Students create exotic state of matter

By Bennett McIntosh

IN THE SUMMER OF 2015, Princeton students Joseph Scherrer and Adam Bowman experienced something few undergraduates can claim: they built, from scratch, a laser system capable of coaxing lithium atoms into a rare, highly excited state of matter to reveal their quantum nature.

When they joined Assistant Professor of Physics Waseem Bakr’s lab in the spring of 2014, Scherrer and Bowman had little experience in optics or quantum physics. Their task was to convince lithium atoms to enter a state of matter known as the Rydberg state. In this state, each atom has a very high-energy electron located far from the atom’s nucleus. The separation of the electron’s negative charge from the nucleus’ positive charge creates a dipole, like a magnet’s north and south poles.

To give the electrons the right amount of energy to create the Rydberg state, Scherrer and Bowman hit the atoms with two carefully tuned lasers, first blue and then red. To prove that the lithium atoms had indeed entered the Rydberg state, the two researchers needed a way to detect them. They trawled the scientific literature for a sensitive enough detection method, and eventually implemented a technique called electromagnetically induced transparency. With this technique, the Rydberg atoms interfere with the absorbance of certain wavelengths of light, so if the gas is transparent in those wavelengths, the Rydberg atoms are present.

The undergraduates designed and built the device independently, Bakr said. “I wasn’t planning on starting this, and suddenly it grew into a whole project, largely due to their efforts,” he said.

“It was a turning point in our scientific development,” said Scherrer, who graduated in 2016 with a degree in physics. “For me, it was a realization of what you can do with quantum optics.” Scherrer was awarded a Fulbright grant to join a team in Munich, Germany, where he is building electron microscopes to image the brain. He will next head to the Massachusetts Institute of Technology to pursue a Ph.D. in physics. Bowman, a physics major in the Class of 2017, continues to study the physics of electronically interesting materials, and spent his junior year and the summer of 2016 working on a new project with Ali Yazdani, Princeton’s Class of 1909 Professor of Physics. There, Bowman built a device that works like an inkjet printer for atoms to print superconductors layer-by-layer.

Atom catcher: With lasers and magnets, Waseem Bakr traps atoms for study under the microscope

By Bennett McIntosh

THE COLDEST SPOT on the Princeton campus is a cluster of a few thousand atoms suspended above a table in Waseem Bakr’s laboratory. When trapped in a lattice of intersecting lasers at just millionths of a degree above absolute zero — and roughly one-millionth the density of air — atoms become very still, enabling Bakr, an assistant professor of physics, to study them through a microscope.

At these frigid temperatures and ultralow densities, atoms begin to act very strangely. They function less like individual particles and instead behave like waves that blur and overlap, losing their individual identity and trading the physics of the everyday world for the laws of quantum mechanics. The resulting state, known as a degenerate Fermi gas, can yield insights into new states of matter that someday may lead to applications such as superconductors and quantum computers.

Bakr uses a system of lasers and magnetic fields to cool and trap the ultracold atoms in a crystal-like lattice made from light. He then manipulates and observes the atoms using a quantum-gas microscope, a device that he helped invent during his graduate studies with Markus Greiner at Harvard University, and further improved when he was a postdoctoral researcher with Martin Zwierlein at the Massachusetts Institute of Technology.

“We use lasers to create artificial crystals in which we place these quantum-mechanical atoms where the spacing between atoms is 10,000 times larger than what you find in real crystals,” Bakr said. “We are essentially engineering the behaviors of atoms using light.”

Bakr and his team first heat a block of lithium to 800 degrees Fahrenheit to liberate individual atoms that then fly into a long tube. There, the particles collide head-on with a laser beam pointed in the opposite direction, which rapidly slows and cools them. The atoms then flow into a chamber where the intersection of several laser beams creates an electromagnetic field that confines the atoms in an “optical trap.” The trap allows the fastest-moving (and warmest) atoms to escape, further cooling the ultracold gas. The resulting cluster of atoms, Bakr said, is “the coldest stuff you can find in the universe.”

Using the microscope, Bakr can agitate a single atom to watch the disturbance propagate, or he can rearrange the entire system to simulate a different material. “If I decide I want to study graphene today,” he said, “I can arrange my lasers to make a graphene-like lattice, and suddenly the physics that I’m looking at are very different.” This precise control could hold the key to another advance, he said. “If you have 1,000 atoms, and you have control over every single atom and their interactions, these are the basic building blocks of a quantum computer,” Bakr said.

Cold atoms

Trapped by lasers and magnets, lithium atoms form a fluorescent red ball at the center of this image. In this initial stage of laser cooling, about 1 billion atoms are brought from a temperature of 350 degrees Celsius to a thousandth of a degree above absolute zero.

