New finding helps explain rainforests’ influence on global climate
By Catherine Zandonella, Office of the Dean for Research
Despite their diversity, the structure of most tropical rainforests is highly predictable. Scientists have described the various sizes of the trees by a simple mathematical relationship called a power law.
In a new study using data from a rainforest in Panama, researchers determined that competition for sunlight is the underlying cause of this common structure, which is observed in rainforests around the globe despite differences in plant species and geography. The new finding can be used in climate simulations to predict how rainforests absorb excess carbon dioxide from the atmosphere.
The researchers found that the rainforest structure stems from what happens after a tall tree falls and creates a gap in the canopy. The gap enables sunlight to reach the forest floor and fuel the rapid growth of small trees. Over time, the trees’ crowns grow to fill the gap until the point where not all of the trees can fit in the sunlit patch. Some will be left behind in the shade of their competitors.
“This process of moving from fast growth in the sun to slow growth in the shade sets up this characteristic size structure that is common across tropical rainforests, despite the differences in their environments,” said Caroline Farrior, first author of the study who is a postdoctoral fellow at the National Institute for Mathematical and Biological Synthesis and will soon be an assistant professor of integrative biology at the University of Texas-Austin.
(View a video interview with Dr. Farrior courtesy of the National Institute for Mathematical and Biological Synthesis.)
“Rainforests store about twice as much carbon as other forests,” Pacala said. “About half of that is due to huge trees, but the other half is all that stuff in the middle. It is not possible to build an accurate climate model without getting that right.”
To gain an understanding of how rainforests grow, Farrior and colleagues analyzed decades of tree census data from a 50-hectare plot on Barro Colorado Island in the Panama Canal. From these data, they identified the mechanism most important in driving the observed size structure in tropical rainforests.
“With this new understanding of tropical forests, we can go on to build better models, we can make more accurate estimates of the carbon storage that’s currently in tropical forests, and we can go on to more accurately predict the pace of climate change in the future,” Farrior said.
The research included work by Stephanie Bohlman, an assistant professor at the University of Florida and a research associate at the Smithsonian Tropical Research Institute (STRI), and Stephen Hubbell, a staff scientist at STRI.
The study was supported by Princeton’s Carbon Mitigation Initiative and the National Institute for Mathematical and Biological Synthesis (NSF grant no. DBI-1300426) at the University of Tennessee-Knoxville. The Barro Colorado Island forest dynamics research project was founded by Stephen Hubbell, Robin Foster and Richard Condit of STRI.
The study, “Dominance of the suppressed: Power-law size structure in tropical forests,” by Caroline Farrior, Stephanie Bohlman, Stephen Hubbell and Stephen Pacala, appeared in the journal Science on Jan. 8, 2016.
Scientists at the U.S. Department of Energy’s Princeton Plasma Physics Laboratory (PPPL) have produced self-consistent computer simulations that capture the evolution of an electric current inside fusion plasma without using a central electromagnet, or solenoid.
The computer simulations of the process, known as non-inductive current ramp-up, were performed using TRANSP, the gold-standard code developed at PPPL. The results were published in October 2015 in the journal Nuclear Fusion. The research was supported by the DOE Office of Science.
In traditional donut-shaped tokamaks, a large solenoid runs down the center of the reactor. By varying the electrical current in the solenoid scientists induce a current in the plasma. This current starts up the plasma and creates a second magnetic field that completes the forces that hold the hot, charged gas together.
But spherical tokamaks, a compact variety of fusion reactor that produces high plasma pressure with relatively low magnetic fields, have little room for solenoids. Spherical tokamaks look like cored apples and have a smaller central hole for the solenoid than conventional tokamaks do. Physicists, therefore, have been trying to find alternative methods for producing the current that starts the plasma and completes the magnetic field in spherical tokamaks.
One such method is known as coaxial helicity injection (CHI). During CHI, researchers switch on an electric coil that runs beneath the tokamak. Above this coil is a gap that opens into the tokamak’s vacuum vessel and circles the tokamak’s floor. The switched-on electrical current produces a magnetic field that connects metal plates on either side of the gap.
Researchers next puff gas through the gap and discharge a spark across the two plates. This process causes magnetic reconnection — the process by which the magnetic fields snap apart and reconnect. This reconnection creates a magnetic bubble that fills the tokamak and produces the vital electric current that starts up the plasma and completes the magnetic field.
This current must be nurtured and fed. According to lead author Francesca Poli, the new computer simulations show that the current can best be sustained by injecting high-harmonic radio-frequency waves (HHFWs) and neutral beams into the plasma.
HHFW’s are radio-frequency waves that can heat both electrons and ions. The neutral beams, which consist of streams of hydrogen atoms, become charged when they enter the plasma and interact with the ions. The combination of the HHFWs and neutral beams increases the current from 300 kiloamps to 1 mega amp.
But neither HHFWs nor neutral beams can be used at the start of the process, when the plasma is relatively cool and not very dense. Poli found that HHFWs would be more effective if the plasma were first heated by electron cyclotron waves, which transfer energy to the electrons that circle the magnetic field lines.
“With no electron cyclotron waves you would have to pump in four megawatts of HHFW power to create 400 kiloamps of current,” she said. “With these waves you can get the same amount of current by pumping in only one megawatt of power.
“All of this is important because it’s hard to control the plasma at the start-up,” she added. “So the faster you can control the plasma, the better.”
