Category Archives: Research

When less is more: Death in moderation boosts population density in nature (Trends in Ecology and Evolution)

A study by Princeton researchers and European colleagues found that the positive effect that mortality can have on populations depends on the size and developmental stage of the creatures that die. The finding could aid the management of wildlife and fish such as the Atlantic cod (Image source: NOAA).

A study by Princeton researchers and European colleagues found that the positive effect that mortality can have on populations depends on the size and developmental stage of the creatures that die. The finding could aid the management of wildlife and fish such as Atlantic cod (Image source: NOAA).

By Morgan Kelly, Office of Communications

In nature, the right amount of death at the right time might actually help boost a species’ population density, according to new research that could help in understanding animal populations, pest control and managing fish and wildlife stocks.

In a paper in the journal Trends in Ecology and Evolution, a Princeton University researcher and European colleagues conclude that the kind of positive population effect an overall species experiences from a loss of individuals, or mortality, depends on the size and developmental stage of the creatures that die.

If many juveniles perish, more adults are freed up to reproduce, but if more adults die, the number of juveniles that mature will increase because density dependence is relaxed, explained co-author Anieke van Leeuwen, a postdoctoral researcher in Princeton’s Department of Ecology and Evolutionary Biology. Van Leeuwen worked with first author Arne Schröder, a postdoctoral research fellow at the Leibniz-Institute of Freshwater Ecology and Inland Fisheries in Berlin, and Tom Cameron, a lecturer in aquatic community ecology at the University of Essex in the United Kingdom.

This dynamic wherein the loss of individuals in one developmental stage translates to more robust individuals in another stage can be important to managing wildlife, pests or resource stocks, van Leeuwen said. For instance, targeting the adults of an invasive insect could have a counterproductive effect of making more food available to growing larvae, she said.

“It doesn’t matter which developmental stage you target, if you impose mortality on one you will get overcompensation on the opposite end of the size range,” van Leeuwen said. “This effect can be especially advantageous in situations where we want to manage resources we want to harvest. Knowing that there are potential effects that result in an increase in that segment of the population we want to encourage is highly relevant.”

At a certain point, of course, mortality becomes too high and the species as a whole declines, the researchers report.

The researchers compared existing theoretical and experimental work on the effect of mortality on population density to resolve various inconsistencies between the two. Existing mathematical models have predicted this phenomenon, and laboratory and field studies have shown that the effect holds true for a variety of animal species.

Many ecological theories and models, however, have ignored differences in body size and development, and predicted that a modest amount of mortality would result in an increase in the total number of individuals, the researchers wrote. On the other hand, experiments have predominantly shown — along with certain models — that mortality has a positive effect within certain life stages or size classes. The researchers concluded that the overlap of experimental and theoretical data indicates that the benefit of mortality is likely divided by developmental stage. In addition, the number of species in which the phenomenon has been observed makes it commonplace in the natural world.

This work was supported by the Journal of Experimental Biology; the Swedish Research Council and the Leibniz-Institute of Freshwater Ecology and Inland Fisheries; the University of Leeds, the National Environment Research Council (grant no. NE/C510467/1) and the European Commission Intra-European Fellowship (FANTISIZE, #275873); and the National Science Foundation (grant no. 1115838).

Read the abstract.

Citation: Schröder, Arne, Anieke van Leeuwen, Thomas C. Cameron. 2014. When less is more: Positive population-level effects of mortality. Trends in Ecology and Evolution. Published in November 2014 edition: Vol. 29, issue 11, pp. 614–624. DOI: 10.1016/j.tree.2014.08.006

Scientists use plasma shaping to control turbulence in stellarators (Phys. Rev. Lett.)

By John Greenwald, Princeton Plasma Physics Laboratory

Stellerator

Magnetic field strength in a turbulence-optimized stellarator design. Regions with the highest strength are shown in yellow. (Source: PPPL)

Researchers at the U.S. Department of Energy’s Princeton Plasma Physics Laboratory (PPPL) and the Max Planck Institute of Plasma Physics in Germany have devised a new method for minimizing turbulen

ce in bumpy donut-shaped experimental fusion facilities called stellarators. This week in Physical Review Letters, these authors describe an advanced application of the method that could help physicists overcome a major barrier to the production of fusion energy in such devices, and could also apply to their more widely used symmetrical donut-shaped cousins called tokamaks. This work was supported by the DOE Office of Science.

