Quantum computing moves forward (Science)

By Catherine Zandonella, Office of the Dean for Research

New technologies that exploit quantum behavior for computing and other applications are closer than ever to being realized due to recent advances, according to a review article published this week in the journal Science.

A silicon chip levitates individual atoms used in quantum information processing. Photo: Curt Suplee and Emily Edwards, Joint Quantum Institute and University of Maryland. Credit: Science.

These advances could enable the creation of immensely powerful computers as well as other applications, such as highly sensitive detectors capable of probing biological systems. “We are really excited about the possibilities of new semiconductor materials and new experimental systems that have become available in the last decade,” said Jason Petta, one of the authors of the report and an associate professor of physics at Princeton University.

Petta co-authored the article with David Awschalom of the University of Chicago, Lee Basset of the University of California-Santa Barbara, Andrew Dzurak of the University of New South Wales and Evelyn Hu of Harvard University.

Two significant breakthroughs are enabling this forward progress, Petta said in an interview. The first is the ability to control quantum units of information, known as quantum bits, at room temperature. Until recently, temperatures near absolute zero were required, but new diamond-based materials allow spin qubits to be operated on a table top, at room temperature. Diamond-based sensors could be used to image single molecules, as demonstrated earlier this year by Awschalom and researchers at Stanford University and IBM Research (Science, 2013).

The second big development is the ability to control these quantum bits, or qubits, for several seconds before they lapse into classical behavior, a feat achieved by Dzurak’s team (Nature, 2010) as well as Princeton researchers led by Stephen Lyon, professor of electrical engineering (Nature Materials, 2012). The development of highly pure forms of silicon, the same material used in today’s classical computers, has enabled researchers to control a quantum mechanical property known as “spin”. At Princeton, Lyon and his team demonstrated the control of spin in billions of electrons, a state known as coherence, for several seconds by using highly pure silicon-28.

Quantum-based technologies exploit the physical rules that govern very small particles — such as atoms and electrons — rather than the classical physics evident in everyday life. New technologies based on “spintronics” rather than electron charge, as is currently used, would be much more powerful than current technologies.

In quantum-based systems, the direction of the spin (either up or down) serves as the basic unit of information, which is analogous to the 0 or 1 bit in a classical computing system. Unlike our classical world, an electron spin can assume both a 0 and 1 at the same time, a feat called entanglement, which greatly enhances the ability to do computations.

A remaining challenge is to find ways to transmit quantum information over long distances. Petta is exploring how to do this with collaborator Andrew Houck, associate professor of electrical engineering at Princeton. Last fall in the journal Nature, the team published a study demonstrating the coupling of a spin qubit to a particle of light, known as a photon, which acts as a shuttle for the quantum information.

Yet another remaining hurdle is to scale up the number of qubits from a handful to hundreds, according to the researchers. Single quantum bits have been made using a variety of materials, including electronic and nuclear spins, as well as superconductors.

Some of the most exciting applications are in new sensing and imaging technologies rather than in computing, said Petta. “Most people agree that building a real quantum computer that can factor large numbers is still a long ways out,” he said. “However, there has been a change in the way we think about quantum mechanics – now we are thinking about quantum-enabled technologies, such as using a spin qubit as a sensitive magnetic field detector to probe biological systems.”

Read the abstract.

Awschalom D.D., Bassett L.C., Dzurak A.S., Hu E.L. & Petta J.R. (2013). Quantum spintronics: engineering and manipulating atom-like spins in semiconductors. Science 339 (6124) 1174-1179. PMID: 23471400

The research at Princeton University was supported by the Alfred P. Sloan Foundation, the David and Lucile Packard Foundation, US Army Research Office grant W911NF-08-1-0189, DARPA QuEST award HR0011-09-1-0007 and the US National Science Foundation through the Princeton Center for Complex Materials (DMR-0819860) and CAREER award DMR-0846341.

Researchers discover workings of brain’s ‘GPS system’ (Nature)

By Catherine Zandonella, Office of the Dean for Research

Just as a global positioning system (GPS) helps find your location, the brain has an internal system for helping determine the body’s location as it moves through its surroundings.

