Observation of Confinement Phenomenon in Condensed Matter

Sunday, November 29, 2009

Force of interaction between magnetic particles grows stronger with increasing distance

An experiment has confirmed that spinons, particle-like magnetic excitations, can be confined in a magnetic insulator similar to the way elementary quarks are confined within individual protons and neutrons. The finding, in a well-described magnetic system, may offer new ways to explore Quantum Chromodynamics, the theory that describes the fundamental interactions of quarks.

The observations of spinon confinement were made at the Science and Technology Facilities Council’s Rutherford Appleton Laboratory in the United Kingdom by an international team of physicists. The team realized serendipitously that a theory developed 12 years earlier by theoretical physicist Alexei Tsevelik, now at the U.S. Department of Energy’s Brookhaven National Laboratory, and collaborators accurately predicted the current findings. Together, the scientists describe the theory and their new observations in the November 29th issue of Nature Physics.

“The concept of confinement is one of the central ideas in modern physics, being at the core of the theory of nuclear forces,” Tsvelik said. “In certain systems, when constituent particles are bound together by an interaction whose strength increases with increasing particle separation, individual particles cannot exist in a free state and therefore can be observed only indirectly.”

The most famous example of confinement is of quarks which are held together in protons and neutrons, for example, by the strong force, a force that grows stronger with increasing distance.

“It has been interesting for us that a similar situation of confinement can be modeled in condensed matter systems,” Tsvelik said. “Instead of quarks being confined in protons and neutrons, we have other quantum entities that act just like particles — elementary excitations of magnetic systems called spinons.”

In the case of the current experiment, the spinons exist on parallel chains of copper-oxide separated by inert calcium. Spinons on individual chains are not confined, but as soon as two chains are brought together to form ladder-like arrangements, the inter-ladder interactions confine the spinons.

“That is, the spinons can appear now only in pairs and cannot fly away from each other too far,” Tsvelik said. “The result of this confinement is a particle we call a ‘magnon.’ It is like two quarks pairing up to form a meson.”

The original theory paper published by Tsvelik and collaborators 12 years ago described the magnetic excitation spectrum of such a system in detail. The team performing the experiments at Rutherford observed a signature that fit that description.

“Now that we have an example of confinement in a condensed matter system, our next step is to check further predictions of the theory to make sure there are no unpleasant surprises,” Tsvelik said. The scientists will also measure the responses in other compounds to see if they observe similar effects.

Tsvelik’s research is funded by the DOE Office of Science.

New Hydrogen-Storage Method Discovered

Monday, November 23, 2009

Scientists at the Carnegie Institution have found for the first time that high pressure can be used to make a unique hydrogen-storage material. The discovery paves the way for an entirely new way to approach the hydrogen-storage problem. The researchers found that the normally unreactive, noble gas xenon combines with molecular hydrogen (H₂) under pressure to form a previously unknown solid with unusual bonding chemistry. The experiments are the first time these elements have been combined to form a stable compound. The discovery debuts a new family of materials, which could boost new hydrogen technologies. The paper is published in the November 22, 2009, advanced online publication of Nature Chemistry.

Xenon has some intriguing properties, including its use as an anesthesia, its ability to preserve biological tissues, and its employment in lighting. Xenon is a noble gas, which means that it does not typically react with other elements.

As lead author Maddury Somayazulu, research scientist at Carnegie’s Geophysical Laboratory, explained: “Elements change their configuration when placed under pressure, sort of like passengers readjusting themselves as the elevator becomes full. We subjected a series of gas mixtures of xenon in combination with hydrogen to high pressures in a diamond anvil cell. At about 41,000 times the pressure at sea level (1 atmosphere), the atoms became arranged in a lattice structure dominated by hydrogen, but interspersed with layers of loosely bonded xenon pairs. When we increased pressure, like tuning a radio, the distances between the xenon pairs changed–the distances contracted to those observed in dense metallic xenon.”

The researchers imaged the compound at varying pressures using X-ray diffraction, infrared and Raman spectroscopy. When they looked at the xenon part of the structure, they realized that the interaction of xenon with the surrounding hydrogen was responsible for the unusual stability and the continuous change in xenon-xenon distances as pressure was adjusted from 41,000 to 255,000 atmospheres.

