Research Blog

A second crack at the nature of glass

On August 13, 2012

In Computers/Technology, Faculty, Field Research, Mathematics, Physics, Visualization

By Ashley Yeager

Glassblowers shape molten silica before the glass transitions from liquid to a more solid structure. Credit: handblownglass.com.

Patrick Charbonneau and his collaborators have taken another crack at understanding the nature of glass. Their latest simulations show that a key assumption of theoretical chemists and physicists to explain the molecular structure of glass is wrong.

Glass forms when liquids are slowly compressed or super-cooled, but don’t crystallize the way cooled water turns to ice. The liquidy pre-cursors to glass, like molten silica, do become hard like a solid, but the atoms in the material don’t organize themselves into a perfect crystal pattern.

The result is a substance that is as hard as a solid but has the molecular arrangement of a liquid — a phenomenon that scientists can’t quite explain, yet.

Previous theories assumed that at the transition point between a liquid and glass, the material’s atoms become caged by each other in a “simple” Gaussian shape. This same shape describes the distribution of people’s height in the U.S. and is known as a bell-shaped curve.

But new simulations, described online Aug. 13 in PNAS, suggest this assumption is wrong. The simulations model the interactions of glass particles in multiple dimensions and show the shape of the particle cage is much more complex than a Gaussian distribution.

The discovery is a “paradigm shift in the sense that so many people have been having the same, wrong, conception for so long, and they should now revisit that basic assumption,” says Charbonneau, a theoretical chemist at Duke. “The assumption was actually constraining how they thought about the problem.”

Even with a new shine on the way scientists think about glass, it is not clear how close or far the theorists are from writing an accurate description of what happens at the liquid-glass transition. But “the path to get there seems clearer than it has been in a long time,” Charbonneau says.

The next step in the research is to understand the relationship between glassy states of matter and those that are jammed, like pieces of cereal wedged in a grain hopper. Charbonneau and collaborators are already at work about how to study the connections between the two forms of matter.

Citation:
“Dimensional study of the caging order parameter at the glass transition.” 2012. Charbonneau, P., et al. PNAS Early Edition. DOI: 10.1073/pnas.1211825109

Reading between the lines of light

By Ashley Yeager

On August 10, 2012

In Computers/Technology, Engineering, Faculty, Nanotech, Physics

By Ashley Yeager

Harry Potter's invisibility cloak is not exactly what scientists have in mind for their light tricks. Credit: Warner Brothers.

The way we understand light is largely based on how we see it. To our eyes, light is like a stream of particles.

Scientists usually study these particle streams by measuring their wavelengths and how they interact with objects. But over the last decade, researchers have begun to realize that light particles can interact with objects within wavelengths too.

Now, scientists are looking inside wavelengths to control and manipulate light, which is transforming the traditional field of optics, according to Duke engineer David Smith and his colleagues.

They describe the changes to the field of optics in a review article appearing online Aug. 2 in Science, and they describe how, at a tenth or even a hundredth of the wavelength of visible light, the classic picture of how we see breaks down.

In this regime, streams of light particles can bend away from an object, essentially tricking the eye into thinking the object is not there. As a result, scientists can no longer think of light in terms of particle streams. Instead, they must think of it as a manipulation of electric and magnetic field lines.

Thinking of light this way, Smith and other scientists are beginning to understand how they can hide one object within another and even harvest energy. The new understanding “will be the design tool of choice” as scientists continue to play with the forces between electrically charged particles, the authors argue.

Citation:

“Transformation Optics and Subwavelength Control of Light.” Pendry, J., et. al. 2012. Science 337: 549-552.
DOI: 10.1126/science.1220600

Lemurs Most Threatened Mammals on the Planet

By Karl Bates

On July 24, 2012

In Animals, Biology, Environment/Sustainability, Lemurs

By Karl Leif Bates

Things seem to be going from bad to worse for the lemurs of Madagascar.