Turbulence allows the hot, charged plasma gas that fuels fusion reactions to escape from the magnetic fields that confine the gas in stellarators and tokamaks. This turbulent transport occurs at comparable levels in both devices, and has long been recognized as a challenge for both in producing fusion power economically.

“Confinement bears directly on the cost of fusion energy,” said physicist Harry Mynick, a PPPL coauthor of the paper, “and we’re finding how to reshape the plasma to enhance confinement.”

The new method uses two types of advanced computer codes that have only recently become available. The authors modified these codes to address turbulent transport, evolving the starting design of a fusion device into one with reduced levels of turbulence. The current paper applies the new method to the Wendelstein 7-X stellarator, soon to be the world’s largest when construction is completed in Greifswald, Germany.

Results of the new method, which has also been successfully applied to the design of smaller stellarators and tokamaks, suggest how reshaping the plasma in a fusion device could produce much better confinement. Equivalently, improved plasma shaping could produce comparable confinement with reduced magnetic field strength or reduced facility size, with corresponding reductions in the cost of construction and operation.

The simulations further suggest that a troublesome characteristic called “stiffness” could occur in reactor-sized stellarators. Stiffness, the tendency for heat to rapidly escape as the plasma temperature gradient rises above a threshold, has been observed in tokamaks but less so in stellarators. The possibility that stiffness might be present in reactor-sized stellarators, wrote the authors, could stimulate efforts “toward further optimizing stellarator magnetic fields for reduced turbulence.”

PPPL, on Princeton University’s Forrestal Campus in Plainsboro, New Jersey, 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. Fusion takes place when atomic nuclei fuse and release a burst of energy. This compares with the fission reactions in today’s nuclear power plants, which operate by splitting atoms apart.

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 single largest 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.

Read the abstract.

Xanthopoulos, P.; Mynick, H.E.; Helander, P.; Turkin, Y.; Plunk, G.G.; Jenko, F.; Görler, T.; Told, D.; Bird, T.; J.H.E. Controlling turbulence in present and future stellarators. Article published in Physical Review Letters on Oct. 7, 2014.

Unstoppable magnetoresistance (Nature)

Mazhar Ali (left) and Steven Flynn (right), co-authors on the Nature paper. Photo by C. Todd Reichert.

Mazhar Ali (left) and Steven Flynn (right), co-authors on the Nature paper. Photo by C. Todd Reichart.

by Tien Nguyen, Department of Chemistry

Mazhar Ali, a fifth-year graduate student in the laboratory of Robert Cava, the Russell Wellman Moore Professor of Chemistry at Princeton University, has spent his academic career discovering new superconductors, materials coveted for their ability to let electrons flow without resistance. While testing his latest candidate, the semimetal tungsten ditelluride (WTe2), he noticed a peculiar result.

Ali applied a magnetic field to a sample of WTe2, one way to kill superconductivity if present, and saw that its resistance doubled. Intrigued, Ali worked with Jun Xiong, a student in the laboratory of Nai Phuan Ong, the Eugene Higgins Professor of Physics at Princeton, to re-measure the material’s magnetoresistance, which is the change in resistance as a material is exposed to stronger magnetic fields.

“He noticed the magnetoresistance kept going up and up and up—that never happens.” said Cava. The researchers then exposed WTe2 to a 60-tesla magnetic field, close to the strongest magnetic field mankind can create, and observed a magnetoresistance of 13 million percent. The material’s magnetoresistance displayed unlimited growth, making it the only known material without a saturation point. The results were published online on September 14 in the journal Nature.