Bakr and his team are using ultracold atoms to study the behavior of superfluids with imbalanced spin populations. In a paper published in the August 24, 2016, issue of Physical Review Letters, Bakr and his team showed that the two-dimensional gas separates into two phases, a superfluid in the center of the trap and a  normal gas at its periphery, like the phase  separation that happens when mixing oil and  water. “Observing this phase separation is the first step in a search for exotic types of superfluidity that were predicted over 50 years ago,”

The Bakr lab’s work is supported by grants from the Air Force Office of Scientific Research, the National Science Foundation and the Alfred P.  Sloan Foundation.

Princeton part of $40 million Simons Observatory

PRINCETON RESEARCHERS will have an integral role in the Simons Observatory, a new astronomy facility in South America recently established with a $38.4 million grant from the Simons Foundation. The observatory will investigate cosmic microwave background (CMB) radiation to better understand the physics of the Big Bang, the nature of dark energy and dark matter, the properties of neutrinos, and the formation of structure in the universe.

The project is a collaboration between Princeton, the University of California-San Diego, the University of California-Berkeley, the University of Pennsylvania and the Lawrence Berkeley National Laboratory, all of which will provide financial support. The Heising-Simons Foundation will provide an additional $1.7 million of support. The observatory will be located in Chile’s Atacama Desert, a longtime site for astronomy and CMB research because of its elevation and near absence of precipitation.

The project manager for the Simons Observatory will be located at Princeton, and Princeton faculty also will oversee the development, design, testing and manufacture of many of the observatory’s camera components.

Suzanne Staggs, Princeton’s project lead for the observatory and the Henry DeWolf Smyth Professor of Physics, said the mission of the Simons Observatory builds on the University’s long history of advancing the understanding of the CMB. Princeton faculty members Lyman Page, the James S. McDonnell Distinguished University Professor in Physics and department chair, and David Spergel, the Charles A. Young Professor of Astronomy on the Class of 1897 Foundation, also will participate in the Simons Observatory. –By Staff

F. Duncan Haldane receives Nobel Prize in Physics

F. Duncan Haldane, Princeton’s Eugene Higgins Professor of Physics, was awarded the 2016 Nobel Prize in Physics “for theoretical discoveries of topological phase transitions and topological phases of matter.” Considered key to finally realizing highly efficient and powerful quantum computers, topological materials exhibit unique properties, particularly great stability and efficient particle movement. Haldane shares the prize with David Thouless of the University of Washington and J. Michael Kosterlitz of Brown University.



ROBERTO CAR receives American Chemistry Society national award

Roberto Car

Roberto Car (Photo by Frank Wojciechowski)

Roberto Car, the Ralph W. *31 Dornte Professor in Chemistry, was recognized for his innovative research by the American Chemical Society (ACS) during a ceremony March 15, 2016. He received the ACS Award in Theoretical Chemistry for the “depth, originality and scientific significance” of his work.

Car’s research explores materials at the level of atoms and electrons. He uses theoretical tools and numerical simulations to gain insight into the chemical and physical processes underlying chemical reactions. While Car’s research is theoretical and fundamental, his discoveries may have technological implications that can aid in the design of new materials and devices with desirable properties. Car, who is a professor of chemistry and the Princeton Institute for the Science and Technology of Materials, is known for the invention of an ab initio moleculardynamics method with Italian physicist Michele Parrinello that is now a standard tool for molecular simulation. The method has been applied to a variety of problems in condensed matter and chemical physics, materials science, geosciences, chemistry and biochemistry.


SIMON LEVIN wins National Medal of Science for unraveling ecological complexity

Simon Levin

Simon Levin (Photo by Brian Wilson)

Simon Levin, the James S. McDonnell Distinguished University Professor in Ecology and Evolutionary Biology, received a National Medal of Science, the nation’s highest scientific honor. Levin was honored at a White House ceremony in early 2016 along with eight fellow Medal of Science recipients, and eight recipients of the National Medal of Technology and Innovation.

Levin focuses his research on complexity, particularly how large-scale patterns — such as at the ecosystem level — are maintained by small-scale behavioral and evolutionary factors at the level of individual organisms. His work uses observational data and mathematical models to explore topics such as biological diversity, the evolution of structure and organization, and the management of public goods and shared resources. While primarily related to ecology, Levin’s work also has analyzed conservation, financial and economic systems, and the dynamics of infectious diseases and antibiotic resistance.