Why was the compound so stable? “We were taken off guard by both the structure and stability of this material,” said Przemek Dera, the lead crystallographer who looked at the changes in electron density at different pressures using single-crystal diffraction. As electron density from the xenon atoms spreads towards the surrounding hydrogen molecules, it seems to stabilize the compound and the xenon pairs.

“Xenon is too heavy and expensive to be practical for use in hydrogen-storage applications,” remarked Somayazulu. “But by understanding how it works in this situation, researchers can come up with lighter substitutes.”

“It’s very exciting to come up with new hydrogen-rich compounds, not just for our interest in simple molecular systems, but because such discoveries can be the foundation for important new technologies,” commented Russell Hemley, director of the Geophysical Laboratory and a co-author. “This hydrogen-rich solid represents a new pathway to forming novel hydrogen storage compounds and the new pressure-induced chemistry opens the possibility of synthesizing new energetic materials.”

This research was funded by the Department of Energy, Basic Energy Sciences hydrogen storage, and the National Science Foundation, Division of Materials Research.

Scientists Challenged to Create Better Tools for Image Analysis

Thursday, April 9, 2009

The Allen Institute for Brain Science, the Howard Hughes Medical Institute (HHMI), and the Krasnow Institute for Advanced Study at George Mason University are launching an international scientific challenge to speed development of new computational tools that accurately and automatically reconstruct the “shape” of brain cells from available light microscopy data.

The organizers hope the DIADEM Challenge—short for Digital Reconstruction of Axonal and Dendritic Morphology—will lead to innovative solutions to a frustrating problem that has slowed efforts to create a functional atlas of the brain. Neuroscientists agree that a systematic characterization of neurons with their dendrites and axons is essential, since these tree-like structures are highly correlated with the electric activity of, and precise connections between, neurons and are thus linked to the functions of specific brain circuits. But scientists currently spend weeks—and, in some cases, months—tracing the intricate neuronal processes by hand, using data supplied by imaging studies.

“Manual tracing of neurons has created an intolerable bottleneck and is currently limiting the pace of discovery in neural circuit analysis.”
Giorgio A. Ascoli

“Manual tracing of neurons has created an intolerable bottleneck and is currently limiting the pace of discovery in neural circuit analysis,” said Giorgio A. Ascoli of the Krasnow Institute for Advanced Study. “Automating this process will open the exciting path to the comprehensive characterization of neuronal structure and connectivity.”

The DIADEM Challenge is open to individuals and teams from the private sector and academic laboratories. The organizers will award a $75,000 cash prize to the winning individual or team whose algorithm is judged to perform the best in tests using real data. Funding for the prize is provided by HHMI and the Allen Institute.

“Solving this computational bottleneck will be key for larger scale studies of brain wiring and to generate an atlas of connections in the brain,” said Allan Jones of the Allen Institute. “Sponsoring the DIADEM Challenge fits in well with the Allen Institute’s mission of providing broad enabling tools and data to the scientific community.”

Competitors will have a year to implement an algorithm for digital reconstruction of neuronal morphology and to test it against manual reconstruction, which is the current “gold standard.” Up to five finalists will compete in a final round at HHMI’s Janelia Farm Research Campus in Ashburn, Virginia, in August 2010.

The National Institutes of Health is providing partial support to a scientific conference that is independent of—but held in conjunction with—the final round of the DIADEM Challenge. Yuan Liu, program director for Computational Neuroscience and Neuroinformatics at the National Institute of Neurological Disorders and Stroke, is co-organizing the scientific conference with Ascoli and Karel Svoboda of Janelia Farm.

The idea for the DIADEM Challenge was originally discussed in 2007 at a scientific workshop at Janelia Farm. Scientists at the meeting noted that progress in understanding neural circuits was being slowed by the tedious task of tracing the structure of individual nerve cells by hand.

Even with the advent of computer technology that enables mapping in three dimensions, the full reconstruction of single neurons may take months. The vast majority of axons (the long neuronal projections that transmit information to neighboring cells) and dendrites (the branches on nerve cells that receive information from neighboring cells) must be traced manually. Researchers trace axons and dendrites that have been labeled with markers, such as green fluorescent protein, and imaged using a variety of microscopy techniques.