A report issued two weeks ago by a working group in Antananarivo, Madagascar’s capital, concludes that these prosimian primate cousins of ours are THE most endangered mammals on the planet with 91 percent of all lemurs on the Red List of threatened status.

The 5,000-acre Betampona Nature Reserve in the eastern rainforest region is the smallest and oldest of Madagascar's officially protected areas. It looks like a green island surrounded by damaged forests and subsistence farming. The reserve is jointly managed by the Madagascar Fauna Group, of which the Duke Lemur Center is a founding partner, and was the site of first reintroduction of lemurs which had been bred in captivity at DLC.

In a poor and poorly governed country, humans are steadily chewing away at lemur habitat and at the lemurs themselves.

One species, the northern sportive lemur, is down to just 18 individuals on a tiny speck of habitat at the extreme northern end of the island. There are none in captivity.

“When these species disappear from Madagascar, they are lost forever,” Lemur Center Director Anne Yoder said. Captive breeding programs, like the one at the Duke Lemur Center, are a poor substitute for the protection lemurs really need.

The warning is unfortunately all too familiar to the faculty, staff and volunteers of the DLC, and it casts their work in conservation, education and research as even more critical.

In addition to its crucial work in Durham, DLC has been working on the ground in Madagascar for more than 20 years to preserve habitat and build a corps of conservation-minded citizens. Post-doctoral researcher Erik Patel participated in the Antananarivo workshop and reported on the meeting last week.

Learn More:

Anne Yoder and Charlie Welch on Duke Lemur Center blog.

Russ Mittermeier, chairman of the Madagascar Primate Specialist Group and President of Conservation International in the Huffington Post.

The Duke Lemur Center's breeding population becomes ever more important as wild lemurs disappear.

Hands-On Lab Experience Helps Student Set Goals

By Karl Bates

On July 23, 2012

In Biology, Guest Post, Students

Story and Photos by Gabriel Aikens, NCCU Summer intern

The bubbling of reactions and the sight of stern-looking, goggle-wearing scientists with lab coats on the verge of discovering the next big cure is what goes on in Duke’s biology labs, right? No, not at all.

Besides seeing lab coats and a variety of beakers, one might be surprised to also find people in hoodies or khaki shorts and sneakers listening to their favorite songs and joking with each other.

Morgan Morrison has been working with the plant Arabidopsis thaliana in the lab of Xinnian Dong in Duke Biology.

Don’t be fooled by the relaxed environment however. These graduate and undergraduate students are hard at work, including intern Morgan Morrison, a North Carolina Central University senior from Charlotte interning at Duke’s Institute of Genome Sciences & Policy (IGSP) Summer Fellowship Program. Morrison and her colleagues spend their days transferring samples into geno-grinders (machines that grind plant tissue), carefully extracting chemicals with pipettes, and handling subzero nitrogen which sizzles and hisses loudly as samples are lowered into it..

Morrison was accepted into other summer internships but chose Duke’s because of her interest in genomics and her attraction to the university.

This internship is offered to a select few students from around the nation to take on various projects. Morrison is undergoing two projects, observing plant-microbe interactions and cloning plants to study their transcription of genes.

“I’m observing the microbes (microscopic organisms) to find useful plant-derived compounds for combatting infections,” says Morrison. “I’m cloning plants to see how resistant they are to a given disease.”

Morrison is doing molecular cloning, which is different from making genetically identical copies like cloning in the movies. Molecular cloning is the engineering of transgenic plants, which are plants containing genes transferred from another species. The plant she works with is Arabidopsis, a small flowering plant that’s a member of the mustard family.

To perform molecular cloning, she first identifies a protein of interest (POI) that might confer resistance to the Arabidopsis and then through a series of steps inserts the DNA coding sequence of that POI into the DNA of Arabidopsis. Then she conducts experiments test whether the new protein conferred resistance.

Morrison developed a fascination with scientific research after an AP Biology II course where she worked with Drosophila (fruit flies).