Crystal structure of WTe2 (Source: Nature)

Crystal structure of WTe2 (Source: Nature)

Electronic information storage is dependent on the use of magnetic fields to switch between distinct resistivity values that correlate to either a one or a zero. The larger the magnetoresistance, the smaller the magnetic field needed to change from one state to another, Ali said. Today’s devices use layered materials with so-called “giant magnetoresistance,” with changes in resistance of 20,000 to 30,000 percent when a magnetic field is applied. “Colossal magnetoresistance” is close to 100,000 percent, so for a magnetoresistance percentage in the millions, the researchers hoped to coin a new term.

Their original choice was “ludicrous” magnetoresistance, which was inspired by “ludicrous speed,” the fictional form of fast-travel used in the comedy “Spaceballs.” They even included an acknowledgement to director Mel Brooks. After other lab members vetoed “ludicrous,” the researchers considered “titanic” before Nature editors ultimately steered them towards the term “large magnetoresistance.”

Terminology aside, the fact remained that the magnetoresistance values were extraordinarily high, a phenomenon that might be understood through the structure of WTe2. To look at the structure with an electron microscope, the research team turned to Jing Tao, a researcher at Brookhaven National Laboratory.

“Jing is a great microscopist. They have unique capabilities at Brookhaven,” Cava said. “One is that they can measure diffraction at 10 Kelvin (-441 °F). Not too many people on Earth can do that, but Jing can.”

Electron microscopy experiments revealed the presence of tungsten dimers, paired tungsten atoms, arranged in chains responsible for the key distortion from the classic octahedral structure type. The research team proposed that WTe2 owes its lack of saturation to the nearly perfect balance of electrons and electron holes, which are empty docks for traveling electrons. Because of its structure, WTe2 only exhibits magnetoresistance when the magnetic field is applied in a certain direction. This could be very useful in scanners, where multiple WTe2 devices could be used to detect the position of magnetic fields, Ali said.

“Aside from making devices from WTe2, the question to ask yourself as a scientist is: How can it be perfectly balanced, is there something more profound,” Cava said.

Read the abstract.

Ali, M. N.; Xiong, J.; Flynn, S.; Tao, J.; Gibson, Q. D.; Schoop, L. M.; Haldolaarachchige, N.; Hirschberger, M.; Ong, N. P.; Cava, R. J. “Large, non-saturating magnetoresistance in WTe2.” Nature. Published online September 14. 514, 205–208 (09 October 2014).

This research was supported by the Army Research Office, grants W911NF-12-1-0461 and W911NF-11-1-0379, and the NSF MRSEC Program Grant DMR-0819860. This work was supported by the US Department of Energy’s Basic Energy Sciences (DOE BES) project “Science at 100 Tesla.” The electron microscopy study at Brookhaven National Laboratory was supported by the DOE BES, by the Materials Sciences and Engineering Division under contract DE-AC02-98CH10886, and through the use of the Center for Functional Nanomaterials.

Study questions the prescription for drug resistance (Proceedings of the Royal Society B)

A drug-resistant strain of bacteria known as MRSA. Photo by James Gathany

A new study examines the question of aggressive versus moderate drug treatment on the emergence of drug-resistant pathogens. Shown is a strain of bacteria known as methicillin-resistant Staphylococcus aureus (MRSA). Photo by James Gathany

By Catherine Zandonella, Office of the Dean for Research

In response to the rise of drug-resistant pathogens, doctors are routinely cautioned against overprescribing antimicrobials. But when a patient has a confirmed bacterial infection, the advice is to treat aggressively to quash the infection before the bacteria can develop resistance.

A new study questions the accepted wisdom that aggressive treatment with high drug dosages and long durations is always the best way to stem the emergence and spread of resistant pathogens. The review of nearly 70 studies of antimicrobial resistance, which was authored by researchers at Princeton and other leading institutions and published last week in the journal Proceedings of the Royal Society B, reveals the lack of evidence behind the practice of aggressive treatment in many cases.