Participants in the DIADEM Challenge will have the opportunity to test their algorithms on the latest data supplied by neuroscientists. Thus, they will have a chance to assess their solutions in a real-world environment.

Ascoli, Liu, and Svoboda believe the DIADEM Challenge and associated conference could lead to significant scientific and technical advancements.

“It will certainly result in a critical assessment of the remaining obstacles to a complete solution,” said Svoboda. “This will be an exciting opportunity to bring computational and experimental scientists together to see if they can solve this problem.”

How the Retina Works

Tuesday, April 7, 2009

Like a Multi-layered Jigsaw Puzzle of Receptive Fields

About 1.25 million neurons in the retina -- each of which views the world only through a small jagged window called a receptive field -- collectively form the seamless picture we rely on to navigate our environment. Receptive fields fit together like pieces of a puzzle, preventing “blind spots” and excessive overlap that could blur our perception of the world, according to researchers at the Salk Institute for Biological Studies.

In the April 7 issue of the journal Public Library of Science, Biology, the scientists say their findings suggest that the nervous system operates with higher precision than previously appreciated and that apparent irregularities in individual cells may actually be coordinated and finely tuned to make the most of the world around us.

Previously, the observed irregularities of individual receptive fields suggested that the collective visual coverage might be uneven and irregular, potentially posing a problem for high-resolution vision. “The striking coordination we found when we examined a whole population indicated that neuronal circuits in the retina may sample the visual scene with high precision, perhaps in a manner that approaches the optimum for high-resolution vision,” says senior author E.J. Chichilnisky, Ph.D., an associate professor in the Systems Neurobiology Laboratories.

All visual information reaching the brain is transmitted by retinal ganglion cells. Each of the 20 or so distinct ganglion cell types is thought to transmit a complete visual image to the brain, because the receptive fields of each type form a regular lattice covering visual space. However, within each regular lattice, the individual cells’ receptive fields have irregular and inconsistent shapes, which could potentially result in patchy coverage of the visual field.

To understand how the visual system overcomes this problem, postdoctoral researcher and first author Jeffrey L. Gauthier, Ph.D., used a microscopic electrode array to record the activity of ganglion cells in isolated patches of retina, the tissue lining the back of the eye.

After monitoring hundreds of ganglion cells over several hours, he distinguished between different cell types based on their light response properties. “Often people record from many cells simultaneously but they don’t know which cell belongs to which type,” says Gauthier. Without this information, he says, he wouldn’t have been able to observe that the receptive fields of neighboring cells of a specific type interlock, complementing each others’ irregular shapes.

“The receptive fields of all four cell types we examined were precisely coordinated,” he says, “but we saw no coordination between cells of different types, emphasizing the importance of clearly distinguishing one cell type from another when studying sensory encoding by a population of neurons.”

Researchers who also contributed to the work include postdoctoral fellows Greg D. Field, Ph.D., Martin Greschner, Ph.D., and Jonathon Shlens, Ph.D., all in the Chichilnisky Laboratory, as well as postdoctoral researcher Alexander Sher, Ph.D., and professor Alan M. Litke, Ph.D., both at the Santa Cruz Institute for Particle Physics, University of California, Santa Cruz.

This work was supported by the National Institutes of Health, the National Science Foundation, the Chapman Foundation, the Helen Hay Whitney Foundation, the Burroughs Wellcome Fund, the Deutscher Akademischer Austauschdienst and the McKnight Foundation.

The Salk Institute for Biological Studies in La Jolla, California, is an independent nonprofit organization dedicated to fundamental discoveries in the life sciences, the improvement of human health and the training of future generations of researchers. Jonas Salk, M.D., whose polio vaccine all but eradicated the crippling disease poliomyelitis in 1955, opened the Institute in 1965 with a gift of land from the City of San Diego and the financial support of the March of Dimes.

Under Embargo Till: 17:00 UTC January 28, 2009
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Newborn Brain Cells “Time-Stamp” Memories

Wednesday, January 28, 2009

“Remember when…?” is how many a wistful trip down memory lane begins. But just how the brain keeps tabs on what happened and when is still a matter of speculation. A computational model developed by scientists at the Salk Institute for Biological Studies now suggests that newborn brain cells—generated by the thousands each day—add a time-related code, which is unique to memories formed around the same time.