A new study from researchers at Princeton University provides evidence for how the brain performs this feat. The study, published in the journal Nature, indicates that certain position-tracking neurons — called grid cells — ramp their activity up and down by working together in a collective way to determine location, rather than each cell acting on its own as was proposed by a competing theory.

Grid cells are neurons that become electrically active, or “fire,” as animals travel in an environment. First discovered in the mid-2000s, each cell fires when the body moves to specific locations, for example in a room. Amazingly, these locations are arranged in a hexagonal pattern like spaces on a Chinese checker board. (See figure.)

As the mouse moves around in a square arena (left), a single grid cell in the mouse’s brain becomes active, or spikes, when the animal arrives at particular locations in the arena (right). These locations are arranged in a hexagonal pattern. The red dots indicate the mouse’s location in the arena when the grid cell fired. (Image credit: Cristina Domnisoru, Princeton University)

“Together, the grid cells form a representation of space,” said David Tank, Princeton’s Henry L. Hillman Professor in Molecular Biology and leader of the study. “Our research focused on the mechanisms at work in the neural system that forms these hexagonal patterns,” he said. The first author on the paper was graduate student Cristina Domnisoru, who conducted the experiments together with postdoctoral researcher Amina Kinkhabwala.

Domnisoru measured the electrical signals inside individual grid cells in mouse brains while the animals traversed a computer-generated virtual environment, developed previously in the Tank lab. The animals moved on a mouse-sized treadmill while watching a video screen in a set-up that is similar to video-game virtual reality systems used by humans.

She found that the cell’s electrical activity, measured as the difference in voltage between the inside and outside of the cell, started low and then ramped up, growing larger as the mouse reached each point on the hexagonal grid and then falling off as the mouse moved away from that point.

This ramping pattern corresponded with a proposed mechanism of neural computation called an attractor network. The brain is made up of vast numbers of neurons connected together into networks, and the attractor network is a theoretical model of how patterns of connected neurons can give rise to brain activity by collectively working together. The attractor network theory was first proposed 30 years ago by John Hopfield, Princeton’s Howard A. Prior Professor in the Life Sciences, Emeritus.

The team found that their measurements of grid cell activity corresponded with the attractor network model but not a competing theory, the oscillatory interference model. This competing theory proposed that grid cells use rhythmic activity patterns, or oscillations, which can be thought of as many fast clocks ticking in synchrony, to calculate where animals are located. Although the Princeton researchers detected rhythmic activity inside most neurons, the activity patterns did not appear to participate in position calculations.

Read the abstract.

Domnisoru, Cristina, Amina A. Kinkhabwala & David W. Tank. 2013. Membrane potential dynamics of grid cells. Nature. doi:10.1038/nature11973. Published online Feb. 10, 2013.

This work was supported by the National Institute of Neurological Disorders and Stroke under award numbers 5RC1NS068148-02 and 1R37NS081242-01, the National Institute of Mental Health under award number 5R01MH083686-04, a National Institutes of Health Postdoctoral Fellowship grant F32NS070514-01A1 (A.A.K.), and a National Science Foundation Graduate Research Fellowship (C.D.).

How do bacteria clog medical devices? Very quickly. (PNAS)

stone-figure-2D_540 A new study has examined how bacteria clog medical devices, and the result isn’t pretty. The microbes join to create slimy ribbons that tangle and trap other passing bacteria, creating a full blockage in a startlingly short period of time.

The finding could help shape strategies for preventing clogging of devices such as stents — which are implanted in the body to keep open blood vessels and passages — as well as water filters and other items that are susceptible to contamination. The research was published in Proceedings of the National Academy of Sciences.

Click on the image to view movie. Over a period of about 40 hours, bacterial cells (green) flowed through a channel, forming a green biofilm on the walls. Over the next ten hours, researchers sent red bacterial cells through the channel. The red cells became stuck in the sticky biofilm and began to form thin red streamers. Once stuck, these streamers in turn trapped additional cells, leading to rapid clogging. (Image source: Knut Drescher)

Using time-lapse imaging, researchers at Princeton University monitored fluid flow in narrow tubes or pores similar to those used in water filters and medical devices. Unlike previous studies, the Princeton experiment more closely mimicked the natural features of the devices, using rough rather than smooth surfaces and pressure-driven fluid instead of non-moving fluid.