“We found that while there are many studies that test for resistance emergence between different drug regimes, surprisingly few have looked at the topic of how varying drug dosage might affect the emergence and spread of resistance,” said Ruthie Birger, a Princeton graduate student who works with C. Jessica Metcalf, an assistant professor of ecology and evolutionary biology and public affairs at Princeton’s Woodrow Wilson School, and Bryan Grenfell, the Kathryn Briger and Sarah Fenton Professor of Ecology and Evolutionary Biology and Public Affairs in Princeton’s Woodrow Wilson School. Birger, Metcalf and Grenfell coauthored the paper with colleagues from 16 universities. “We are a long way from having the evidence for the best treatment decisions with respect to resistance for a range of diseases,” Birger said.

Microbes such as bacteria and parasites can evade today’s powerful drugs by undergoing genetic mutations that enable them to avoid being killed by the drug. For example, bacteria can develop enzymes that degrade certain antibiotics. The logic behind aggressive treatment goes something like this: kill off as many microbes as you can so that few will be around to evolve into resistant forms.

But some scientists have observed a different outcome in mice infected with both an already-resistant strain of malaria and a non-resistant strain. The high-dose drug treatment killed off the non-resistant malarial parasites, leaving the resistant strains to multiply and make the mice even sicker.

The idea that aggressive treatment may backfire against malarial parasites led the authors of the current study to comb the scientific literature to examine whether the same may be true for other types of microbes such as bacteria. The few studies that they found — mostly in laboratory cell cultures rather than animal models or patients — suggest that the picture is complicated, and depends on whether the resistance is new or existing, how many mutations are necessary for the pathogen to become resistant, and how long the drugs have been in use. “It’s remarkable how little we know about this topic,” said Metcalf. “The malaria study conducted by Silvie Huijben and colleagues at Pennsylvania State University is an inspiring step towards developing an evidence base for these important issues.”

In the current analysis, the study authors found that drug resistance is governed by two factors: the abundance of the pathogen and the strength of the selection pressure that drives the pathogen to evolve. Aggressive treatment deals with the first factor by killing off as much pathogen as possible, while moderate treatment may, for some pathogens, reduce the ability for the resistant pathogen to thrive (for example, by maintaining the competitive advantage of a co-infecting drug-sensitive strain of the pathogen) but still reduce total pathogen levels sufficiently that the patient can recover.

Finding the ideal dose and duration of treatment, one that cures the patient without aiding the spread of resistance, will likely be done on a disease by disease basis, the authors found.

One possibility is that moderate treatment might be best used against already-resistant microbes to prevent their spread. Moderate treatment may also be best for drugs that have been on the market for several years with plenty of time for resistant strains to develop.

Aggressive treatment might be best for pathogens that develop resistance slowly, over the course of several mutations. High doses early in the process could be effective at heading off the development of resistance.

Read the abstract.

Roger D. Kouyos, C. Jessica E. Metcalf, Ruthie Birger, Eili Y. Klein, Pia Abel zur Wiesch, Peter Ankomah, Nimalan Arinaminpathy, Tiffany L. Bogich, Sebastian Bonhoeffer, Charles Brower, Geoffrey Chi-Johnston, Ted Cohen, Troy Day, Bryan Greenhouse, Silvie Huijben, Joshua Metlay, Nicole Mideo, Laura C. Pollitt, Andrew F. Read, David L. Smith, Claire Standley, Nina Wale and Bryan Grenfell. Proc. R. Soc. B: Biological Sciences, 281, 20140566. Published Sept. 24, 2014

The work emerged from two workshops held at Princeton University and funded by the RAPIDD program of the Science and Technology Directorate, Department of Homeland Security and the Fogarty International Center, National Institutes of Health; Science and Technology Directorate, Department of Homeland Security; contract HSHQDC-12-C-00058

Longstanding bottleneck in crystal structure prediction solved (Science)

By Tien Nguyen, Department of Chemistry

benzene crystal

Orthographic projections of a cluster cut from the benzene crystal along the two directions (Image courtesy of Science/AAAS)

Two years after its release, the HIV-1 drug Ritonavir was pulled from the market. Scientists discovered that the drug had crystallized into a slightly different form—called a polymorph—that was less soluble and made it ineffective as a treatment.