“By labeling contemporary events as similar, new neurons allow us to recall events from a certain period,” speculates Fred H. Gage, Ph.D., a professor in the Laboratory for Genetics, who led the study published in the Jan. 29, 2009, issue of the journal Neuron. Unlike the kind of time stamp found on digital photographs, however, the neuronal time code only provides relative time.

Ironically, Gage and his team had not set out to explain how the brain stores temporal information. Instead they were interested in why adult brains continually spawn new brain cells in the dentate gyrus, the entryway to the hippocampus. The hippocampus, a small seahorse-shaped area of the brain, distributes memory to appropriate storage sections in the brain after readying the information for efficient recall.

“At least one percent of all cells in the dentate gyrus are immature at any given time,” explains lead author Brad Aimone, a graduate student in the Computational Neuroscience Program at the University of California, San Diego. “Intuitively we feel that those new brain cells have to be good for something, but nobody really knows what it is.”

Each of these newborn neurons undergoes a prolonged maturation process, during which it changes from hyper-excitable to composed and reaches out to mature brain cells that are already well-connected within the established circuitry. Exercise, learning, and environmental enrichment increase proliferation and survival of new neurons, while pathological (chronic) stress and age send their numbers plummeting. Despite an increasing understanding of how new neurons become part of the existing dentate gyrus network, it is still unclear what their exact function is.

Trying to ascertain the newcomers’ job in adult brains, the Salk researchers took every piece of available biological information and fed it into a computer program designed to simulate the neuronal circuits in the dentate gyrus. “Most modelers test a specific hypothesis and build a model around it,” says Aimone. “We tried not to make any big assumptions about the function of new neurons. Instead we asked, ‘What is the biology, and what does the math suggest?’”

It quickly became clear that overly excitable youngsters respond indiscriminately to incoming information. “The circuit in the dentate gyrus is designed to separate incoming memories into distinct events, a process called pattern separation, but immature cells get into the way by blurring the lines,” says Aimone. “And if they keep muddling the picture, there’s almost no point.”

But nothing lasts forever. Even the most highly strung nerve cells that used to get excited by just about anything will eventually quiet down. As they mature into fully functional granule cells, they take their place in the existing circuitry while the next generation of newborn neurons takes their place firing away at new events.

Yet, independent events that had nothing in common but the fact that they occurred around the same time will now be connected forever in our minds—explaining why discussing the movie we saw a couple of months ago might bring back the name of the café we visited afterward but whose name has been eluding us.

“Current thinking holds that when we bring up a certain memory, it passes back to the dentate gyrus, which pulls all related bits of information from their offsite storage,” says Gage. “Our hypothesis suggests that cells that were easily excitable bystanders when the memory was formed are engaged as well, providing a hyperlink between all events that happened during their hyperactive youth.”

The study was funded by the James S. McDonell Foundation, the Kavli Institute for Brain and Mind, the NSF Temporal Dynamics of Learning Center, and the U.S. National Institutes of Health.

Janet Wiles, Ph.D, a professor at the School of Information Technology and Electrical Engineering, University of Brisbane, Australia, also contributed to the study.

Study of Ancient and Modern Plagues Finds Common Features

Saturday, November 22, 2008

In 430 B.C., a new and deadly disease — its cause remains a mystery — swept into Athens. The walled Greek city-state was teeming with citizens, soldiers and refugees of the war then raging between Athens and Sparta. As streets filled with corpses, social order broke down. Over the next three years, the illness returned twice and Athens lost a third of its population. It lost the war too. The Plague of Athens marked the beginning of the end of the Golden Age of Greece.

The Plague of Athens is one of 10 historically notable outbreaks described in an article in The Lancet Infectious Diseases by authors from the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health. The phenomenon of widespread, socially disruptive disease outbreaks has a long history prior to HIV/AIDS, severe acute respiratory syndrome (SARS), H5N1 avian influenza and other emerging diseases of the modern era, note the authors.

