An explanation for the mysterious onset of a universal process (Physics of Plasmas)

Solar flares
Magnetic reconnection happens in solar flares on the surface in the sun, as well as in experimental fusion energy reactors here on Earth. Image credit: NASA.

By John Greenwald, Princeton Plasma Physics Laboratory Communications

Scientists have proposed a groundbreaking solution to a mystery that has puzzled physicists for decades. At issue is how magnetic reconnection, a universal process that sets off solar flares, northern lights and cosmic gamma-ray bursts, occurs so much faster than theory says should be possible. The answer, proposed by researchers at the U.S. Department of Energy’s (DOE) Princeton Plasma Physics Laboratory (PPPL) and Princeton University, could aid forecasts of space storms, explain several high-energy astrophysical phenomena, and improve plasma confinement in doughnut-shaped magnetic devices called tokamaks designed to obtain energy from nuclear fusion.

Magnetic reconnection takes place when the magnetic field lines embedded in a plasma — the hot, charged gas that makes up 99 percent of the visible universe — converge, break apart and explosively reconnect. This process takes place in thin sheets in which electric current is strongly concentrated.

According to conventional theory, these sheets can be highly elongated and severely constrain the velocity of the magnetic field lines that join and split apart, making fast reconnection impossible. However, observation shows that rapid reconnection does exist, directly contradicting theoretical predictions.

Detailed theory for rapid reconnection

Now, physicists at PPPL and Princeton University have presented a detailed theory for the mechanism that leads to fast reconnection. Their paper, published in the journal Physics of Plasmas in October, focuses on a phenomenon called “plasmoid instability” to explain the onset of the rapid reconnection process. Support for this research comes from the National Science Foundation and the DOE Office of Science.

Plasmoid instability, which breaks up plasma current sheets into small magnetic islands called plasmoids, has generated considerable interest in recent years as a possible mechanism for fast reconnection. However, correct identification of the properties of the instability has been elusive.

Luca Comisson, PPPL
Luca Comisso, lead author of the study. Photo courtesy of PPPL.

The Physics of Plasmas paper addresses this crucial issue. It presents “a quantitative theory for the development of the plasmoid instability in plasma current sheets that can evolve in time” said Luca Comisso, lead author of the study. Co-authors are Manasvi Lingam and Yi-Min Huang of PPPL and Princeton, and Amitava Bhattacharjee, head of the Theory Department at PPPL and Princeton professor of astrophysical sciences.

Pierre de Fermat’s principle

The paper describes how the plasmoid instability begins in a slow linear phase that goes through a period of quiescence before accelerating into an explosive phase that triggers a dramatic increase in the speed of magnetic reconnection. To determine the most important features of this instability, the researchers adapted a variant of the 17th century “principle of least time” originated by the mathematician Pierre de Fermat.

Use of this principle enabled the researchers to derive equations for the duration of the linear phase, and for computing the growth rate and number of plasmoids created. Hence, this least-time approach led to a quantitative formula for the onset time of fast magnetic reconnection and the physics behind it.

The paper also produced a surprise. The authors found that such relationships do not reflect traditional power laws, in which one quantity varies as a power of another. “It is common in all realms of science to seek the existence of power laws,” the researchers wrote. “In contrast, we find that the scaling relations of the plasmoid instability are not true power laws – a result that has never been derived or predicted before.”

PPPL, on Princeton University’s Forrestal Campus in Plainsboro, N.J., is devoted to creating new knowledge about the physics of plasmas — ultra-hot, charged gases — and to developing practical solutions for the creation of fusion energy. The Laboratory is managed by Princeton University for the U.S. Department of Energy’s Office of Science, which is the largest single supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit

Read the abstract here: Comisso, L.; Lingam, M.; Huang, Y.-M.; Bhattacharjee, A. General theory of the plasmoid instability. Physics of Plasmas 23, 2016. DOI: 10.1063/1.4964481





Outlook for subtropical rainfall under climate change not so gloomy (Nature Climate Change)

Researchers found a clear difference in the rate of global surface warming (left panel) and the rate of subtropical rainfall decline (indicated by the brown shading in the right panel) when forced with an instantaneous increase of CO2. This is the main evidence to show that the subtropical rainfall decline is unrelated to the global surface warming. Credit: Jie He, Ph.D., Princeton University and Brian J. Soden, Ph.D., University of Miami Rosenstiel School of Marine and Atmospheric Science
Researchers found a clear difference in the rate of global surface warming (left panel) and the rate of subtropical rainfall decline (indicated by the brown shading in the right panel) when forced with an instantaneous increase of CO2. (Credit: Jie He, Ph.D., Princeton University and Brian J. Soden, Ph.D., University of Miami Rosenstiel School of Marine and Atmospheric Science)