The team of biologists and engineers introduced a small number of bacteria known to be common contaminants of medical devices. Over a period of about 40 hours, the researchers observed that some of the microbes — dyed green for visibility — attached to the inner wall of the tube and began to multiply, eventually forming a slimy coating called a biofilm. These films consist of thousands of individual cells held together by a sort of biological glue.

Over the next several hours, the researchers sent additional microbes, dyed red, into the tube. These red cells became stuck to the biofilm-coated walls, where the force of the flowing liquid shaped the trapped cells into streamers that rippled in the liquid like flags rippling in a breeze. During this time, the fluid flow slowed only slightly.

At about 55 hours into the experiment, the biofilm streamers tangled with each other, forming a net-like barrier that trapped additional bacterial cells, creating a larger barrier which in turn ensnared more cells. Within an hour, the entire tube became blocked and the fluid flow stopped.

The study was conducted by lead author Knut Drescher with assistance from technician Yi Shen. Drescher is a postdoctoral research associate working with Bonnie Bassler, Princeton’s Squibb Professor in Molecular Biology and a Howard Hughes Medical Institute Investigator, and Howard Stone, Princeton’s Donald R. Dixon ’69 and Elizabeth W. Dixon Professor of Mechanical and Aerospace Engineering.

“For me the surprise was how quickly the biofilm streamers caused complete clogging,” said Stone. “There was no warning that something bad was about to happen.”

By constructing their own controlled environment, the researchers demonstrated that rough surfaces and pressure driven flow are characteristics of nature and need to be taken into account experimentally. The researchers used stents, soil-based filters and water filters to prove that the biofilm streams indeed form in real scenarios and likely explain why devices fail.

The work also allowed the researchers to explore which bacterial genes contribute to biofilm streamer formation. Previous studies, conducted under non-realistic conditions, identified several genes involved in formation of the biofilm streamers. The Princeton researchers found that some of those previously identified genes were not needed for biofilm streamer formation in the more realistic habitat.

Read the abstract.

Drescher, Knut, Yi Shen, Bonnie L. Bassler, and Howard A. Stone. 2013. Biofilm streamers cause catastrophic disruption of flow with consequences for environmental and medical systems. Proceedings of the National Academy of Sciences. Published online February 11.

This work was supported by the Howard Hughes Medical
Institute, National Institutes of Health grant 5R01GM065859, National Science Foundation (NSF) grant MCB-0343821, NSF grant MCB-1119232, and the Human Frontier Science Program.

Where the wild things go (Folia Primatologica)

A lack of fresh water makes swamp life hard for animals such as the endangered Zanzibar red colobus monkey, pictured here drinking from a container of fresh water provided by locals. (Photo by Katarzyna Nowak)

by Morgan Kelly, Office of Communications

Ecologists have evidence that some endangered primates and large cats faced with relentless human encroachment will seek sanctuary in the sultry thickets of mangrove and peat swamp forests. These harsh coastal biomes are characterized by thick vegetation — particularly clusters of salt-loving mangrove trees — and poor soil in the form of highly acidic peat, which is the waterlogged remains of partially decomposed leaves and wood. As such, swamp forests are among the few areas in many African and Asian countries that humans are relatively less interested in exploiting (though that is changing).

Yet conservationists have been slow to consider these tropical hideaways when keeping tabs on the distribution of threatened animals such as Sumatran orangutans and Javan leopards, according to a recent Princeton University study in the journal Folia Primatologica. To draw attention to peat and mangrove swamps as current — and possibly future — wildlife refuges, Katarzyna Nowak, a former postdoctoral researcher of ecology and evolutionary biology at Princeton, compiled a list of 60 primates and 20 felids (the large-cat family that includes tigers and leopards) known to divide their time between their natural forest habitats and some 47 swamp forests in Africa and Asia.

Because swamp forests often lack food sources, fresh water and easy mobility, few mammals are exclusive to these areas, Nowak reported. Consequently, conservation groups have not intensely monitored the animals’ swamp use.