PAUL CHIRIK receives Presidential Green Chemistry Challenge Award


Paul Chirik (Photo by C. Todd Reichart)

Paul Chirik, the Edwards S. Sanford Professor of Chemistry, was among five recipients nationwide of the 2016 Presidential Green Chemistry Challenge Awards presented by the U.S. Environmental Protection Agency. Chirik was recognized for discovering a new class of catalysts that produce silicones without using hard-to-obtain platinum, which could dramatically reduce the mining of ore and reduce costs, greenhouse-gas emissions and waste. The winners were recognized during a ceremony June 13, 2016.

Big answers from small creatures

A graduate student tracks the spread of viruses from bats to humans in Madagascar

By Cara Brook

IT IS SPRINGTIME in the Makira-Masoala peninsula of northeastern Madagascar, and the lychee trees are in full fruit. I sit crouched with my research team in camping chairs as dusk settles, our eyes intent on Rousettus madagascariensis, one of three species of endemic Malagasy fruit bat. The fox-faced bats flit deftly amongst the leafy branches, dodging our nets as they search out juicy pink fruits for their evening meal.

Our quiet vigil is interrupted by the arrival of a whistling gray-haired man from the nearby village who carries a net strung on a pole in one hand and a garish yellow plastic fuel can in the other. With a nod to us, he strides up to a neighboring tree and expertly scoops five of the feasting bats, pins the net to the ground with a bare hand, and coaxes the bats one-by-one into his yellow can. Mission accomplished, he straightens up with a wink and turns back home, rattling his can of bats in time to his whistle as he walks.

Handeha hihinina andrehy izy?” I ask my Malagasy colleagues in astonishment. Is he going to eat the bats? Laughing at my horror, they nod in affirmation.

Bats as reservoirs

I study zoonotic diseases, infections that transmit from wildlife to humans, as a graduate student in Princeton’s Department of Ecology and Evolutionary Biology. Bats are native reservoir hosts — meaning they host viruses without getting sick — for a number of the world’s most dangerous human diseases, including rabies, Ebola and SARS. I want to understand how bats host these viruses without getting sick and what factors contribute to the viruses’ spillover to human populations.

Field lab

Graduate student Cara Brook (rear) and colleague Christian Ranaivoson, a graduate student at the University of Antananarivo and an intern with the Pasteur Institute of Madagascar, process fresh bat fluids in their field lab in Maromizaha, Madagascar, in September 2014. (Photo by Deborah Bower.)

A lot of my work involves building mathematical models to understand disease. When I started graduate school, I barely understood what a “model” was. Four years later, I recognize that a model is simply a representation of reality — it can be physical, like a model of the solar system; experimental, like a mouse that a scientist infects to monitor disease progression; or mathematical, like the equations we use to describe disease transmission in my field of disease ecology.

The goal is to build simple models that still adequately represent reality. One of my professors, Bryan Grenfell, once told me, “If you apply a complex model to a complex system, then you have two things that you don’t understand.” If we can understand our models, then we can learn by observing the differences between these models and the more complex reality.

In disease ecology, our simple models are mathematical equations that class all potential disease hosts — bats, in my research — into three categories: (1) susceptible to infection; (2) currently infected; or (3) recovered from infection and now immune. We use our equations to predict how the proportion of hosts within each category changes over time, and then we collect data to determine whether our predictions match reality.

Remote corners

One of the ideas we are testing is whether bats are fundamentally different from other mammals in their capacity for resisting or tolerating viral infections. I build models depicting the spread of infected cells within individual bats and explore the physiological processes that might allow a bat cell to host a replicating virus without experiencing the cellular damage that causes the host to feel sick.

In the lab, I grow layers of bat cells, infect them with virus, and monitor cell-to-cell viral spread. Then I compare these data with what is predicted in my models. If the data match the model, then maybe the mechanism for disease mitigation that I chose for my model also is the one used in real life.

At a population level, bat-virus transmission, including spillover, peaks in the winter, and we want to know why. I build population-level transmission models that incorporate different seasonal pathways to cause winter infections, then I try to match those models to data. Collecting field data is hard — I spend years trekking to remote corners of Madagascar, mastering obscure Malagasy dialects, and rigging complex pulley systems out of nets, fishing lines and carabiners.

At the end of it all, like the man in Makira- Masoala, I catch a few bats. Instead of cooking them for dinner, however, I use fine-gauge needles, cryogenic vials and sterile swabs to collect their blood and other bodily fluids before I let them go. I haul the fluids in vats of liquid nitrogen to the laboratories of the Pasteur Institute of Madagascar in the capital city of Antananarivo. From there, samples are shipped to collaborators in London, Berlin, New York and Washington, D.C., while others remain in-country. My collaborators and I perform a variety of tests on these transported fluids to ascertain whether the bats were susceptible, infected or recovered from infection at the time of sampling.