F.M. Poli, R.G. Andre, N. Bertelli, S.P. Gerhardt, D. Mueller and G. Taylor. “Simulations towards the achievement of non-inductive current ramp-up and sustainment in the National Spherical Torus Experiment Upgrade.” Nuclear Fusion. Published October 30, 2015. DOI: 10.1088/0029-5515/55/12/123011
Researchers from Princeton University have identified genes important for age-related cognitive declines in memory in adult worm neurons, which had not been studied previously. The research, published in the journal Nature, could eventually point the way toward therapies to extend life and enhance health in aging human populations.
The small soil-dwelling roundworm, Caenorhabditis elegans, contains genes that determine the rate of aging and overall health during aging. Mutations in one of these genetic pathways, the insulin/IGF-1 signaling (IIS) pathway, can double worm lifespan. Similar mutations in humans have been found in long-lived humans.
But studying the IIS mutation in adult worm neurons was difficult because the adults have a thick, durable covering that protects the neurons.
Using a new technique they developed to break up the tough outer covering, researchers at Princeton succeeded in isolating adult neurons, which enabled the detection of the new set of genes regulated by the insulin/IGF-1 signaling pathway.
“Our technique enabled us to study gene expression in adult neurons, which are the cells that govern cognitive aspects such as memory and nerve-regeneration,” said Murphy, whose research on aging is funded in part by the National Institutes of Health. “Prior to this work, researchers were only able to examine gene regulation either using adult worms or individual tissues from young worms.”
The work allowed co-first authors Rachel Kaletsky and Vanisha Lakhina to explore why long-lived IIS mutants maintain memory and neuron-regeneration abilities with age. Until now, the known targets of the insulin longevity pathway were located mostly in the intestine and skin of the worm rather than the neurons. Kaletsky is a postdoctoral research fellow and Lakhina is a postdoctoral research associate in the Lewis-Sigler Institute.
Kaletsky worked out the new way to isolate neurons from adult worms, and with Lakhina, proceeded to profile the gene activity in adult C. elegans neurons for the first time. They discovered that the IIS mutant worms express genes that keep neurons working longer, and that these genes are completely different from the previously known longevity targets. They also discovered a new factor that is responsible for nerve cell (axon) regeneration in adult worms, which could have implications for human traumatic brain injury.
“Kaletsky and Lakhina developed a new technique that is going to be used by the entire worm community, so it really opens up new avenues of research even beyond the discoveries we describe in the paper,” Murphy said.
One of the newly identified genes, fkh-9, regulates both enhanced memory and neuronal regeneration in IIS mutants. Previous studies have detected only one other gene that regulates neuronal regeneration in the mutants, demonstrating the power of the technique to identify new gene regulators. The researchers also found that fkh-9 gene expression is required for long lifespan in many IIS mutants, but it did not play that role in neurons, suggesting the gene governs multiple outcomes in the worm.
Murphy’s lab is now working to understand how fkh-9 works to influence memory, axon regeneration, and lifespan. The gene codes for a protein, FKH-9, that acts as a transcription factor, meaning it controls the expression of other genes and is likely part of a larger regulatory network. FKH-9 also appears to regulate different processes in different tissues: It is required in neurons for memory and axon repair, but not for lifespan. Murphy’s group is working to figure out how FKH-9 acts in distinct tissues to regulate such different processes.
The study provides a more complete picture of how IIS mutants control gene expression in different tissues to promote healthy aging, Murphy said.
“fkh-9 is likely only one of the exciting genes that will emerge from using this technique,” Murphy said. “By identifying the suite of IIS-regulated neuronal genes, there are many candidates for follow-up, only a fraction of which have been characterized in any great detail,” she said.
Other contributors to the study included Rachel Arey, a postdoctoral research fellow; former graduate students April Williams and Jessica Landis; and Jasmine Ashraf, a research specialist in the Lewis-Sigler Institute.
Additional funding for the study was provided by the Keck Foundation, the Ruth L. Kirschstein National Research Service Awards, the National Science Foundation and the New Jersey Commission on Brain Injury Research.
The article, The C. elegans adult neuronal IIS/FOXO transcriptome reveals adult phenotype regulators, by Rachel Kaletsky, Vanisha Lakhina, Rachel Arey, April Williams, Jessica Landis, Jasmine Ashraf and Coleen T. Murphy, was published in the journal Nature online ahead of print on December 14, 2015. doi:10.1038/nature16483.
By Raphael Rosen, Princeton Plasma Physics Laboratory Communications
A team of physicists led by Stephen Jardin of the U.S. Department of Energy’s Princeton Plasma Physics Laboratory (PPPL) has discovered a mechanism that prevents the electrical current flowing through fusion plasma from repeatedly peaking and crashing. This behavior is known as a “sawtooth cycle” and can cause instabilities within the plasma’s core. The results have been published online in Physical Review Letters. The research was supported by the DOE Office of Science.
The team, which included scientists from General Atomics and the Max Planck Institute for Plasma Physics, performed calculations on the Edison computer at the National Energy Research Scientific Computing Center, a division of the Lawrence Berkeley National Laboratory. Using M3D-C1, a program they developed that creates three-dimensional simulations of fusion plasmas, the team found that under certain conditions a helix-shaped whirlpool of plasma forms around the center of the tokamak. The swirling plasma acts like a dynamo — a moving fluid that creates electric and magnetic fields. Together these fields prevent the current flowing through plasma from peaking and crashing.