By Diana Udel, University of Miami

Terrestrial rainfall in the subtropics — including the southeastern United States — may not decline in response to increased greenhouse gases as much as it could over oceans, according to a study from Princeton University and the University of Miami (UM). The study challenges previous projections of how dry subtropical regions could become in the future, and it suggests that the impact of decreased rainfall on people living in these regions could be less severe than initially thought.

“The lack of rainfall decline over subtropical land is caused by the fact that land will warm much faster than the ocean in the future — a mechanism that has been overlooked in previous studies about subtropical precipitation change,” said first author Jie He, a postdoctoral research associate in Princeton’s Program in Atmospheric and Oceanic Sciences who works at the National Oceanic and Atmospheric Administration’s Geophysical Fluid Dynamics Laboratory located on Princeton’s Forrestal Campus.

In the new study, published in the journal Nature Climate Change, He and co-author Brian Soden, a UM professor of atmospheric sciences, used an ensemble of climate models to show that rainfall decreases occur faster than global warming, and therefore another mechanism must be at play. They found that direct heating from increasing greenhouse gases is causing the land to warm faster than the ocean. The associated changes in atmospheric circulation are thus driving rainfall decline over the oceans rather than land.

Subtropical rainfall changes have been previously attributed to two mechanisms related to global warming: greater moisture content in air that is transported away from the subtropics, and a pole-ward shift in air circulation. While both mechanisms are present, this study shows that neither one is responsible for a decline in rainfall.

“It has been long accepted that climate models project a large-scale rainfall decline in the future over the subtropics. Since most of the subtropical regions are already suffering from rainfall scarcity, the possibility of future rainfall decline is of great concern,” Soden said. “However, most of this decline occurs over subtropical oceans, not land, due to changes in the atmospheric circulation induced by the more rapid warming of land than ocean.”

Most of the reduction in subtropical rainfall occurs instantaneously with an increase of greenhouse gases, independent of the warming of the Earth’s surface, which occurs much more slowly. According to the authors, this indicates that emission reductions would immediately mitigate subtropical rainfall decline, even though the surface will continue to warm for a long time.

He is supported by the Visiting Scientist Program at the department of Atmospheric and Oceanic Science, Princeton University.

Read the abstract:

The study, “A re-examination of the projected subtropical precipitation decline,” was published in the Nov. 14 issue of the journal Nature Climate Change.

Researchers’ Sudoku strategy democratizes powerful tool for genetics research (Nature Communications)

Princeton University researchers Buz Barstow (left), graduate student Kemi Adesina and undergraduate researcher Isao Anzai ’17,
Princeton University researchers Buz Barstow (left), graduate student Kemi Adesina and undergraduate researcher Isao Anzai, Class of 2017, with colleagues at Harvard Universiy, have developed a strategy called “Knockout Sodoku” for figuring out gene function.

By Tien Nguyen, Department of Chemistry

Researchers at Princeton and Harvard Universities have developed a way to produce the tools for figuring out gene function faster and cheaper than current methods, according to new research in the journal Nature Communications.

The function of sizable chunks of many organisms’ genomes is a mystery, and figuring out how to fill these information gaps is one of the central questions in genetics research, said study author Buz Barstow, a Burroughs-Wellcome Fund Research Fellow in Princeton’s Department of Chemistry. “We have no idea what a large fraction of genes do,” he said.

One of the best strategies that scientists have to determine what a particular gene does is to remove it from the genome, and then evaluate what the organism can no longer do. The end result, known as a whole-genome knockout collection, provides full sets of genomic copies, or mutants, in which single genes have been deleted or “knocked out.” Researchers then test the entire knockout collection against a specific chemical reaction. If a mutant organism fails to perform the reaction that means it must be missing the particular gene responsible for that task.

It can take several years and millions of dollars to build a whole-genome knockout collection through targeted gene deletion. Because it’s so costly, whole-genome knockout collections only exist for a handful of organisms such as yeast and the bacterium Escherichia coli. Yet, these collections have proven to be incredibly useful as thousands of studies have been conducted on the yeast gene-deletion collection since its release.