The various patterns that atoms of a solid material can adopt, called crystal structures, can have a huge impact on its properties. Being able to accurately predict the most stable crystal structure for a material has been a longstanding challenge for scientists.

“The holy grail of this particular problem is to say, I’ve written down this chemical formula for a material, and then just from the formula be able to predict its structure—a goal since the dawn of chemistry,” said Garnet K. L. Chan, the A. Barton Hepburn Professor of Theoretical Chemistry at Princeton University. One major bottleneck towards achieving this goal has been to compute the lattice energy—the energy associated with a structure—to sufficient accuracy to distinguish between several competing polymorphs.

Chan’s group has now accomplished this task, publishing their results in the journal Science on August 8. The research team demonstrated that new techniques could be used to calculate the lattice energy of benzene, a simple yet important molecule in pharmaceutical and energy research, to sub-kilojoule per mole accuracy—a level of certainty that allows polymorphism to be resolved.

Chan credited this success to the combined application of advances in the field of quantum mechanics over the last 15 years. “Some of these advances allow you to resolve the behavior of electrons more finely, do computations on more atoms more quickly, and allow you to consider more electrons at the same time,” Chan said. “It’s a triumph of the modern field of quantum chemistry that we can now determine the behavior of Nature to this level of precision.”

The group’s next goal is to shorten the time it takes to run the desired calculations. These initial calculations consumed several months of computer time, Chan said, but with some practical modifications, future predictions should take only a few hours.

Chan’s colleagues on the work included first author Jun Yang, an electronic structure theory specialist and lecturer in chemistry, and graduate student Weifeng Hu at Princeton University. Additional collaborators were Denis Usvyat and Martin Schutz of the University of Regensburg and Devin Matthews of the University of Texas at Austin.

The work was supported by the U.S. Department of Energy under grant no. DE-SC0008624, with secondary support from grant no. DE-SC0010530. Additional funding was received from the National Science Foundation under grant no. OCI-1265278 and CHE-1265277. D.M. was supported by the U.S. Department of Energy through a Computational Science Graduate Fellowship, funded by grant no. DE-FG02-97ER25308.

Read the abstract.

Yang J., Hu, W., Usvyat, D., Matthews, D., Schutz, M., Chan, G. K. L. Ab initio determination of the crystalline benzene lattice energy to sub-kilojoule/mol accuracy. Science 2014, 345, 640.

Conservation versus innovation in the fight against antibiotic resistance (Science)

Pills (Image source: NIH)

(Image source: NIH)

“Antibiotic resistance is a problem of managing an open-access resource, such as fisheries or oil,” writes Ramanan Laxminarayan, a research scholar at Princeton University and the director of the Center for Disease Dynamics, Economics & Policy in Washington, D. C., in today’s issue of the journal Science. He goes on to say that individuals have little incentive to use antibiotics wisely, just as people have little incentive to conserve oil when it is plentiful.

As with many other natural resources, maintaining the effectiveness of antibiotics requires two approaches: conserving the existing resource and exploring new sources, Laxminarayan says. These two approaches are linked, however. “Just as incentives for finding new sources of oil reduce incentives to conserve oil,” Laxminarayan writes, “large public subsidies for new drug development discourage efforts to improve how existing antibiotics are used.” Yet new antibiotics tend to cost more than existing ones due to the expense of clinical trials and the fact that the easiest-to-find drugs may have already been discovered.

Laxminarayan’s analysis reveals that the benefits of conserving existing drugs are significant, and argues that the proposed increases in public subsidies for new antibiotics should be matched by greater spending on conservation of antibiotic effectiveness through public education, research and surveillance.

Ramanan Laxminarayan is a research scholar at the Princeton Environmental Institute. His perspective, “Antibiotic effectiveness: Balancing conservation against innovation,” appeared in the September 12, 2014 issue of Science.

Read the article.

Fast-camera image of plasma during magnetic reconnection with rendering of the field lines, shown in white, based on measurements made during the experiment. The converging horizontal lines represent the field lines prior to reconnection. The outgoing vertical lines represent the field lines after reconnection. Image courtesy of Jongsoo Yoo.

