establish an infection. The phenomenon is called quorum sensing.

Yet little is known about how quorum sensing proceeds during infection “Much of what is known about quorum sensing,” Darch says, “comes from studies of large populations of bacteria in an environment that does not compare with the natural infection site.” In infections, for example, bacteria are often found in small, dense clusters, called aggregates. “It’s really important for us as scientists to think about what bacterial growth looks like in an infection,” Darch says.

In a paper in the Proceedings of the National Academy of Sciences USA, Darch, Whiteley, and colleagues describe for the first time how close bacteria need to be to “talk” with each other in an environment similar to an infection. Their findings could reveal new ways to disrupt bacterial signaling and provide other targets to treat infections.

The work was supported by the National Institutes of Health, the Cystic Fibrosis Foundation, Human Frontiers Science, and the Welch Foundation.

Cystic Fibrosis Model

The study uses an environment similar to the chronic infection of the cystic fibrosis (CF) lung.

CF is a genetic disease that causes buildup of sticky mucus in the lung. The viscous setting CF creates makes the organ prime real estate for disease-causing bacteria. Among the most prevalent of these in the CF lung is Pseudomonas aeruginosa.

P. aeruginosa infections pose a huge problem because they are resistant to many antibiotics and are difficult to treat. Often P. aeruginosa infection is what causes death among patients with CF.

The team used a synthetic CF sputum media (SCFM2), based on the makeup of lung secretions from patients. In nutritional content and physical form, the medium is similar to sputum from the lung. Importantly, P. aeruginosa forms aggregates in SCFM2 that are similar in size to those observed in CF lung tissue.

3-D Printed Bacteria

To begin to answer the question “How close do you have to be to talk to your neighbor?” the team collaborated with Jason Shear at the University of Texas, Austin. The Shear Lab had developed a micro-3D-printing platform that could be used to engineer the growth of bacteria to mimic infections.

Bacteria are not uniformly distributed in infections. “Instead we see bacterial aggregates that vary in size and can be separated by large distances,” Whiteley says. “We needed an experimental method to engineer these types of infection landscapes in the lab.”

Using Shear’s micro-3D-printing platform, the team printed bacterial aggregates of exact positions and sizes.

A typical experiment starts by enclosing one producer cell in a picoliter-sized trap, using micro-3D-printing. After multiple cell divisions, the population fills the volume of the trap. Then SCFM2-containing aggregates of responder cells are overlaid the porous trap.

They observe the one-way flow of signals from aggregates in a trap (producers) to aggregates outside receiving signals (responders). They could see the response of completed conversations by responders changing color from red to green.

Implications for Cystic Fibrosis

“We found that bacterial aggregates slightly larger than those in CF lung – containing about 2,000 cells – were not large enough to signal to other aggregates,” Darch says.

Prior to this study, it was thought that bacterial signaling could occur over extended distances. However, in the CF lung, small populations of bacteria are scattered across a large volume and separated by large distances. Aggregates are unlikely to “talk” to each other. 

It took aggregates containing at least 5,000 cells to successfully send signals to neighbors as far away as 176 micrometers. “These aggregates are around five times the size of the average aggregate observed in CF lung tissue” Darch says “From these data, communication is likely confined within an individual aggregate rather than being a population-wide phenomenon”.

Among CF patients who are at least 20 years old, 80% are infected with P. aeruginosa. “Infection with P. aeruginosa remains a significant clinical problem in immunocompromised patients, particularly those with CF,” Darch says. “Understanding better how bacteria communicate has the potential to find ways of disrupting the communication and potentially diminishing bacterial virulence.”

“The study provides benchmark data for how quorum sensing might proceed in an environment similar to the CF lung,” says Whiteley, who is a member of the Parker H. Petit Institute for Bioengineering and Bioscience. “In different settings, where P. aeruginosa and other bacteria exist as aggregates of different sizes, communication may look different. Future studies will involve experimental and modeling work to further examine the spatial parameters of quorum sensing in CF and other infections, such as a chronic wound.”

Figure Caption

(Left) Rendered confocal laser-scanning micrograph of a micro-3D-printed trap (red)  surrounded by P. aeruginosa aggregates responding to quorum-sensing signals (green) in a synthetic CF sputum media (SCFM2).