The researchers found two specific conditions under which the plasma behaves like a dynamo. First, the magnetic lines that circle the plasma must rotate exactly once, both the long way and the short way around the doughnut-shaped configuration, so an electron or ion following a magnetic field line would end up exactly where it began. Second, the pressure in the center of the plasma must be significantly greater than at the edge, creating a gradient between the two sections. This gradient combines with the rotating magnetic field lines to create spinning rolls of plasma that swirl around the tokamak and gives rise to the dynamo that maintains equilibrium and produces stability.
This dynamo behavior arises only under certain conditions. Both the electrical current running through the plasma and the pressure that the plasma’s electrons and ions exert on their neighbors must be in a range that is “not too large and not too small,” said Jardin. In addition, the speed at which the conditions for the fusion reaction are established must be “not too fast and not too slow.”
Jardin stressed that once a range of conditions like pressure and current are set, the dynamo phenomenon occurs all by itself. “We don’t have to do anything else from the outside,” he noted. “It’s something like when you drain your bathtub and a whirlpool forms over the drain by itself. But because a plasma is more complicated than water, the whirlpool that forms in the tokamak needs to also generate the voltage to sustain itself.”
During the simulations the scientists were able to virtually add new diagnostics, or probes, to the computer code. “These diagnostics were able to measure the helical velocity fields, electric potential, and magnetic fields to clarify how the dynamo forms and persists,” said Jardin. The persistence produces the “voltage in the center of the discharge that keeps the plasma current from peaking.”
Physicists have indirectly observed what they believe to be the dynamo behavior on the DIII-D National Fusion Facility that General Atomics operates for the Department of Energy in San Diego and on the ASDEX Upgrade in Garching, Germany. They hope to learn to create these conditions on demand, especially in ITER, the huge multinational fusion machine being constructed in France to demonstrate the practicality of fusion power. “Now that we understand it better, we think that computer simulations will show us under what conditions this will occur in ITER,” said Jardin. “That will be the focus of our research in the near future.”
Learning how to create these conditions will be particularly important for ITER, which will produce helium nuclei that could amplify the sawtooth disruptions. If large enough, these disruptions could cause other instabilities that could halt the fusion process. Preventing the cycle from starting would therefore be highly beneficial for the ITER experiment.
The warming effects of climate change usually conjure up ideas of parched and barren landscapes broiling under a blazing sun, its heat amplified by greenhouse gases. But a study led by Princeton University researchers suggests that hotter nights may actually wield much greater influence over the planet’s atmosphere as global temperatures rise — and could eventually lead to more carbon flooding the atmosphere.
Since measurements began in 1959, nighttime temperatures in the tropics have had a strong influence over year-to-year shifts in the land’s carbon-storage capacity, or “sink,” the researchers report in the journal Proceedings of the National Academy of Sciences. Earth’s ecosystems absorb about 25% of the excess carbon from the atmosphere, and tropical forests account for about one-third of land-based plant productivity.
During the past 50 years, the land-based carbon sink’s “interannual variability” has grown by 50 to 100 percent, the researchers found. The researchers used climate- and satellite-imaging data to determine which of various climate factors — including rainfall, drought and daytime temperatures — had the most effect on the carbon sink’s swings. They found the strongest association with variations in tropical nighttime temperatures, which have risen by about 0.6 degrees Celsius since 1959.
First author William Anderegg, an associate research scholar in the Princeton Environmental Institute, explained that he and his colleagues determined that warm nighttime temperatures lead plants to put more carbon into the atmosphere through a process known as respiration.
Just as people are more active on warm nights, so too are plants. Although plants take up carbon dioxide from the atmosphere, they also internally consume sugars to stay alive. That process, known as respiration, produces carbon dioxide. Plants step up respiration in warm weather, Anderegg said. The researchers found that yearly variations in the carbon sink strongly correlated with variations in plant respiration.
“When you heat up a system, biological processes tend to increase,” Anderegg said. “At hotter temperatures, plant respiration rates go up and this is what’s happening during hot nights. Plants lose a lot more carbon than they would during cooler nights.”
Previous research has shown that nighttime temperatures have risen significantly faster as a result of climate change than daytime temperatures, Anderegg said. This means that in future climate scenarios respiration rates could increase to the point that the land is putting more carbon into the atmosphere than it’s taking out, “which would be disastrous,” he said.
Of course, plants consume carbon dioxide as a part of photosynthesis, during which they convert sunlight into energy. Photosynthesis also is sensitive to rises in temperature, but it occurs only during the day, whereas respiration occurs at all hours and thus is more sensitive to nighttime warming, Anderegg said.
“Nighttime temperatures have been increasing faster than daytime temperatures and will continue to rise faster,” Anderegg said. “This suggests that tropical ecosystems might be more vulnerable to climate change than previously thought, risking crossing the threshold from a carbon sink to a carbon source. But there’s certainly potential for plants to acclimate their respiration rates and that’s an area that needs future study.”
This research was supported by the National Science Foundation MacroSystems Biology Grant (EF-1340270), RAPID Grant (DEB-1249256) and EAGER Grant (1550932); and a National Oceanic and Atmospheric Administration (NOAA) Climate and Global Change postdoctoral fellowship administered by the University Corporation of Atmospheric Research.