But the presence of endangered cats and primates in swamp forests might be seriously overlooked, Nowak found. About 55 percent of Old World monkeys — primates such as baboons and macaques that are native to Africa and Asia — take to the swamps either regularly, seasonally or as needed. In 2008, the Wildlife Conservation Society reported that the inaccessible Lake Télé swamp forest in the Republic of the Congo was home to 125,000 lowland gorillas — more than were thought to exist in the wild. Among big cats, the Bengal tiger, for instance, holds its sole ground in Bangladesh in the Sundarbans, the world’s largest mangrove forest.

Princeton University research compiled 21 swamp forests in Africa (left) and 26 in Asia where primates and felids (a large cat family that includes tigers and leopards) are known to seek refuge from human encroachment. The colored dots indicate the overall “threat score,” or vulnerability, of species living in a particular site. Purple denotes a site with high species diversity, and where some resident primates and felids are likely listed as a conservation concern on the Red List of the International Union for Conservation of Nature. (Image by Katarzyna Nowak)

Life in the swamps can still be harsh for some animals. Species such as the crab-eating macaque and fishing cat can adapt somewhat readily to a life of swimming and foraging for crustaceans. Meanwhile, Zanzibar’s red colobus monkey — driven to coastal mangroves by deforestation — can struggle to find the freshwater it needs, as Nowak reported in the American Journal of Primatology in 2008. Such a trend could result in local extinction of the red colobus nonetheless, she said.

Nowak concludes that swamp forests beg further exploration as places where endangered species such as lowland gorillas and flat-headed cats have preserved their numbers — and where humans could potentially preserve them into the future.

Read the abstract.

Citation: Nowak, Katarzyna. 2013. Mangrove and Peat Swamp Forests: Refuge Habitats for Primates and Felids. Folia Primatologica. Vol. 83, no. 3-6, pp. 361-76.

Forecast is for more snow in polar regions, less for the rest of us (Journal of Climate)

A new climate model predicts declines in snowfall in the U.S. over the next 70 years. Source: GFDL
Click on image to enlarge.

By Catherine Zandonella, Office of the Dean for Research

A new climate model predicts an increase in snowfall for the Earth’s polar regions and highest altitudes, but an overall drop in snowfall for the globe, as carbon dioxide levels rise over the next century.

The decline in snowfall could spell trouble for regions such as the western United States that rely on snowmelt as a source of fresh water.

The projections are the result of a new climate model developed at the National Oceanic and Atmospheric Administration (NOAA) Geophysical Fluid Dynamics Laboratory (GFDL) and analyzed by scientists at GFDL and Princeton University. The study was published in the Journal of Climate.

The model indicates that the majority of the planet would experience less snowfall as a result of warming due to a doubling of atmospheric carbon dioxide. Observations show that atmospheric carbon dioxide has already increased by 40 percent from values in the mid-19th century, and, given projected trends, could exceed twice those values later this century. In North America, the greatest reductions in snowfall will occur along the northeast coast, in the mountainous west, and in the Pacific Northwest. Coastal regions from Virginia to Maine, as well as coastal Oregon and Washington, will get less than half the amount of snow currently received.

In very cold regions of the globe, however, snowfall will rise because as air warms it can hold more moisture, leading to increased precipitation in the form of snow. The researchers found that regions in and around the Arctic and Antarctica will get more snow than they now receive.

The highest mountain peaks in the northwestern Himalayas, the Andes and the Yukon region will also receive greater amounts of snowfall after carbon dioxide doubles. This finding clashes with other models which predicted declines in snowfall for these high-altitude regions. However, the new model’s prediction is consistent with current snowfall observations in these regions.

The model is an improvement over previous models in that it utilizes greater detail about the world’s topography – the mountains, valleys and other features. This new “high-resolution” model is analogous to having a high-definition model of the planet’s climate instead of a blurred picture.

The study was conducted by Sarah Kapnick, a postdoctoral research scientist in the Program in Atmospheric and Oceanic Sciences at Princeton University and jointly affiliated with NOAA’s Geophysical Fluid Dynamics Laboratory in Princeton, and Thomas Delworth, senior physical scientist at GFDL.

Read a plain-language summary of the article on GFDL’s web site.

Read the abstract.

Citation: Kapnick, Sarah B. and Thomas L. Delworth, 2013. Controls of Global Snow Under a Changed Climate. Journal of Climate. Early online release published Feb. 6. http://dx.doi.org/10.1175/JCLI-D-12-00528.1

This work was supported by the Cooperative Institute for Climate Science, a collaborative institute between Princeton University and GFDL.