(Right) Rendered confocal laser-scanning micrograph of responding (green) and non-responding (red) P. aeruginosa aggregates formed in a synthetic CF sputum media (SCFM2).

June 1, 2018

Curvy baseball pitches have surprising things in common with quantum particles described in a new physics study, though the latter fly much more weirdly.

In fact, ultracold paired particles called fermions must behave even weirder than physicists previously thought, according to theoretical physicists from the Georgia Institute of Technology, who mathematically studied their flight patterns. The researchers even predicted that the particles can act like different quantum balls called bosons to mimic the manner that photons, or particles of light, fly.

Already, flying quantum particles were renowned for their weirdness. To understand why, start with similarities to a baseball then add significant differences.

A pitcher imparts spin, momentum, and energy to a baseball when throwing a curveball, a change-up, or a slider. Fermions’ funny flights are likewise carved by spins, momenta, and energies, but also by powerful quantum eccentricities like entanglement, which Albert Einstein once called “spooky action at a distance” between quantum particles.

A simplified explanation of these ultracold paired particles and their odd flights is below.

Light-matter modeling

Those influences all combine to give fermions a trajectory repertoire much odder than that of any master baseball pitcher, and the new study maps it out and opens new ways to observe it experimentally. The Georgia Tech team took the offbeat approach of adding quantum optical -- or light-like – ideas to their predictive calculations of these specks of matter and arrived at eyebrow-raising, insightful results.

“The particle behavior we predicted is just schizophrenic,” said Uzi Landman, Regents’ and Institute Professor and F.E. Callaway Endowed Chair in Georgia Tech’s School of Physics.

Mathematical and theoretical details can be found in the study in the journal Physical Review A, which Landman, first author Benedikt Brandt, who is a graduate research assistant, and senior scientist Constantine Yannouleas published on May 4, 2018. Their research was funded by the Air Force Office of Scientific Research.

Flying fermions explained

Tracing quantum curveballs is counterintuitive by nature with concepts like fermions, bosons, spins, spooky entanglement, and particle-wave duality. So, let’s go step-by-step to understand them and the study’s insights.

This ballgame revolves around fermion pairs. Fermions can be subatomic particles or whole atoms. In this case, the physicists modeled using atoms.

The term fermion refers to quantum-statistical properties that the particle has as opposed the properties of its counterpart particle called a boson, in particular, the particle’s spin, which is called half-integer for fermions and full-integer for bosons. (These spins aren’t exactly like those on a ball. For more, see: Fermions and Bosons for Dummies.)

"Photons and Higgs bosons are examples of bosons," Landman said. "Bosons are gregarious: Two or more bosons can share the exact same space. This allows many of them to be superimposed onto each other on the same tiny spot."

"Fermions, on the other hand, are standoffish. They lay claim to their own space, and don't share it with other particles. Fermions can be stacked upon each other but do not occupy the same space."

Electrons, protons, neutrons, and many atoms are common examples of fermions.

Laser-tweezing baseballs

The theoretical study envisions two fermionic atoms starting out carefully held next to each other by two pairs of “tweezers” made of intersecting laser beams, as is actually done in applicable physics experiments. In the study's theoretical setup, lasers and special magnetic fields would also be used to slow the fermions to a near halt, making them “ultracold” at 0.000000001 degrees Kelvin, or -273.15 degrees Celsius (-459.67 degrees Fahrenheit). 

That’s a sliver above absolute zero, the lowest possible temperature in the universe, and particles that cold do strange things.

“A particle’s motion is usually frantic, but the cooling slows it down almost to a stand-still,” said Landman, who is also director of the Georgia Tech Center for Computational Materials Science. “And these particles also have wave properties, and at that temperature, the wavelength grows enormously long.”

“The waves become microns in size. That would be like a pebble growing to be a third of the size of this country. When that happens, the atom actually becomes visible under an optical microscope.”

The inflated size makes it easier for researchers to know the two particles’ starting locations. When they turn the laser tweezers off, the fermions fly away. The particles’ wave properties also have a lot to do with their weird flights.

“A particle in motion will act as a projectile under certain circumstances. But in others, it will behave like a wave,” Landman said. “We call it the quantum world duality.”

Together or apart

“If you set up two detectors at different positions but the same distance from the particle pair, how often the two fly into the same detector or how often they fly into separate ones says a lot about those particles,” Landman said. “And that’s where our weird findings come in.”