Learning lab skills will help Morgan decide on a career path.

“At the time, I didn’t know which field of science would be best for me, but I especially wanted to be involved in chemistry.”

She’s pursuing a B.S. in Pharmaceutical Science at NC Central University with a concentration in Chemistry, followed by going into a Ph.D program. “Right now, my purpose here at this Duke internship is to determine if I want to do research, and if so, what I’d like to research,” she says.

So far, she finds the internship beneficial and plans to combine her new knowledge with her future plans, which includes going to pharmacy school or becoming a patent lawyer. “As a scientist, I feel that it is good to be well-rounded in every aspect of science, via biology, chemistry, or desk work because basic skills and information are always relevant wherever you go,” she says.

Congo native Musoki Mwimba is mentoring Morrison during the internship. He’s an N.C Central University alumnus and graduate student in Duke’s Department of Biology. His interest is pharmaceutical science and part of his training and pursuit of a doctorate is mentoring newcomers. He says this requirement helps “improve his communication skills with others.”

“Though I like working by myself, working with the mentees is great because I’m learning from them,” Mwimba says. “As I see what their aspirations are, I try to help them reach them.”

As she works alongside Mwimba, Morrison wants to absorb as much as she can from this experience. “I hope to gain better understanding of what people do in this lab and master the projects I’m working on,” she says. “I’m happy I chose to come here.”

Trinity Junior in Phoenix for Summer, Doing Real Research

By sa160@duke.edu

On July 23, 2012

In Biology, Genetics/Genomics, Medicine, Students

By: Nonie Arora

Sonya Jooma, Trinity '14, provided by Steve Yozwiak

Rising Trinity Junior Sonya Jooma is in Phoenix, Arizona this summer working at the Translational Genomics Research Institute (TGen) as an intern in the TGen-Duke Biomedical Futures Program. This is the first year TGen and Duke have partnered to offer a funded biomedical research internship exclusively for Duke students. Jooma and a second Duke undergrad, Geoff Houtz, are the first two students to participate in this pilot program.

The TGen-Duke Biomedical Futures Program joins the growing list of Duke programs for students excited about genomics, such as the Genome FOCUS program and the Institute for Genome Sciences & Policy Summer Fellowship. In fact, the Genome FOCUS spurred Jooma’s enthusiasm for genomics research. Last year, she worked in the John Willis lab researching plant genetics as part of the Howard Hughes Research Fellows Program.

Her project at TGen, in the lab of Dr. Lisa Baumbach-Reardon, centers on the genetic basis of Infantile Spinal Muscular Atrophy. This disease causes muscle weakness and abnormality at birth. Afflicted children often die before their second birthday. According to Jooma, there are cases of this disease for which the genetic basis is unknown. As part of her lab’s exome sequencing project, they hope to identify mutations involved in the disease.

Jooma says her TGen experience has been great so far. She finds it similar to working in a research lab at Duke because of the similar lab hierarchy. However, she appreciates that TGen has overarching specific goals that focus on translating discoveries to clinical diagnostics and therapies. Jooma also looks forward to attending professional development workshops and presenting her work at TGen’s annual intern research symposium in July.

Ultimately, Jooma’s experience at TGen will be one of many exciting research projects: she hopes to pursue a career in biology research.

Hot particles appear in Science

By Ashley Yeager

On July 19, 2012

In Physics

By Ashley Yeager

Protons and neutrons "melt" to produce a plasma of freely interacting quarks and gluons. Credit: RHIC/BNL.

On July 20, readers of the journal Science are in for quite a treat — a clear, concise explanation of what matter looked like in the early universe and how scientists study it.

Science has “published very few articles in this field, as is generally the case in nuclear and particle physics, so it was a nice surprise when they invited us to write the piece,” said Duke theoretical physicist, Berndt Mueller, a co-author of the review article.

Subatomic scientists rarely try to present their latest discoveries in widely accessible terms, which may be why the journal does not run many articles related to nuclear physics, he said.