New light shed on pesky “snakes” that cool fusion reactions (Physical Review Letters)

By John Greenwald, Princeton Plasma Physics Laboratory

Corkscrew-shaped instabilities called “snakes” have long been a common feature of the hot, electrically charged plasma gas that fuels fusion reactions, which could provide a future source of clean and abundant energy for generating electricity. Such snakes trap impurities released from the plasma-facing walls of experimental fusion vessels called tokamaks, and these impurities radiate away copious amounts of energy, cooling the plasma to temperatures below those required to create fusion reactions. Understanding the formation and survival of snakes can thus be essential to eliminating the problem so that fusion can take place.

New experimental data reported today in Physical Review Letters sheds light on how snakes form and survive in fusion plasmas. The paper, whose lead author is Luis Delgado-Aparicio of the U.S. Department of Energy’s Princeton Plasma Physics Laboratory (PPPL), cites recent experiments on the Alcator C-Mod tokamak at the Massachusetts Institute of Technology Plasma Science and Fusion Center (MIT-PSFC). The findings compiled by a multidisciplinary team show that the formation of snakes cannot be explained, as previously thought, by plasma pressure alone. Instead, the formation reflects complex interactions among phenomena that include the separately evolving plasma density and temperature conditions that produce the plasma pressure. This separate evolution of density and temperature also enables the snakes to survive periodic relaxations of plasma pressure known as sawtooth instabilities.

Left: Time sequence of a snake, in red, depicted by x-ray detectors. The sawtooth crash occurs halfway through the sequence and barely perturbs the snake.
Right: X-ray reconstruction of cross-section of crescent snake inside Alcator C-Mod.
Credit: Luis Delgado-Aparicio

Read the abstract.

Citation:
Delgado-Aparicio, Luis; Linda Sugiyama, MIT; Robert Granetz, MIT; David Gates, PPPL; John Rice, MIT; Matthew Reinke, MIT; Manfred Bitter, PPPL; Eric Fredrickson, PPPL; Chi Gao, MIT; Martin Greenwald, MIT; Kenneth Hill, PPPL; Amanda Hubbard, MIT; Jerry Hughes, MIT; Earl Marmar, MIT; Novimir Pablant, PPPL; Yuri Podpaly, MIT; Steven Scott, PPPL; Randy Wilson, PPPL; Steve Wolfe, MIT; and Steve Wukitch, MIT. 2013. Formation and stability of impurity “snakes” in tokamak plasmas. Physical Review Letters 110, 065006.

This work was performed under U.S. DOE contracts including DE-FC02-99ER54512 and others at MIT and DE-AC02-09CH11466 at PPPL. Computational support was provided by the National Energy Research Scientific Computing Center under DE-AC02-05CH11231.

Organizations shape pharmacists’ work as gatekeepers (Social Science and Medicine)

By Michael Hotchkiss, Office of Communications

Pharmacists regularly face a range of ethical dilemmas, from deciding whether to dispense emergency contraception to managing requests for narcotics, and must navigate a range of relationships with other health-care professionals.

Using 95 interviews with pharmacists working in retail and hospital settings, Princeton researcher Elizabeth Chiarello shows how organizations shape the way pharmacists exercise their roles as medical, legal, fiscal and moral gatekeepers. An article by Chiarello based on the research was published online by the journal Social Science and Medicine.

According to the paper by Chiarello, a sociologist working as a postdoctoral research associate at the Office of Population Research within the Woodrow Wilson School of International and Public Affairs, the findings suggest new directions for theorizing about ethical decision-making in medical contexts.

Read the abstract.

Chiarello, Elizabeth. 2013. How Organizational Context Affects Bioethical Decision-Making: Pharmacists’ Management of Gatekeeping Processes in Retail and Hospital Settings. Social Science and Medicine. doi: 10.1016/j.socscimed.2012.11.041

Funding for this research was provided by the Andrew W. Mellon Foundation, the American Council of Learned Societies, the U.S. Department and Health and Human Services Agency for Healthcare Research and Quality, the Princeton University Office of Population Research, the Princeton University Center for Health and Wellbeing, and a grant from the University of California, Irvine Center for Organizational Research.

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