Fermions are expected to fly differently from bosons, but the theoretical physicists’ study on fermions revises this idea. Depending on the degree of quantum entanglement between the two fermions before they’re released and depending on their energy level, they can act like fermions or act like bosons.

“This adds new weirdness to the already established schizophrenic particle-wave duality,” Landman said.

“A pair of photons (which are bosons) fly to the same place. They stay as a pair,” Landman said. “They’re social animals, and you find them either both in the one detector or both in the other. We call this phenomenon ‘bunching.’”

Weirdo flight paths

Fermions are often expected to do the opposite, referred to as anti-bunching, but according to the study, how they fly depends on whether or not they have spooky interaction and, if so, whether the interaction is attractive or repulsive.

“If they’re interacting, and depending on the starting energy level, we predict that they may do strange things when they fly,” Landman said. “That’s new.”

“At the base energy level, called ground state, our two fermions that interact with ultra-strong repulsion behave fermionically, meaning they avoid each other. Now, if they interact with strong attraction, they aggregate the way bosons do,” Landman said. “So far, all as expected.”

But bumping up the trapped particles’ level of energy, or excitation, via an additional laser or a magnetic field, would appear to heighten the particles’ weirdness. The excitation levels can twist the rules of what interactions do to a fermion’s flight, according to the theoretical study.

For example, the above mentioned fermionic behavior usually connected with strong repulsive interaction could turn bosonic, according to the physicists’ calculations. In other words, the two particles would fly to the same detector the way bosons do.

Orderly quantum schizophrenia

“As crazy as all this looks, there appears to be strong reliability in these behaviors that could even be predictably and practically manipulated,” Landman said.

As with a pitcher who finesses a screwball’s path, physicists could determine a fermion’s weird flight using quantum mechanical formulation, advanced computational simulation, and experimentation, the study said.

“It looks like you may even be able to engineer what this quantum weirdness does,” Landman said. "If you know particle states reliably, you may be able to use them as a resource for quantum computations and information storage and retrieval."

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The research was funded by the Air Force Office of Scientific Research (award # FA9550-418 15-1-0519). Findings and opinions are those of the authors and not necessarily of the sponsoring agency. Georgia Tech's Brice Zimmerman contributed baseball background to this report.

Writer & Contact: Ben Brumfield (404-660-1408)

Email: ben.brumfield@comm.gatech.edu

June 1, 2018

David M. Collard, professor and associate dean, will serve as interim dean of the College of Sciences. Collard will officially assume the role Aug. 1, following the departure of the current dean, Paul Goldbart.

“Dr. Collard is a valued member of the faculty and administration in the College of Sciences,” said Rafael L. Bras, provost and executive vice president for Academic Affairs and K. Harrison Brown Family Chair. “We are grateful for his continued leadership and trust the College is in great hands during this transition.”

Collard joined the Georgia Tech faculty in the School of Chemistry and Biochemistry in 1991. He served as the director of Graduate Studies from 1997 to 2005, and then as associate chair from 2005 to 2010.

Academic Leadership

Collard has served as the associate dean for Academic Programs in the College of Sciences since 2010. In this role he coordinates activities related to recruitment, retention, curricula, instructional facilities, scholarships, and awards.

He also directs initiatives to broaden participation in STEM, build capacity for undergraduate research, and foster partnerships with neighboring, predominantly undergraduate institutions.

Research and Instruction

His teaching interests are in the field of organic chemistry, and he maintains a research program in polymer chemistry.

Along with his teaching and research interests, Collard has served in leadership roles of on-campus experiential learning programs including National Science Foundation (NSF) Research Experiences for Undergraduate programs (REU), a 3M Undergraduate Summer Research Program, an NSF Scholarships in STEM & Living-Learning Community, and a number of U.S. Department of Education Graduate Assistantships in Areas of National Need programs (GAANN).

Collard also co-directs the Chemistry Collaborations, Workshops, and Communities of Scholars (cCWCS) faculty development initiative, which has engaged thousands of faculty members from institutions across the United States. 

He has authored or co-authored more than 100 papers in refereed journals. Collard’s commitment to individual student research mentorship has included 24 Ph.D. graduates, 12 M.S. graduates, and 37 undergraduate researchers.

