Research Highlights

In a recent Science paper, researchers led by JILA and NIST Fellow Jun Ye, along with collaborators JILA and NIST Fellow David Nesbitt, scientists from the University of Nevada, Reno, and Harvard University, observed novel ergodicity-breaking in C60, a highly symmetric molecule composed of 60 carbon atoms arranged on the vertices of a “soccer ball” pattern (with 20 hexagon faces and 12 pentagon faces). Their results revealed ergodicity breaking in the rotations of C60. Remarkably, they found that this ergodicity breaking occurs without symmetry breaking and can even turn on and off as the molecule spins faster and faster. Understanding ergodicity breaking can help scientists design better-optimized materials for energy and heat transfer. 

Many everyday systems exhibit “ergodicity” such as heat spreading across a frying pan and smoke filling a room. In other words, matter or energy spreads evenly over time to all system parts as energy conservation allows. On the other hand, understanding how systems can violate (or “break”) ergodicity, such as magnets or superconductors, helps scientists understand and engineer other exotic states of matter.

In a new ACS Nano paper, JILA and NIST Fellow David Nesbitt, along with former graduate student Jacob Pettine and other collaborators, developed a new method for measuring the dynamics of specific particles known as “hot carriers,” as a function of both time and energy, unveiling detailed information that can be used to improve collection efficiencies.

Although one might think it would be simple, the genetics of bacteria can be rather complicated. A bacterium’s genes use a set of regulatory proteins and other molecules to monitor and change genetic expressions within the organism. One such mechanism is the riboswitch, a small piece of RNA that can turn a gene “on” or “off.” In order to “flip” this genetic switch, a riboswitch must bind to a specific ion or molecule, called a ligand, at a special riboswitch site called the aptamer. The ligand either activates the riboswitch (allowing it to regulate gene expression) or inactivates it until the ligand unbinds and leaves the aptamer. Understanding the relationship between ligands and aptamers can have big implications for many fields, including healthcare.  “Understanding riboswitches and gene expression can help us develop better antimicrobial drugs,” explained JILA graduate student Andrea Marton Menendez. “The more we know about how to attack bacteria, the better, and if we can just target one small interaction that prevents or abets a gene from being translated or transcribed, we may have an easier way to treat bacterial infections.”  
To better understand the dynamics of aptamer and ligand binding, Marton Menendez, along with JILA and NIST Fellow David Nesbitt, looked at the lysine (an amino acid) riboswitch in Bacillus subtilis, a common type of bacterium present in environments ranging from cow stomachs to deep sea hydrothermal vents. With this model organism, the researchers studied how different secondary ligands, like, potassium, cesium, and sodium, affect riboswitch activation, or its physical folding. The results have been published in the Journal of Physical Chemistry B.

JILA researchers have upgraded a breathalyzer based on Nobel Prize-winning frequency-comb technology and combined it with machine learning to detect SARS-CoV-2 infection in 170 volunteer subjects with excellent accuracy. Their achievement represents the first real-world test of the technology’s capability to diagnose disease in exhaled human breath.

There are many ways to diagnose health conditions. One of the most common methods is blood testing. This sort of test can look for hundreds of different kinds of molecules in the body to determine if an individual has any diseases or underlying conditions. Not everyone is a fan of needles, however, which makes blood tests a big deal for some people. Another method of diagnosis is breath analysis. In this process, an individual's breath is measured for different molecules as indicators of certain health conditions. Breath analysis has been fast progressing in recent years and is continuing to gain more and more research interest. It is, however, experimentally challenging due to the extremely low concentrations of molecules present in each breath, limited number of detectable molecular species, and the long data-analysis time required. Now, a JILA-based collaboration between the labs of NIST Fellows Jun Ye and David Nesbitt has resulted in a more robust and precise breath-testing apparatus. In combining a special type of laser with a mirrored cavity, the team of researchers was able to precisely measure four molecules in human breath at unprecedented sensitivity levels, with the promise of measuring many more types of molecules. The team published their findings in the Proceedings of the National Academy of Sciences (PNAS).

The basic question of how strands of nucleic acids (DNA and RNA) fold and hybridize has been studied thoroughly by biophysicists around the globe. In particular, there can be unexpected challenges in obtaining accurate kinetic data when studying the physics of how DNA and RNA fold and unfold at the single molecule level. One problem comes from temporal camera blur, as the cameras used to capture single photons emitted by these molecules do so in a finite time window that can blur the image and thereby skew the kinetics. In a paper published in the Journal of Physical Chemistry B, JILA Fellow David Nesbitt, and first author David Nicholson, propose an extremely simple yet broadly effective way to overcome this camera blur. 

Quantum technologies could process information even faster if they could harness the speed of light. Using gold nanostars, the Nesbitt Lab have found a way to use light to steer electric currents. 