William R. L. Anderegg, Ashley P. Ballantyne, W. Kolby Smith, Joseph Majkut, Sam Rabin, Claudie Beaulieu, Richard Birdsey, John P. Dunne, Richard A. Houghton, Ranga B. Myneni, Yude Pan, Jorge L. Sarmiento, Nathan Serota, Elena Shevliakova, Pieter Tan and Stephen W. Pacala. “Tropical nighttime warming as a dominant driver of variability in the terrestrial carbon sink.” Proceedings of the National Academy of Sciences, published online in-advance of print Dec. 7, 2015. DOI: 10.1073/pnas.1521479112.
By Raphael Rosen, Princeton Plasma Physics Laboratory Communications
Physicists at the U.S. Department of Energy’s (DOE) Princeton Plasma Physics Laboratory (PPPL) are proposing a new way to process nuclear waste that uses a plasma-based centrifuge. Known as plasma mass filtering, the new mass separation techniques would supplement chemical techniques. It is hoped that this combined approach would reduce both the cost of nuclear waste disposal and the amount of byproducts produced during the process. This work was supported by PPPL’s Laboratory Directed Research and Development Program.
“The safe disposal of nuclear waste is a colossal problem,” said Renaud Gueroult, staff physicist at PPPL and lead author of the paper that appeared in the Journal of Hazardous Materials in October. “One solution might be to supplement existing chemical separation techniques with plasma separation techniques, which could be economically attractive, ideally leading to a reevaluation of how nuclear waste is processed.”
The immediate motivation for safe disposal is the radioactive waste stored currently at the Hanford Site, a facility in Washington State that produced plutonium for nuclear weapons during the Cold War. The volume of this waste originally totaled 54 million gallons and was stored in 177 underground tanks.
In 2000, Hanford engineers began building machinery that would encase the radioactive waste in glass. The method, known as “vitrification,” had been used at another Cold War-era nuclear production facility since 1996. A multibillion-dollar vitrification plant is currently under construction at the Hanford site.
To reduce the cost of high-level waste vitrification and disposal, it may be advantageous to reduce the number of high-level glass canisters by packing more waste into each glass canister. To reduce the volume to be vitrified, it would be advantageous to separate the nonradioactive waste, like aluminum and iron, out of the waste, leaving less waste to be vitrified. However, in its 2014 report, the DOE Task Force on Technology Development for Environmental Management argued that, “without the development of new technology, it is not clear that the cleanup can be completed satisfactorily or at any reasonable cost.”
The high-throughput, plasma-based, mass separation techniques advanced at PPPL offer the possibility of reducing the volume of waste that needs to be immobilized in glass. “The interesting thing about our ideas on mass separation is that it is a form of magnetic confinement, so it fits well within the Laboratory’s culture,” said physicist Nat Fisch, co-author of the paper and director of the Princeton University Program in Plasma Physics. “To be more precise, it is ‘differential magnetic confinement’ in that some species are confined while others are lost quickly, which is what makes it a high-throughput mass filter.”
How would a plasma-based mass filter system work? The method begins by atomizing and ionizing the hazardous waste and injecting it into the rotating filter so the individual elements can be influenced by electric and magnetic fields. The filter then separates the lighter elements from the heavier ones by using centrifugal and magnetic forces. The lighter elements are typically less radioactive than the heavier ones and often do not need to be vitrified. Processing of the high-level waste therefore would need fewer high-level glass canisters overall, while the less radioactive material could be immobilized in less costly wasteform (e.g., concrete, bitumen).
The new technique would also be more widely applicable than traditional chemical-based methods since it would depend less on the nuclear waste’s chemical composition. While “the waste’s composition would influence the performance of the plasma mass filter in some ways, the effect would most likely be less than that associated with chemical techniques,” said Gueroult.
Gueroult points out why savings by plasma techniques can be important. “For only about $10 a kilogram in energy cost, solid waste can be ionized. In its ionized form, the waste can then be separated into heavy and light components. Because the waste is atomized, the separation proceeds only on the basis of atomic mass, without regard to the chemistry. Since the total cost of chemical-based techniques can be $2,000 per kilogram of the vitrified waste, as explained in the Journal of Hazardous Materials paper, it stands to reason that even if several plasma-based steps are needed to achieve pure enough separation, there is in principle plenty of room to cut the overall costs. That is the point of our recent paper. It is also why we are excited about our plasma-based methods.”
Fisch notes that “our original ideas grew out of the thesis of Abe Fetterman, who began by considering centrifugal mirror confinement for nuclear fusion, but then realized the potential for mass separation. Now the key role on this project is being played by Renaud, who has developed the concept substantially further.”
According to Fisch, the current developments are a variation and refinement of a plasma-based mass separation system first advanced by a private company called Archimedes Technology Group. That company, started by the late Dr. Tihiro Ohkawa, a fusion pioneer, raised private capital to advance a plasma-based centrifuge concept to clean up the legacy waste at Hanford, but ceased operation in 2006 after failing to receive federal funding.
Now an updated understanding of the complexity of the Hanford problem, combined with an increased appreciation of new ideas, has led to renewed federal interest in waste-treatment solutions. Completion of the main waste processing operations, which was in 2002 projected for 2028, has slipped by 20 years over the last 13 years, and the total cleanup cost is now estimated by the Department of Energy to be greater than 250 billion dollars, according to the DOE Office of Inspector General, Office of Audits and Inspections. DOE, which has the responsibility of cleaning up the legacy nuclear waste at Hanford and other sites, conducted a Basic Research Needs Workshop on nuclear waste cleanup in July that both Fisch and Gueroult attended. The report of that workshop, which is expected to highlight new approaches to the cleanup problem, is due out this fall.