Honors and Awards

During his tenure, Collard has received all three of the Institute’s top teaching awards: the Class of 1940 W. Roane Beard Outstanding Teacher Award, the Class of 1940 Howard Ector Outstanding Teacher Award, and the Eichholz Award.

He is also the recipient of the Georgia Tech Class of 1934 Outstanding Use of Educational Technology Award and the Outstanding Ph.D. Advisor Award.

His work in undergraduate education has also garnered awards from the National Science Foundation, the Camille and Henry Dreyfus Foundation, and the Research Corporation for the Advancement of Science.

In 2017, he was the recipient of the University System of Georgia’s Felton Jenkins Jr. Hall of Fame Faculty Award in recognition of his commitment to teaching and student success.

Collard received his Ph.D. in Chemistry from the University of Massachusetts – Amherst in 1989 and a Bachelor of Science in Chemical Sciences from the University of East Anglia, U.K., in 1983.

Collard will serve until a new dean is named. A search chair and advisory committee will be selected in the next several weeks to conduct an international search for the College’s next leader. Jennifer Herazy, associate provost for Operations, will serve as search director.

EDITOR'S NOTE: This item is a slightly modified version of the original story by Susie Ivy published on June 1, 2018, in the Georgia Tech News Center.

June 4, 2018

There’s a long way to go before neuroscience can fathom the vastness of human consciousness, but researchers pushing that envelope have uncovered a mechanism that helps create a simple visual awareness. In a new study, they describe brain functions that give you confidence that you did see what you just saw.

Though that may be a very modest level of awareness that humans perhaps share with hamsters, psychologists at the Georgia Institute of Technology were fascinated to observe how two regions of the brain work together to produce this visual confidence.

“We had already thought of the prefrontal cortex (PFC) as producing that confidence, but we haven’t previously distinguished two regions of it as having distinct, separate roles,” said Dobromir Rahnev, an assistant professor in Georgia Tech’s School of Psychology.

Awareness of seeing

The observed phenomenon is a type of metacognition, which is broadly defined as when the brain registers, i.e. becomes aware of, something else that the brain is doing. Metacognition can be as complex as pondering your own thoughts or as simple as knowing you feel itchy, or that you just saw something.

The two regions of the PFC that the researchers studied were the dorsolateral prefrontal cortex (DLPFC) and the anterior prefrontal cortex (aPFC). The aPFC is about two inches above the eyebrow, near the top of the forehead and DLPFC is about a few inches directly behind aPFC.

The upper area collects visual sensory input, according to the study, and when it has strong inputs, it signals down to the aPFC, which usually correctly and confidently registers – yes, I’m aware I see that.

“The aPFC takes the evidence from the DLPFC and matches it to a level of confidence of what is being seen,” said graduate research assistant Medha Shekhar.

Rahnev and Shekhar published their study in May in the Journal of Neuroscience.

Two-stage signoff

Though they have separate roles, neither region appears to lay claim to being the chief confidence maker of having seen something.

“I would say that it’s both parts together,” Rahnev said. “The whole process of generating a confidence rating can be thought of as metacognition, so both the DLPFC and aPFC contribute to the process.”

The DLPFC collects all the inputs. Then it nudges the aPFC to put the stamp on the final confidence rating, according to the psychologists’ model.

To do that, the aPFC probably pulls in additional data from elsewhere in the brain.

“There is research that suggests that we take into account other, non-perceptual factors when making our confidence judgment,” Shekhar said. “Our previous confidence about past things we’ve seen influences current confidence about what we’re seeing now. We hypothesize that there are other things like attention and arousal that the aPFC is taking into account.”

Running brain interference

Researchers currently can’t directly see the processes that interested them, since neurological imaging technologies are not yet that far along, so the psychologists had to come up with creative ways of observing the mechanisms. They used transcranial magnetic stimulation (TMS), which some people know from its application to treat depression, to interfere with activity in one brain region then separately in the other.

“By dissociating the contributions made by the two regions, we could discern some mechanisms in these processes we were interested in,” Shekhar said.

To track the effects of the dissociation caused by the magnetism, the psychologists had volunteers look at two faint patterns on a drab, gray background that appeared in sequence, and then indicate what they saw. It was nothing fancy, just a series of lined patterns like this one \\\\ or this one ////.

“These are very standard visual inputs for an experiment like this,” Rahnev said. “They’re the most boring stimuli one can imagine. They’re called Gabor patches. We use them because we want to minimize interfering neurological activity by not encouraging the brain to do a lot of additional things.”