JILA researchers have created a laser-controlled "electron faucet", which emits a stable stream of low-energy electrons. These faucets have many applications for ultrafast switches and ultrafast electron imaging. The electron faucet starts with gold, spherical nanoshells. “They are glass cores with a thin, gold layer over them,” said Jacob Pettine, the graduate student on the project. These nanoshells are truly on the nanoscale, measuring less than 150 nanometers in diameter, which is “something like a thousandth of the size of a human hair,” said Pettine.

The Nesbitt group has invented a nifty technique for exploring the physics and chemistry of a gas interacting with molecules on the surface of a liquid. The group originally envisioned the technique because it’s impossible to overestimate the importance of understanding surface chemistry. For instance, ozone depletion in the atmosphere occurs because of chemical reactions of hydrochloric acid on the surface of ice crystals and aerosols in the upper atmosphere. Interstellar chemistry takes place on the surface of tiny grains of dust.

A wildly successful JILA (Nesbitt Group)-NIH collaboration is opening the door to studies of RNA behavior, including binding, folding and other factors that affect structural changes of RNA from living organisms. Such structural changes determine RNA enzymatic functions, including the regulation of genetic information.

Biomolecules may not always behave the same way in test tubes as they do in living cells, a fact underscored by important new work by former research associate Nick Dupuis, graduate student Erik Holmstrom, and Fellow David Nesbitt. The researchers found that under crowded conditions that begin to mimic those found in cells, single RNA molecules folded 35 times faster than in the dilute solutions typically used in test-tube experiments.

Graduate student Erik Holmstrom and Fellow David Nesbitt have applied their laboratory research on the rates of RNA folding and unfolding to the medically important enzyme telomerase. Telomerase employs both protein and RNA components to lengthen chromosomes, which are shortened every time they are copied.

The Nesbitt group has figured out the central role of “plasmon resonances” in light-induced emission of electrons from gold or silver nanoparticles. Plasmons are rapid-fire electron oscillations of freely moving (conduction) electrons in metals. They are caused by light of just the “right frequency.”

The interface between a gas and a solid is a remarkable environment for new investigations. Lots of fascinating chemistry takes place there, including catalysis. Catalysis is acceleration of a chemical reaction that is caused by an element like platinum that remains unchanged by a chemical reaction. For instance platinum catalyzes the transformation of carbon monoxide (CO) into carbon dioxide (CO2) in automobile catalytic converters. A better understanding of catalysis could improve the efficiency of manufacturing important chemicals as well as expanding our fundamental knowledge of chemistry.

The Nesbitt group has been investigating RNA folding since the early 2000s. The group’s goal has been to gain a detailed understanding of the relationship between structure and function in this important biomolecule. One challenge has been figuring out how unfolded RNA molecules assume the proper three-dimensional (3D) shape to perform their biological activities. To accomplish this, the researchers have shown how biologically active RNA is able to neutralize negative charges that end up in close proximity to each other after folding into a 3D structure.

The Nesbitt group wants to figure out how chemistry works in outer space. In particular, the group wants to understand the “cosmo”-chemistry leading to the generation of soot, which is similar to products of combustion here on Earth.

In microscopic studies of single biological molecules or nanoparticles, it’s useful to be able to precisely control the temperature around the sample. Until now, heating has required electric currents that warm up microscope stages, slides, and optics in addition to the specimen under study. Such methods are slow and hard to control, not to mention capable of accidentally altering the chemistry or structure of the sample. Now there is a better solution for keeping samples nice and warm: The nanobathtub.

Quantum dots are tiny structures made of semiconductor materials. With diameters of 1–5 nm, they are small enough to constrain their constituents in all three dimensions. This constraint means that when a photon of light knocks an electron into the conduction band and creates an electron/hole pair, the pair can’t get out of the dot.

Imagine being able to study how molecules form on the quantum level. It turns out that researchers have already figured out some nifty techniques involving lasers and jets of reactive atoms for doing just that in a gaseous environment. Now graduate student Alex Zolot, former Visiting Fellow Paul Dagdikian of Johns Hopkins University, and Fellow David Nesbitt have taken this kind of study into a whole different arena: They recently probed the molecules that form when the surface of a liquid is bombarded with a very reactive gas.

For many years, chemists have explored the differences between liquids and solids. One difference is that liquid surfaces tend to be softer than solid surfaces (from the perspective of molecules crashing onto them). Another difference is that the surface of at least one oily liquid (perfluorinated polyether, or PFPE) actually gets stickier as it gets hotter, according to a new study by graduate student Brad Perkins and Fellow David Nesbitt. This behavior contrasts with solid surfaces, which usually get stickier when they get colder!