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. Results of PPPL research have ranged from a portable nuclear materials detector for anti-terrorist use to universally employed computer codes for analyzing and predicting the outcome of fusion experiments. The Laboratory is managed by the 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 science.energy.gov.
Renaud Gueroult, David T. Hobbs, Nathaniel J. Fisch. “Plasma filtering techniques for nuclear waste remediation.” Journal of Hazardous Materials, published October 2015. doi:10.1016/j.jhazmat.2015.04.058.
Stopping the outbreak of a disease hinges on a wealth of data such as what makes a suitable host and how a pathogen spreads. But gathering these data can be difficult for diseases in remote areas of the world, or for epidemics involving wild animals.
A new study led by Princeton University researchers and published in the Journal of the Royal Society Interface explores an approach to studying epidemics for which details are difficult to obtain. The researchers analyzed the 2013 outbreak of dolphin morbillivirus — a potentially fatal pathogen from the same family as the human measles virus — that resulted in more than 1,600 bottlenose dolphins becoming stranded along the Atlantic coast of the United States by 2015. Because scientists were able to observe dolphins only after they washed up on shore, little is known about how the disease transmits and persists in the wild.
The researchers used a Poisson process — a statistical tool used to model the random nature of disease transmission — to determine from sparse data how dolphin morbillivirus can spread. They found that individual bottlenose dolphins may be infectious for up to a month and can spread the disease over hundreds of miles, particularly during seasonal migrations. In 2013, the height of disease transmission occurred toward the end of summer around an area offshore of Virginia Beach, Virginia, where multiple migratory dolphin groups are thought to cross paths.
In the interview below, first author Sinead Morris, a graduate student in ecology and evolutionary biology, explains what the researchers learned about the dolphin morbillivirus outbreak, and how the Poisson process can help scientists understand human epidemics. Morris is in the research group of co-author Bryan Grenfell, Princeton’s Kathryn Briger and Sarah Fenton Professor of Ecology and Evolutionary Biology and Public Affairs.
Q: How does the Poisson process track indirectly observed epidemics and what specific challenges does it overcome?
A: One of the main challenges in modeling indirectly observed epidemics is a lack of data. In our case, we had information on all infected dolphins that had been found stranded on shore, but had no data on the number of individuals that became infected but did not strand. The strength of the Poisson process is that its simple framework means it can be used to extract important information about the how the disease is spreading across space and time, despite having such incomplete data. Essentially the way the process works is that it keeps track of where and when individual dolphins stranded, and then at each new point in the epidemic it uses the history of what has happened before to project what will happen in the future. For example, an infected individual is more likely to transmit the disease onwards to other individuals in close spatial proximity than to those far away. So, by keeping track of all these infections the model can identify where and when the largest risk of new infections will be.
Q: Why was this 2013-15 outbreak of dolphin morbillivirus selected for study, and what key insights does this work provide?
A: The recent outbreak of dolphin morbillivirus spread rapidly along the northwestern Atlantic coast from New York to Florida, causing substantial mortality among coastal bottlenose dolphin populations. Despite the clear detrimental impact that this disease can have, however, it is still poorly understood. Therefore, our aim in modeling the epidemic was to gain much needed information about how the virus spreads. We found that a dolphin may be infectious for up to 24 days and can travel substantial distances (up to 220 kilometers, or 137 miles) within this time. This is important because such long-range movements — for example, during periods of seasonal migration — are likely to create many transmission opportunities from infected to uninfected individuals, and may have thus facilitated the rapid spread of the virus down the Atlantic coast.
Q: Can this model be used for human epidemics?
A: The Poisson process framework was originally developed to model the occurrence of earthquakes, and has since been used in a variety of other contexts that also tend to suffer from noisy, indirectly observed data, such as urban crime distribution. To model dolphin morbillivirus, we adapted the framework to incorporate more biological information, and similar techniques have also been applied to model meningococcal disease in humans, which can cause meningitis and sepsis. Generally, the data characterizing human epidemics are more detailed than the data we had for this project and, as such, models that can incorporate greater complexity are more widely used. However, we hope that our methods will stimulate the greater use of Poisson process models in epidemiological systems that also suffer from indirectly observed data.
This research was supported by the RAPIDD program of the Science and Technology Directorate of the Department of Homeland Security; the National Institutes of Health Fogarty International Center; the Bill and Melinda Gates Foundation; and the Marine Mammal Unusual Mortality Event Contingency Fund and John H. Prescott Marine Mammal Rescue Assistance Grant Program operated by the National Oceanic and Atmospheric Administration.
Sinead E. Morris, Jonathan L. Zelner, Deborah A. Fauquier, Teresa K. Rowles, Patricia E. Rosel, Frances Gulland and Bryan T. Grenfell. “Partially observed epidemics in wildlife hosts: modeling an outbreak of dolphin morbillivirus in the northwestern Atlantic, June 2013–2014.” Journal of the Royal Society Interface, published Nov. 18 2015. DOI: 10.1098/rsif.2015.0676
By John Greenwald, Princeton Plasma Physics Laboratory Communications
For fusion reactions to take place efficiently, the atomic nuclei that fuse together in plasma must be kept sufficiently hot. But turbulence in the plasma that flows in facilities called tokamaks can cause heat to leak from the core of the plasma to its outer edge, causing reactions to fizzle out.