The volunteers pressed buttons to say that the respective line patterns that they saw pointed up to the left \\\\ or up to the right //// and how sure they were about what they saw.

Confidence up and down

While the volunteers did this, the researchers used TMS to run interference in the volunteers’ DLPFC and then their aPFC. The TMS affected whether subjects got the line direction right or wrong and how sure subjects felt about what they were seeing.

Applying TMS to the DLPFC caused the subjects’ confidence levels to sink, presumably because that interfered with it gathering or passing on enough data to trigger confidence. TMS to the aPFC, which had to be applied for a longer period to have relevant effect, actually increased visual metacognitive ability.

The two effects were strong evidence that the two brain regions were carrying out separate roles in visual metacognition. The researchers also computationally modeled the brain processes, and their simulation concurred with the experimental results.

Peeking at consciousness

Did the researchers observe a piece of what makes consciousness work?

“Consciousness is tricky because so many processes feed it and help generate it, so we stay agnostic about this and stick with the immediate phenomenon we observe,” Rahnev said.

But he did think it may be fair to say that this kind of metacognition stands in the threshold of what we humans like to think of as consciousness.

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June 4, 2018

By Mallory Rosten, Student Communications Assistant, College of Sciences

Students major in the College of Sciences because they’re curious about the natural world. They want to know why things are the way they are. They want to solve problems, to explain the mysteries of the universe, and to use science and technology to better people’s lives.

At the end of the Spring 2018 semester, 11 of those students received awards for outstanding achievements.

“We take great pleasure in recognizing and nurturing the outstanding, well-rounded students in our care,” says College of Sciences Dean and Sutherland Chair Paul M. Goldbart. “They are the reason we are constantly striving to strengthen and diversify the educational experiences and research opportunities that we offer.”

“I cannot say a more heartfelt thank you to the benefactors of these awards and scholarships,” Goldbart says.  “Their generosity marvelously expands our ability to support deserving students and retain them in the College.”  

Outstanding Undergraduate Researcher Award

This award recognizes undergraduates who are committed to research. Ann Johnson, a biology major, and Calvin Runnels, a biochemistry major, are the 2018 recipients in the College of Sciences.

Johnson is passionate about changing global health and interested in engineering for the developing world. She has conducted research with Joe Brown,  in the School of Civil and Environmental Engineering, with Omer Inan, in the School of Electrical and Computer Engineering, and at Johns Hopkins University. “It’s so important to intersect an understanding of humanities and science in order to look at culture and how it impacts people,” Johnson says.

The intersection of science and people also fascinates Runnels. He conceived and implemented the Undergraduate Research Fair to connect labs with students. He tirelessly advocated for marginalized and LGBTQ students.

Runnels conducted research on the origins of protein folding in the lab of Loren Williams, in the School of Chemistry and Biochemistry. His work yielded a yet-unpublished manuscript about the nature of biopolymers of which he is the first author

Runnels graduated in May 2018 and is headed to Oxford University as a Rhodes Scholar. According to one professor, Runnels is “a once-in-a-decade student” who displays empathy as well as a command of science.

Gretzinger Undergraduate Research Initiation Award

The award focuses on students just getting started in research. The award seeks to early involvement and broaden the recipient’s participation in research. Keith Creech, a biochemistry major, is the 2018 recipient. He will begin research with Robert Dickson, in the School of Chemistry and Biochemistry, in summer 2019.

Mehta Phingbodhipakkiya Memorial Scholarship

The scholarship honors the top junior in the College of Sciences. Sara Brockmeier is the 2018 recipient. Brockmeier majors in psychology with a business option.

Brockmeier conducts research in the joint lab of Phillip Ackerman and Ruth Kanfer, also called the PARK Lab, in the School of Psychology. She studies the influence of factors affecting workplace learning, behavior, and performance. She helped pilot a study of test-retest reliability aptitude tests used by the U.S. Navy.

Brockmeier hopes to apply her research to a career in industrial and organizational psychology.

Larry O’Hara Graduate Scholarship

The award recognizes outstanding graduate students. The 2018 recipients are Joel Mumma and Jennifer Pentz.

Joel Mumma, a psychology Ph.D. student, also hopes to use psychology to improve people’s lives. Winning this award, he’s doing a bit more than hoping. Mumma has written a paper that will save lives, according to his advisor, Frank Durso.