The Princeton and Harvard researchers are the first to create a collection quickly and affordably, doing so in less than a month for several thousand dollars. Their strategy, called “Knockout Sudoku,” relies on a combination of randomized gene deletion and a powerful reconstruction algorithm. Though other research groups have attempted this randomized approach, none have come close to matching the speed and cost of Knockout Sudoku.

“We sort of see it as democratizing these powerful tools of genetics,” said Michael Baym, a co-author on the work and a Harvard Medical School postdoctoral researcher. “Hopefully it will allow the exploration of genetics outside of model organisms,” he said.

Their approach began with steep pizza bills and a technique called transposon mutagenesis that ‘knocks out’ genes by randomly inserting a single disruptive DNA sequence into the genome. This technique is applied to large colonies of microbes to ensure the likelihood that every single gene is disrupted. For example, the team started with a colony of about 40,000 microbes for the bacterium Shewanella oneidensis, which has approximately 3,600 genes in its genome.

Barstow recruited undergraduates and graduate students to manually transfer 40,000 mutants out of laboratory Petri dishes into separate wells using toothpicks. He offered pizza as an incentive, but after a full day of labor, they only managed to move a couple thousand mutants. “I thought to myself, ‘Wait a second, this pizza is going to ruin me,’” Barstow said.

Instead, they decided to rent a colony-picking robot. In just two days, the robot was able to transfer each mutant microbe to individual homes in 96-well plates, 417 plates in total.

But the true challenge and opportunity for innovation was in identifying and cataloging the mutants that could comprise a whole-genome knockout collection in a fast and practical way.

DNA amplification and sequencing is a straightforward way to identify each mutant, but doing it individually quickly gets very expensive and time-consuming. So the researchers’ proposed a scheme in which mutants could be combined into groups that would only require 61 amplification reactions and a single sequencing run.

But still, after sequencing each of the pools, the researchers had an incredible amount of data. They knew the identities of all the mutants, but now they had to figure exactly where each mutant came from in the grid of plates. This is where the Sudoku aspect of the method came in. The researchers built an algorithm that could deduce the location of individual mutants through its repeated appearance in various row, column, plate-row and plate-column pools.

Knockout sodoku helps find genes' functions.

But there’s a problem. Because the initial gene-disruption process is random, it’s possible that the same mutant is formed more than once, which means that playing Sudoku wouldn’t be simple. To find a solution for this issue, Barstow recalled watching the movie, “The Imitation Game,” about Alan Turing’s work on the enigma code, for inspiration.

“I felt like the problem in some ways was very similar to code breaking,” he said. There are simple codes that substitute one letter for another that can be easily solved by looking at the frequency of the letter, Barstow said. “For instance, in English the letter A is used 8.2 percent of the time. So, if you find that the letter X appears in the message about 8.2 percent of the time, you can tell this is supposed to be decoded as an A. This is a very simple example of Bayesian inference.”

With that same logic, Barstow and colleagues developed a statistical picture of what a real location assignment should look like based on a mutant that only appeared once and used that to rate the likelihood of possible locations being real.

“One of the things I really like about this technique is that it’s a prime example of designing a technique with the mathematics in mind at the outset which lets you do much more powerful things than you could do otherwise,” Baym said. “Because it was designed with the mathematics built in, it allows us to get much, much more data out of much less experiments,” he said.

Using their expedient strategy, the researchers created a collection for microbe Shewanella oneidensis. These microbes are especially good at transferring electrons and understanding their powers could prove highly valuable for developing sustainable energy sources, such as artificial photosynthesis, and for environmental remediation in the neutralization of radioactive waste.

Using the resultant collection, the team was able to recapitulate 15 years of research, Barstow said, bolstering their confidence in their method. In an early validation test, they noticed a startlingly poor accuracy rate. After finding no fault with the math, they looked at the original plates to realize that one of the researchers had grabbed the wrong sample. “The least reliable part of this is the human,” Barstow said.

The work was supported by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund and Princeton University startup funds and Fred Fox Class of 1939 funds.

Read the full article here:

Baym, M.; Shaker, L.; Anzai, I. A.; Adesina, O.; Barstow, B. “Rapid construction of a whole-genome transposon insertion collection for Shewanella oneidensis by Knockout Sudoku.” Nature Comm. Available online on Nov. 10, 2016.