In the piece, Mueller and his co-author, Barbara Jacak, an experimental physicist at Stony Brook University, describe the most recent discoveries and remaining questions about matter in the early universe, a primordial soup called the quark-gluon plasma.

One of the most puzzling questions for physicists in this field how the subatomic particles that make matter — quarks and gluons — behave when they are “liberated,” or broken apart, as they were in the early phase of the cosmos. “We now know, thanks to the experiments at the Relativistic Heavy Ion Collider (RHIC), that they behave completely differently than theorists thought, but we only know some aspects, many others remain to be explored,” Mueller said.

The “big” question is what structure the primordial soup of quarks and gluons takes at extremely high temperatures‚ beyond two trillion degrees Celsius. “We don’t know. It’s somehow made up of quarks and gluons. It’s like saying that liquid water is made up of the elements hydrogen and oxygen, but not knowing that they form water, or H2O molecules, and that those again cluster in teaming little molecular clusters,” Mueller said.

Gold particles collide, forming a soup of quarks and gluons. Click the image to watch a more-detailed video about the quark-gluon soup.Credit: RHIC/BNL.

Answering the structure question may also help to better explain how some atoms at the opposite extreme of the temperature scale‚ a minute fraction of a degree above absolute zero, act as a nearly perfect fluid, flowing almost without resistance, just as the quark-gluon plasma does. The answer could also offer ways to comprehend black holes, string theory, and extra dimensions.

To make those connections, the authors argue that physicists will need to explore how quark matter evolves over a range of energies, temperatures and densities. They can use the Large Hadron Collider (LHC) in Europe to probe the universe’s primordial soup at the highest range of energies. But RHIC seems to be able to operate at the energy “sweet spot” for exploring the transition from ordinary matter to the quark-gluon plasma.

The scientists will talk more about future plans and research at RHIC and LHC at the Quark Matter 2012 conference in Washington, D.C. on August 12-18, which the Duke nuclear theory group helped to organize. Jacak, the leader of a 500-member international collaboration performing experiments at RHIC and a member of the National Academy of Sciences, will be at Duke on Sept. 5 to give a talk about hot nuclear matter research.

Citation: The Exploration of Hot Nuclear Matter. Jacak, B., and Mueller, B. 2012. Science. 337: 310-314.
DOI: 10.1126/science.1215901

Sleuths Take Over Science This Summer

By Karl Bates

On July 17, 2012

In Animals, Biology, Science Communication & Education, Students

Story and Photos by Gabriel Aikens, NCCU Summer Intern

Science Sleuths Lance Cook, Alex St. Bernard, and staff member Emily Milligan work together on dissecting a cow's ankle, called the fetlock.

While many teens spend their summer days playing Xbox and watching cartoons, some eighth and ninth graders are constructing catapults and dissecting cow knuckles as part of Summer Science Sleuths at Duke, a two-week program that exposes kids from across the country to science in fun and creative ways.

On a recent Thursday morning inside the Biological Sciences Building, the kids dissected cow fetlocks, which are similar to the upper knuckle joints in a human hand. There were looks of amazement, curiosity, and disgust as Dean Aguiar, program director at The Hartwell Foundation, demonstrated proper procedure with the fetlock.

“Feel free to take one home to barbeque,” Aguiar joked. Some of the kids weakly smiled, but overcame their queasy feelings the more they operated on the fetlock with their scalpels.

“It was cool,” said ninth grader Samantha Goetz from Cream Ridge, New Jersey. “The activity is similar to what I want to do when I get older, like surgery and such.”

Dean Aguiar, program director at The Hartwell Foundation, demonstrated proper procedure on the fetlock to sleuth Natalia LeMay.

The point of the dissection was to have a better understanding of joint movement, as well as identify bone cartilage, ligaments, and synovial fluid, which is a lubricating liquid inside the joint that provides nutrients to joint tissues.