Mumma led the risk analyses of protocols that health care providers follow to protect themselves from dangerous pathogens, such as Ebola. The paper, in Clinical Infectious Diseases, is filled with “a number of nuanced and surprising findings that tell us a little more about the psychology of human error,” Durso says. Hospitals are already putting to the results to practice. This paper, Durso adds, is just the beginning for this “rising star.”

Jennifer Pentz is a biology Ph.D. student. Using yeast cells, she studies the origins of multicellularity with William Ratcliff, in the School of Biological Sciences. It was during her undergraduate research at the University of Minnesota that Pentz discovered an interest in ecological and evolutionary questions.

At Tech, Pentz co-authored a study finding that physical stress may have been critical in the rise of multicellular organisms from single cells. Her work with yeast brought her to the Atlanta Science Festival, where she demonstrated the “Science of Beer”.

A. Joyce Nickelson and John C. Sutherland Undergraduate Research Award

Daniel Gurevich is the 2018 winner. The award recognizes excellence at the interface of mathematics and physics.  

No stranger to solving real-world problems, Gurevich is interested in data analysis. An algorithm he developed has helped discover new mechanisms for ventricular fibrillation. This heart disorder is fatal within minutes if not treated.  He also wants to be able to predict when patients in intensive care units might crash based on their vital signs.

An author of two research papers, Gurevich is triple majoring in physics, mathematics, and industrial and systems engineering. This broad perspective gives him an edge. He says it helps him find patterns in data.

Perhaps his love for problem solving comes from chess. He started playing at age five, and now he’s an International Master.

Roger M. Wartell and Stephen E. Brossette Award for Multidisciplinary Studies in Biology, Physics, and Mathematics

Being able to study more than one field – and to synthesize them – is an extraordinary skill. This award recognizes students studying at the interface of physics or mathematics with biology.

Harsh V. Patel, a biology major and computer science minor, is the 2018 recipient of the award. A School of Biological Sciences student ambassador with a keen analytical mind, Patel conducted research with Patrick McGrath and Greg Gibson, in the School of Biological Sciences.

When he first started research, Patel hoped to revolutionize genotype-phenotype mapping using machine learning. His computer science background allowed him to apply machine learning and probabilistic models to biology studies.

Virginia C. and Herschel V. Clanton Jr. Scholarship

Deep curiosity about the foundations of life also drives Nancy Park, the 2018 recipient. The scholarship goes to a top pre-health junior in the College of Sciences. Park is majoring in biology with a minor in physiology and a pre-health designation.

Park is a Fast-Track to Research Scholar and the president of Student Hospital Connections. She conducts research with Terry Snell, in the School of Biological Sciences.

“She really enjoys experimentation and discovery, and is constantly thinking of ways to improve techniques,” Snell says of Park. In Snell’s lab, Park has studied the sequencing of DNA from various rotifers and the metal toxicity to Proales similis.

Cynthia L. Bossart and James Efron Scholarship

This award recognizes the top out-of-state junior in the College of Sciences. The 2018 recipient is Katherine Wei. The biology major and health and medical sciences minor hopes to be a dentist.

In Todd Streelman’s lab, Wei studies the cichlid fish genome to explore the divergence of behavioral genes. Wei has had an integral role in advancing the understanding the genetic mechanisms of sex determination, a mentor says.

According to another mentor, Wei “only seems to express excitement as she dives into- and solves- new challenges and always has a positive impact on her projects and those around her.”

Wei serves as vice president of membership of the Pre-Dental Society and Stamps Health Services ambassador.

Robert A. Pierotti Memorial Scholarship

When it comes to solving challenges, Libby Taylor excels. She’s the 2018 recipient of the scholarship, which recognizes a top graduating senior in the College of Sciences. Taylor has already won the Alice T. Schafer Mathematics Prize, a prestigious nationwide award.

One of Taylor’s first challenges was taking Georgia Tech classes while still in high school. As an undergraduate, she went on to take several graduate level classes.

Taylor conducted research in combinatorics, tropical geometry, matroid theory, and random graph theory. According to her professors, when she came upon a foreign concept, she learned it on her own. One professor is “amazed at her ability to quickly pick up sophisticated ideas.” Another looks “forward to seeing what Taylor’s future holds.”

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