Researchers at the U.S. Department of Energy’s (DOE) Princeton Plasma Physics Laboratory (PPPL) have for the first time modeled previously unsuspected sources of turbulence in spherical tokamaks, an alternative design for producing fusion energy. The findings, published online in October in Physics of Plasmas, could influence the development of future fusion facilities. This work was supported by the DOE Office of Science.
Spherical tokamaks, like the recently completed National Spherical Torus Experiment-Upgrade (NSTX-U) at PPPL, are shaped like cored apples compared with the mushroom-like design of conventional tokamaks that are more widely used. The cored-apple shape provides some distinct characteristics for the behavior of the plasma inside.
The paper, with PPPL principal research physicist Weixing Wang as lead author, identifies two important new sources of turbulence based on data from experiments on the National Spherical Torus Experiment prior to its upgrade. The discoveries were made by using state-of-the-art large-scale computer simulations. These sources are:
Instabilities caused by plasma that flows faster in the center of the fusion facility than toward the edge when rotating strongly in L-mode — or low confinement — regimes. These instabilities, called “Kelvin-Helmholtz modes” after physicists Baron Kelvin and Hermann von Helmholtz, act like wind that stirs up waves as it blows over water and are for the first time found to be relevant for realistic fusion experiments. Such non-uniform plasma flows have been known to play favorable roles in fusion plasmas in conventional and spherical tokamaks. The new results from this study suggest that we may also need to keep these flows within an optimized level.
Trapped electrons that bounce between two points in a section of the tokamak instead of swirling all the way around the facility. These electrons were shown to cause significant leakage of heat in H-mode — or high-confinement — regimes by driving a specific instability when they collide frequently. This type of instability is believed to play little role in conventional tokamaks but can provide a robust source of plasma turbulence in spherical tokamaks.
Most interestingly, the model predicts a range of trapped electron collisions in spherical tokamaks that can be turbulence-free, thus improving the plasma confinement. Such favorable plasmas could possibly be achieved by future advanced spherical tokamaks operating at high temperature.
Findings of the new model can be tested on the NSTX-U and will help guide experiments to identify non-traditional sources of turbulence in the spherical facility. Results of this research can shed light on the physics behind key obstacles to plasma confinement in spherical facilities and on ways to overcome them in future machines.
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. Results of PPPL research have ranged from a portable nuclear materials detector for anti-terrorist use to universally employed computer codes for analyzing and predicting the outcome of fusion experiments. 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 science.energy.gov.
An international team of researchers has predicted the existence of a new type of particle called the type-II Weyl fermion in metallic materials. When subjected to a magnetic field, the materials containing the particle act as insulators for current applied in some directions and as conductors for current applied in other directions. This behavior suggests a range of potential applications, from low-energy devices to efficient transistors.
The researchers theorize that the particle exists in a material known as tungsten ditelluride (WTe2), which the researchers liken to a “material universe” because it contains several particles, some of which exist under normal conditions in our universe and others that may exist only in these specialized types of crystals. The research appeared in the journal Naturethis week.
The new particle is a cousin of the Weyl fermion, one of the particles in standard quantum field theory. However, the type-II particle exhibits very different responses to electromagnetic fields, being a near perfect conductor in some directions of the field and an insulator in others.
The particle’s existence was missed by physicist Hermann Weyl during the initial development of quantum theory 85 years ago, say the researchers, because it violated a fundamental rule, called Lorentz symmetry, that does not apply in the materials where the new type of fermion arises.
Particles in our universe are described by relativistic quantum field theory, which combines quantum mechanics with Einstein’s theory of relativity. Under this theory, solids are formed of atoms that consist of a nuclei surrounded by electrons. Because of the sheer number of electrons interacting with each other, it is not possible to solve exactly the problem of many-electron motion in solids using quantum mechanical theory.
Instead, our current knowledge of materials is derived from a simplified perspective where electrons in solids are described in terms of special non-interacting particles, called quasiparticles, that move in the effective field created by charged entities called ions and electrons. These quasiparticles, dubbed Bloch electrons, are also fermions.
Just as electrons are elementary particles in our universe, Bloch electrons can be considered the elementary particles of a solid. In other words, the crystal itself becomes a “universe,” with its own elementary particles.
In recent years, researchers have discovered that such a “material universe” can host all other particles of relativistic quantum field theory. Three of these quasiparticles, the Dirac, Majorana, and Weyl fermions, were discovered in such materials, despite the fact that the latter two had long been elusive in experiments, opening the path to simulate certain predictions of quantum field theory in relatively inexpensive and small-scale experiments carried out in these “condensed matter” crystals.
These crystals can be grown in the laboratory, so experiments can be done to look for the newly predicted fermion in WTe2 and another candidate material, molybdenum ditelluride (MoTe2).
“One’s imagination can go further and wonder whether particles that are unknown to relativistic quantum field theory can arise in condensed matter,” said Bernevig. There is reason to believe they can, according to the researchers.
The universe described by quantum field theory is subject to the stringent constraint of a certain rule-set, or symmetry, known as Lorentz symmetry, which is characteristic of high-energy particles. However, Lorentz symmetry does not apply in condensed matter because typical electron velocities in solids are very small compared to the speed of light, making condensed matter physics an inherently low-energy theory.
“One may wonder,” Soluyanov said, “if it is possible that some material universes host non-relativistic ‘elementary’ particles that are not Lorentz-symmetric?”