On other days during the two-week camp, the Sleuths created solar ovens, built rafts, and visited the Videri Chocolate Factory in Raleigh to learn how chocolate is made. The kids were housed in dorms at Duke and had picnics and cookouts on campus, as well as dinner at the Durham Bulls Athletic Park.

To be considered for selection to participate in Summer Science Sleuths at Duke, campers completed a survey on attitudes toward science, had a parent submit an application and had a teacher complete the recommendation form.

“This is the second year of the Summer Science Sleuths at Duke program,” said Chris Adamcyzk, executive director of the Duke Center for Science Education and creator of the program. “We want to make science fun for the kids,” she says. “ We carefully design the curriculum so that they can be introduced to a breadth of science, while making connections to their real world. Although they do experiments in the lab, they also interview scientists and take field trips to connect interesting science with everyday life.”

Fetlocks are similar to human knuckles, but a whole lot larger.

Making science fun for the kids is also the goal of Frederick Dombrose, President of The Hartwell Foundation, which funds the program.

“This wasn’t designed for kids who were at the top of their science class,” he said. “We created this for bright kids who have an interest in science so we can inspire them. This is an opportunity that most of them would’ve never been exposed to, so we want them to enjoy themselves and take advantage of this.”

'Chicken' Logic Secures Planes, Trains and Ports

By Ashley Yeager

On July 13, 2012

In Business/Economics, Computers/Technology, Lecture, Mathematics, Science Communication & Education, Students

By Ashley Yeager

U.S. goalkeeper Hope Solo deflects a penalty kick. Credit: AP

Soccer penalty kicks, ‘Chicken’ and other games may thwart terrorist attacks, drug smugglers and even freeloaders trying to board trains without tickets.

It’s not so much the intensity and adrenaline of the games that lead to better security, but the logic the players use, says Vincent Conitzer, a professor of computer science and economics at Duke.

This logic is called game theory and now scientists are using it to compute solutions for security issues, Conitzer explained at a July 11 talk with undergraduates completing summer research projects on campus.

During the talk, Conitzer gave a brief overview of game theory using real-world examples, such as penalty kicks in soccer and a set of drivers playing chicken. In the soccer example, he described a “zero-sum game” between the goalie and the kicker, where no matter the outcome, one player wins and the other loses.

But in the case of chicken, in which two cars drive straight at each other until one of the drivers “chickens out” and diverts course, the stakes of each choice are a bit higher. If both drivers stay straight, they crash. It’s no longer a zero-sum game.

When it comes to preventing security problems, there are more angles of attack, smuggler entry points and ways to board a train than the simple left, right or straight of these game examples.

Cars and buses wait to clear a security checkpoint at LAX. Credit: cardatabase.net

To make predictions about what the bad guys will do in the security scenarios, Conitzer is working with Milind Tambe and his group at USC. The team has designed game theory algorithms to set the schedule of security checkpoints and canine rounds at LAX airport, smuggler-scouting in Boston Harbor and even methods for preventing terrorist attacks in Mumbai.

Tambe “treats the problem of Mumbai personally” since that is his home city, Conitzer said, adding that he is only directly involved in this project with the USC group.

While the talk focused mainly on security applications, Conitzer also thinks that some “surprising new applications have yet to emerge” from the work. The new uses won’t necessarily help win a game of chicken or score a penalty kick.

But they could help scientists understand how to better use incentives to designgames with only good outcomes, such as encouraging smart energy use.

Citation: “Computing Game-Theoretic Solutions and Applications to Security.” Conitzer, V. In Proceedings of the 26th National Conference on Artificial Intelligence (AAAI-12), Toronto, ON, Canada, 2011.

Fermilab's final findings on Higgs, it exists

By Ashley Yeager

On July 2, 2012

In Physics

By Ashley Yeager

This graphic shows the simulation of a Higgs boson decay. Credit: Fermilab.