PPPL scientists take key step toward solving a major astrophysical mystery

By John Greenwald, Princeton Plasma Physics Laboratory

Magnetic reconnection in the Earth and sun’s atmospheres can trigger geomagnetic storms that disrupt cell phone service, damage satellites and blackout power grids. Understanding how reconnection transforms magnetic energy into explosive particle energy has been a major unsolved problem in plasma astrophysics.

Scientists at the Princeton Plasma Physics Laboratory (PPPL) and Princeton University have taken a key step toward a solution, as described in a paper published this week in the journal Nature Communications. In research conducted on the Magnetic Reconnection Experiment (MRX) at PPPL, the scientists not only identified how the mysterious transformation takes place, but measured experimentally the amount of magnetic energy that turns into particle energy. The work is supported by the U. S. Department of Energy as well as the NSF-funded Center for Magnetic Self-Organization.

Fast-camera image of plasma during magnetic reconnection with rendering of the field lines, shown in white, based on measurements made during the experiment. The converging horizontal lines represent the field lines prior to reconnection. The outgoing vertical lines represent the field lines after reconnection. Image courtesy of Jongsoo Yoo.

Fast-camera image of plasma during magnetic reconnection with rendering of the field lines, shown in white, based on measurements made during the experiment. The converging horizontal lines represent the field lines prior to reconnection. The outgoing vertical lines represent the field lines after reconnection. Image courtesy of Jongsoo Yoo.

Magnetic field lines represent the direction, and indicate the shape, of magnetic fields. In magnetic reconnection, the magnetic field lines in plasma snap apart and violently reconnect. The MRX, built in 1995, allows researchers to study the process in a controlled laboratory environment.

The new research shows that reconnection converts about 50 percent of the magnetic energy, with one-third of the conversion heating the electrons and two-thirds accelerating the ions — or atomic nuclei — in the plasma. In large bodies like the sun, such converted energy can equal the power of millions of tons of TNT.

“This is a major milestone for our research,” said Masaaki Yamada, a research physicist, the principal investigator for the MRX and first author of the Nature Communications paper. “We can now see the entire picture of how much of the energy goes to the electrons and how much to the ions in a proto-typical reconnection layer.”

The findings also suggested the process by which the energy conversion occurs. Reconnection first propels and energizes the electrons, according to the researchers, and this creates an electrically charged field that “becomes the primary energy source for the ions,” said Jongsoo Yoo, an associate research physicist at PPPL and co-author of the paper.

The other contributors to the paper were Hantao Ji, professor of astrophysical sciences at Princeton; Russell Kulsrud, professor of astrophysical sciences, emeritus, at Princeton; and doctoral candidates in astrophysical sciences Jonathan Jara-Almonte and Clayton Myers.

If confirmed by data from space explorations, the PPPL results could help resolve decades-long questions and create practical benefits. These could include a better understanding of geomagnetic storms that could lead to advanced warning of the disturbances and an improved ability to cope with them. Researchers could shut down sensitive instruments on communications satellites, for example, to protect the instruments from harm.

Next year NASA plans to launch a four-satellite mission to study reconnection in the magnetosphere — the magnetic field that surrounds the Earth. The PPPL team plans to collaborate with the venture, called the Magnetospheric Multiscale (MMS) Mission, by providing MRX data to it. The MMS probes could help to confirm the laboratory’s findings.

PPPL, on Princeton University’s Forrestal Campus in Plainsboro, New Jersey, 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. Fusion takes place when atomic nuclei fuse and release a burst of energy. This compares with the fission reactions in today’s nuclear power plants, which operate by splitting atoms apart.

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 single largest 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.

Read the abstract.

Yamada, M; Yoo J.; Jara-Almonte, J.; Ji, H.; Kulsrud, R.M.; Myers, C.E. Conversion of magnetic energy in the magnetic reconnection layer of a laboratory plasma. Nature Communications. Article published online Sept. 10, 2014. DOI: NCOMMS5774