"There appear to be common determinants of disease emergence that transcend time, place and human progress," says NIAID Director Anthony S. Fauci, M.D., one of the study authors. For example, international trade and troop movement during wartime played a role in both the emergence of the Plague of Athens as well as in the spread of influenza during the pandemic of 1918-19. Other factors underlying many instances of emergent diseases are poverty, lack of political will, and changes in climate, ecosystems and land use, the authors contend. "A better understanding of these determinants is essential for our preparedness for the next emerging or re-emerging disease that will inevitably confront us," says Dr. Fauci.

"The art of predicting disease emergence is not well developed," says David Morens, M.D., another NIAID author. "We know, however, that the mixture of determinants is becoming ever more complex, and out of this increased complexity comes increased opportunity for diseases to reach epidemic proportions quickly."

For example, more people travel more often over greater distances and in less time now than at any time in the past. One consequence of the increased mobility in the modern age can be seen in the 2003 outbreak of the novel illness SARS, which rapidly spread from Hong Kong to Toronto and elsewhere as infected passengers traveled by air.

To better understand and predict disease emergence, Dr. Morens and his coauthors stress the need for research aimed at broadly understanding infectious diseases as well as specifically understanding how disease-causing microorganisms make the jump from animals to humans.

In a narrow sense, epidemics are caused by particular microorganisms, and the study of infectious disease has historically been microbe-focused. For example, the Black Death (bubonic plague), which killed some 34 million Europeans in the middle of the 14^th century, was caused by the bacterium Yersinia pestis. In a broader sense, however, epidemics are caused by complex and not fully predictable interactions between the disease-causing microbe, the human host and multiple environmental factors, the authors note. The Black Death, for instance, was borne westward along newly established land and sea trade routes from its probable origin, China, into multiple European countries. Similarly, patterns of human movement along trade routes, specifically truck routes throughout Africa, played a role in the spread of HIV throughout that continent. Greater consideration must be given, say the NIAID authors, to broader, interlinked factors such as climate, urbanization, increased international travel and the rise of drug-resistant microbes, and the ways in which these factors combine to spark new epidemics.

Aside from commerce and travel, the NIAID authors point to several other factors that underlie many notable emerging diseases: poverty, the breakdown of public hygiene practices, and susceptibility of human populations to microbes against which they have no pre-existing immunity. This last factor played a key role in the smallpox epidemic that afflicted the Aztecs of 16^th century Mexico. Smallpox had ravaged European communities for centuries, but until the Spanish arrived on the Yucatan coast in 1519, the disease was unknown in the New World. Historians believe that some 3.5 million people in central Mexico died in the first year of the epidemic.

Epidemics also can spur advances in public health, note the authors. They point to the yellow fever epidemics of 1793-98, which began in the then-U.S. capital, Philadelphia. Though the entire federal government and most Philadelphians fled, those who remained formed an emergency government and mobilized such marginalized groups as African-Americans and immigrants to fight the outbreak. In 1798, Congress established the Marine Hospital System — forerunner of the modern U.S. Public Health Service — to provide, at public expense, medical care for sick and injured merchant seamen. Historians generally agree that a prime impetus for creating the Marine Hospital System was the yellow fever epidemics.

Modern epidemiology began in reaction to another epidemic, says Dr. Morens. In the early 1830s, as cholera made its way along waterways from Asia towards Europe, French officials attempted to prepare their country in advance of an outbreak. Teams of scientists were sent to Poland and Russia to observe the outbreaks there. Throughout France, coastal health agencies and new quarantine stations were established; in Paris, a network of health inspection offices was created to coordinate inspection of wells, cesspools and latrines of both public and private buildings. Despite these efforts, cholera arrived in Paris on March 29, 1832, with explosive effect — within two weeks, there were 1,000 cases, 85 percent of them fatal. Daily newspapers published lists of cases allowing armchair epidemiologists to see trends in illness and deaths. "For the first time in history," write the NIAID authors, "a large-scale emerging epidemic was scientifically investigated in 'real time' using census data in a prospective population-based approach that featured analyses of morbidity and mortality stratified by age-group, sex, occupation, socioeconomic status and location."

NIAID conducts and supports research — at NIH, throughout the United States, and worldwide — to study the causes of infectious and immune-mediated diseases, and to develop better means of preventing, diagnosing and treating these illnesses.