This question was answered positively by the work of the international collaboration. The work started when Soluyanov and Dai were visiting Bernevig in Princeton in November 2014 and the discussion turned to strange unexpected behavior of certain metals in magnetic fields (Nature 514, 205-208, 2014, doi:10.1038/nature13763). This behavior had already been observed by experimentalists in some materials, but more work is needed to confirm it is linked to the new particle.
The researchers found that while relativistic theory only allows a single species of Weyl fermions to exist, in condensed matter solids two physically distinct Weyl fermions are possible. The standard type-I Weyl fermion has only two possible states in which it can reside at zero energy, similar to the states of an electron which can be either spin-up or spin-down. As such, the density of states at zero energy is zero, and the fermion is immune to many interesting thermodynamic effects. This Weyl fermion exists in relativistic field theory, and is the only one allowed if Lorentz invariance is preserved.
The newly predicted type-2 Weyl fermion has a thermodynamic number of states in which it can reside at zero energy – it has what is called a Fermi surface. Its Fermi surface is exotic, in that it appears along with touching points between electron and hole pockets. This endows the new fermion with a scale, a finite density of states, which breaks Lorentz symmetry.
The discovery opens many new directions. Most normal metals exhibit an increase in resistivity when subject to magnetic fields, a known effect used in many current technologies. The recent prediction and experimental realization of standard type-I Weyl fermions in semimetals by two groups in Princeton and one group in IOP Beijing showed that the resistivity can actually decrease if the electric field is applied in the same direction as the magnetic field, an effect called negative longitudinal magnetoresistance. The new work shows that materials hosting a type-II Weyl fermion have mixed behavior: While for some directions of magnetic fields the resistivity increases just like in normal metals, for other directions of the fields, the resistivity can decrease like in the Weyl semimetals, offering possible technological applications.
“Even more intriguing is the perspective of finding more ‘elementary’ particles in other condensed matter systems,” the researchers say. “What kind of other particles can be hidden in the infinite variety of material universes? The large variety of emergent fermions in these materials has only begun to be unraveled.”
Researchers at Princeton University were supported by the U.S. Department of Defense, the U.S. Office of Naval Research, the U.S. National Science Foundation, the David and Lucile Packard Foundation and the W.M. Keck Foundation. Researchers at ETH Zurich were supported by Microsoft Research, the Swiss National Science Foundation and the European Research Council. Xi Dai was supported by the National Natural Science Foundation of China, the 973 program of China and the Chinese Academy of Sciences.
The article, “Type II Weyl Semimetals,” by Alexey A. Soluyanov, Dominik Gresch, Zhijun Wang, QuanSheng Wu, Matthias Troyer, Xi Dai, and B. Andrei Bernevig was published in the journal Nature on November 26, 2015.
Columns of workers penetrate the forest, furiously gathering as much food and supplies as they can. They are a massive army that living things know to avoid, and that few natural obstacles can waylay. So determined are these legions that should a chasm or gap disrupt the most direct path to their spoils they simply build a new path — out of themselves.
Without any orders or direction, individuals from the rank and file instinctively stretch across the opening, clinging to one another as their comrades-in-arms swarm across their bodies. But this is no force of superhumans. They are army ants of the species Eciton hamatum, which form “living” bridges across breaks and gaps in the forest floor that allow their famously large raiding swarms to travel efficiently.
Researchers from Princeton University and the New Jersey Institute of Technology (NJIT) report for the first time that these structures are more sophisticated than scientists knew. The ants exhibit a level of collective intelligence that could provide new insights into animal behavior and even help in the development of intuitive robots that can cooperate as a group, the researchers said.
Ants of E. hamatum automatically form living bridges without any oversight from a “lead” ant, the researchers report in the journal Proceedings of the National Academy of the Sciences. The action of each individual coalesces into a group unit that can adapt to the terrain and also operates by a clear cost-benefit ratio. The ants will create a path over an open space up to the point when too many workers are being diverted from collecting food and prey.
“These ants are performing a collective computation. At the level of the entire colony, they’re saying they can afford this many ants locked up in this bridge, but no more than that,” said co-first author Matthew Lutz, a graduate student in Princeton’s Department of Ecology and Evolutionary Biology.
“There’s no single ant overseeing the decision, they’re making that calculation as a colony,” Lutz said. “Thinking about this cost-benefit framework might be a new insight that can be applied to other animal structures that people haven’t thought of before.”
The research could help explain how large groups of animals balance cost and benefit, about which little is known, said co-author Iain Couzin, a Princeton visiting senior research scholar in ecology and evolutionary biology, and director of the Max Planck Institute for Ornithology and chair of biodiversity and collective behavior at the University of Konstanz in Germany.
Previous studies have shown that single creatures use “rules of thumb” to weigh cost-and-benefit, said Couzin, who also is Lutz’s graduate adviser. This new work shows that in large groups these same individual guidelines can eventually coordinate group-wide, he said — the ants acted as a unit although each ant only knew its immediate circumstances.
“They don’t know how many other ants are in the bridge, or what the overall traffic situation is. They only know about their local connections to others, and the sense of ants moving over their bodies,” Couzin said. “Yet, they have evolved simple rules that allow them to keep reconfiguring until, collectively, they have made a structure of an appropriate size for the prevailing conditions.
“Finding out how sightless ants can achieve such feats certainly could change the way we think of self-configuring structures in nature — and those made by man,” he said.