New data announced Monday by the Tevatron particle accelerator at Fermilab suggests the Higgs boson exists. But it will take results from experiments at the Large Hadron Collider(LHC) in Europe to establish a firm discovery of the particle.

Fortunately, you won’t have to wait long. LHC scientists are expected to release their latest Higgs results two days later, on July 4.

The new Tevatron data suggests that the Higgs particle has a mass between 115 and 135 GeV/c^2, or about 130 times the mass of the proton.

The estimated mass is calculated from data taken from two Tevatron experiments and aligns with LHC-based Higgs’ mass estimates announced in December 2011 and March 2012.

The Tevatron searches are “particularly sensitive” to the Higgs boson decaying to a pair of bottom quarks, said Bo Jayatilaka, a post-doctoral scientist working with Duke physics professor Ashutosh Kotwal. “This is the largest predicted decay of the Higgs boson at the masses being considered. The nature of collisions at the LHC makes it very hard to see this particular decay over background,” he said.

Jayatilaka, who heads one of the Higgs analysis groups at Fermilab, said the Tevatron results “give a glimpse into this important decay channel of bottom quarks substantially earlier than the LHC will be able to.” It will require much more data to see this decay at LHC, he said.

The Tevatron stopped taking data in the fall of 2011, so the new Fermilab-Higgs results are final. As a result, “the most complete Higgs picture will emerge by putting together the pieces of the jigsaw puzzle from both Fermilab and CERN,” Kotwal said.

CSI-House teams could make better medical diagnoses

By Ashley Yeager

On June 28, 2012

In Biology, Cardiology, Computers/Technology, Genetics/Genomics, Lecture, Medicine

By Ashley Yeager

Comparing a child's DNA to his parents' could help with identification of hard-to-diagnose genetic diseases. Credit: Henrik Jonsson/iStockphoto

Dr. Gregory House, star of House, M.D., and the lab techs on CSI never fail at their jobs. But that’s Hollywood. In real life, diagnosing illnesses and sequencing DNA isn’t so straightforward. It doesn’t always lead to a happy ending either, especially for children who are sick but can’t be diagnosed, even by gifted, real-life doctors.

That’s exactly why geneticist David Goldstein has teamed with pediatrician Vandana Shashi to combine a little House and CSI to identify apparent genetic diseases and quickly end some families’ diagnostic odysseys.

So far, the team has provided likely genetic diagnoses in six of 12 children it has worked with, said Goldstein at a Cardiovascular Research Center Seminar Series talk on June 27.

The children were referred to Shashi for a pilot study where she would record their symptoms, or phenotypic behavior, much like House. Then, Goldstein and his team at the Center for Human Genome Variation collected DNA samples from the children and both of their biological parents.

Using next-generation genetic sequencers, as well as traditional DNA scanners, Goldstein and his team looked for genetic variations between the children’s and parents’ complete genome. Like looking at DNA to identify a criminal, Goldstein and his genetics team are scouring the sequences for genetic fingerprints of the diseases disrupting the children’s lives.

Once variations were identified, the entire team looked for known diseases with similar gene mutations and symptoms. Goldstein explained that the study not only pinpointed the undiagnosed congenital diseases in some patients but also presented new genes that could also be linked to the illnesses. The study’s success has led to the creation of the Genome Sequencing Clinic.

The clinic will begin to help the families of the 50,000 children (out of the four million) born each year in the US with difficult-to-diagnose genetic diseases. These types of studies will likely be the “earliest drivers for large-scale genetic sequencing,” Goldstein said.

But, he cautioned, “there’s a whole lot of junk,” or variation, in DNA. Every genome has the narrative potential for devastating diseases, and that means that House-CSI teams, like Shashi and Goldstein’s, need to be extremely careful when making diagnoses, especially if the results will influence treatment, he said.

Citation: Clinical application of exome sequencing in undiagnosed genetic conditions. Need, A. et. al. 2012. J. Med Genet. 49:6 353-361. doi:10.1136/jmedgenet-2012-100819