When all is said and done, the results are sometimes difficult to interpret. Science is a gradual process, and the goal is to always narrow the window of possible hypotheses at least a little bit.

For me, science is a recognition of, as John Steinbeck put it, “how man is related to the whole thing.” I’m still trying to understand how humans fit into the zoonotic cycle of disease. I’m nearing the end of my Ph.D., but I have enough questions to keep me going for a lifetime.

Cara Brook is a fifth-year doctoral student. Her advisers are Andrew Dobson, professor of ecology and evolutionary biology; Bryan Grenfell, the Kathryn Briger and Sarah Fenton Professor of Ecology and Evolutionary Biology and Public Affairs; Andrea Graham, associate professor of ecology and evolutionary biology; and C. Jessica Metcalf, assistant professor of ecology and evolutionary biology and public affairs. Brook’s research is funded by the National Science Foundation, the National Geographic Society and PIVOT, a Madagascar-based health care nongovernmental society.

Exploring collective interactions of matter and antimatter

STRIP AWAY ELECTRONS FROM THEIR ATOMS and you get a plasma — a collection of negatively charged electrons and positively charged ions. But at high energies around compact cosmic objects such as black holes, quasars and pulsars, curious plasmas may form that, instead of ions, contain positrons, the antimatter counterparts of electrons.

Scientists are searching for ways of distinguishing this type of plasma from others, both in astrophysical environments and in laboratories on Earth. Julia Mikhailova, an assistant professor of mechanical and aerospace engineering, and Matthew Edwards, a graduate student in her lab, together with Professor of Astrophysical Sciences Nathaniel Fisch, found that, contrary to earlier claims, an electron-positron plasma would scatter some wavelengths of light surprisingly intensely via a process called Brillouin scattering.

This fundamental insight into the unusual behavior of matter-antimatter plasmas, published in the journal Physical Review Letters Jan. 8, 2016, may help to find such plasmas in space, or validate methods for creating them in the lab. The work was funded in part by the National Science Foundation and the National Nuclear Security Administration. –By Bennett McIntosh

In cells, self-destructive behavior suggests strategy for fighting cancer

SOMETIMES, TO SURVIVE, our cells destroy their own ribonucleic acid (RNA), the part of our genetic instruction code that helps turn genes into proteins. Cells do this as part of the first line of defense against pathogens and damage. New research suggests how this mechanism could form the basis of a strategy against cancer.

The mechanism is part of the body’s innate immune system, which kicks into gear minutes after infection. The innate immune system holds pathogens at bay for the critical few days needed to make antibodies.

One of the mysterious weapons in the innate immune system is an enzyme called RNase L that chops up strands of RNA, an intermediate step between genes and their final products, proteins. Because viruses lack the machinery to make copies of themselves to spread infection, they hijack a cell’s reproductive technology and force it to make viral RNA and proteins. To fight back, the body sends RNase L. (The “ase” is a common ending for enzymes, and the “L” is for latent, because RNase L lies in wait for infection or damage signals.)

RNase L chops up the viral RNA, but it also shears the body’s own RNA. This self-mutilation is necessary for good health. Mice that lack RNase L are obese, diabetic and have signs of inflammation.

“This cleavage of the cell’s own RNA has a protective function. It does not always kill the cell, but when it does it eliminates only damaged or infected cells, which repairs the tissue. It ultimately means animals survive better,” said Alexei Korennykh, an associate professor of molecular biology. His lab was the first to solve the crystal structure of human RNase L, a result they published in the journal Science March 14, 2014.

Korennykh’s research is funded by the National Institutes of Health, the Sidney Kimmel Foundation, the Burroughs Wellcome Fund and the Vallee Foundation.

With the 3-D structure in hand, Korennykh and his team turned to the question of how RNase L works. Korennykh wondered if RNase L chops up every RNA that comes along, or just certain ones. To find out, the researchers sequenced every piece of RNA made in a typical human cell and evaluated them to see which ones were susceptible to RNase L.

What they found surprised them. RNase L chops up RNA strands that govern the rapid division of cells, as well as how well cells stick to each other. These two activities — when cells proliferate and attach themselves in new locations — are two of the key steps in the spread of cancer. They published the findings Dec. 29, 2015, in the Proceedings of the National Academy of Sciences.

The link between RNase L and cancer made sense because RNase L mutations are common in individuals from families with a hereditary predisposition for prostate cancer, Korennykh said. The team is exploring how to turn this discovery into a strategy for inhibiting cancer’s spread using small drug-like molecules to boost RNase L’s activity against cell proliferation and attachment.

“We really stumbled on this approach very unexpectedly,” Korennykh said. “Often the best experiments are the ones where you didn’t get the results you expected.” –By Catherine Zandonella