Ant-colony behavior has been the basis of algorithms related to telecommunications and vehicle routing, among other areas, explained co-first author Chris Reid, a postdoctoral research associate at the University of Sydney who conducted the work while at NJIT. Ants exemplify “swarm intelligence,” in which individual-level interactions produce coordinated group behavior. E. hamatum crossings assemble when the ants detect congestion along their raiding trail, and disassemble when normal traffic has resumed.
The video below shows how E. hamatum confronted a gap they encountered on an apparatus that Lutz and Reid built and deployed in the forests of Barro Colorado Island, Panama. Previously, scientists thought that ant bridges were static structures — their appearance over large gaps that ants clearly could not cross in midair was somewhat of a mystery, Reid said. The researchers found, however, that the ants, when confronted with an open space, start from the narrowest point of the expanse and work toward the widest point, expanding the bridge as they go to shorten the distance their compatriots must travel to get around the expanse.
“The amazing thing is that a very elegant solution to a colony-level problem arises from the individual interactions of a swarm of simple worker ants, each with only local information,” Reid said. “By extracting the rules used by individual ants about whether to initiate, join or leave a living structure, we could program swarms of simple robots to build bridges and other structures by connecting to each other.
“These robot bridges would exhibit the beneficial properties we observe in the ant bridges, such as adaptability to local conditions, real-time optimization of shape and position, and rapid construction and deconstruction without the need for external building materials,” Reid continued. “Such a swarm of robots would be especially useful in dangerous and unpredictable conditions, such as natural disaster zones.”
Radhika Nagpal, a professor of computer science at Harvard University who studies robotics and self-organizing biological systems, said that the findings reveal that there is “something much more fundamental about how complex structures are assembled and adapted in nature, and that it is not through a supervisor or planner making decisions.”
Individual ants adjusted to one another’s choices to create a successful structure, despite the fact that each ant didn’t necessarily know everything about the size of the gap or the traffic flow, said Nagpal, who is familiar with the research but was not involved in it.
“The goal wasn’t known ahead of time, but ’emerged’ as the collective continually adapted its solution to the environmental factors,” she said. “The study really opens your eyes to new ways of thinking about collective power, and has tremendous potential as a way to think about engineering systems that are more adaptive and able to solve complex cost-benefit ratios at the network level just through peer-to-peer interactions.”
She compared the ant bridges to human-made bridges that automatically widened to accommodate heavy vehicle traffic or a growing population. While self-assembling road bridges may be a ways off, the example illustrates the potential that technologies built with the same self-assembling capabilities seen in E. hamatum could have.
“There’s a deep interest in creating robots that don’t just rely on themselves, but can exploit the group to do more — and self-assembly is the ultimate in doing more,” Nagpal said. “If you could have small simple robots that were able to navigate complex spaces, but could self-assemble into larger structures — bridges, towers, pulling chains, rafts — when they face something they individually did not have the ability to do, that’s a huge increase in power in what robots would be capable of.”
The spaces E. hamatum bridges are not dramatic by human standards — small rifts in the leaf cover, or between the ends of two sticks. Bridges will be the length of 10 to 20 ants, which is only a few centimeters, Lutz said. That said, E. hamatum swarms form several bridges during the course of a day, which can see the back-and-forth of thousands of ants. Many ants pass over a living bridge even as it is assembling.
“The bridges are something that happen numerous times every day. They’re creating bridges to optimize their traffic flow and maximize their time,” Lutz said.
“When you’re moving hundreds of thousands of ants, creating a little shortcut can save a lot of energy,” he said. “This is such a unique behavior. You have other types of ants forming structures out of their bodies, but it’s not such a huge part of their lives and daily behavior.”
The research also included Scott Powell, an army-ant expert and assistant professor of biology at George Washington University; Albert Kao, a postdoctoral fellow at Harvard who received his doctorate in ecology and evolutionary biology from Princeton in 2015; and Simon Garnier, an assistant professor of biological sciences at NJIT who studies swarm intelligence and was once a postdoctoral researcher in Couzin’s lab at Princeton.
To conduct their field experiments, Lutz and Reid constructed a 1.5-foot-tall apparatus with ramps on both sides and adjustable arms in the center with which they could adjust the size of the gap. They then inserted the apparatus into active E. hamatum raiding trails that they found in the jungle in Panama. Because ants follow one another’s chemical scent, Lutz and Reid used sticks and leaves from the ants’ trail to get them to reform their column across the device.
Lutz and Reid observed how the ants formed bridges across gaps that were set at angles of 12, 20, 40 and 60 degrees. They gauged how much travel-distance the ants saved with their bridge versus the surface area (in centimeters squared) of the bridge itself. Twelve-degree angles shaved off the most distance (around 11 centimeters) while taking up the fewest workers. Sixty-degree angles had the highest cost-to-benefit ratio. Interestingly, the ants were willing to expend members for 20-degree angles, forming bridges up to 8 centimeters squared to decrease their travel time by almost 12 centimeters, indicating that the loss in manpower was worth the distance saved.
Lutz said that future research based on this work might compare these findings to the living bridges of another army ant species, E. burchellii, to determine if the same principles are in action.
The paper, “Army ants dynamically adjust living bridges in response to a cost-benefit trade-off,” was published Nov. 23 by Proceedings of the National Academy of Sciences. The work was supported by the National Science Foundation (grant nos. PHY-0848755, IOS0-1355061 and EAGER IOS-1251585); the Army Research Office (grant nos. W911NG-11-1-0385 and W911NF-14-1-0431); and the Human Frontier Science Program (grant no. RGP0065/2012).