Author: Ashley Yeager Page 5 of 7

Solving cells' social networks

On March 1, 2012

By Ashley Yeager

Rick Durrett is looking at the math underlying the most challenging biological problems. Credit: Les Todd, Duke Photography.

“Cancers are complicated systems, and you want to figure out how they work,” says mathematician Rick Durrett in a Q&A in the latest editions of the Proceedings of the National Academy of Sciences.

Durrett, who was recently elected to the Academy, came to Duke in the summer of 2010 and has been collaborating with researchers to here, using the tools of probability theory to look for ways to study cancer questions through computer simulations rather than large experimental trials.

One of the greatest challenges is to understand how cells use social networking to survive and adapt to their environment. Durrett has been working with biologists to describe mathematically how individual cells secrete chemicals that affect the behavior of nearby cells.

“This may be important for the spread of cancers. It’s an interesting area, and one I’m learning more about now,” he said in the PNAS interview.

You can read the full interview here.

Physicist's thesis now 'famous'

By Ashley Yeager

On February 22, 2012

In Faculty, Physics, Students

By Ashley Yeager

Physicist Ashutosh Kotwal's thesis paper is now famous in the high-energy physics field. Image courtesy of Ashutosh Kotwal.

Physicist Ashutosh Kotwal spent his days in graduate school making particles scatter. Little did he know that his 1996 thesis on protons, deuterons and muons would become famous.

Kotwal, now a full professor at Duke, recently learned from a former mentor, Northwestern physicist Heidi Schellman,that his Ph.D thesis earned “famous paper” distinction in his field of high-energy physics. The honor is based on the number of times other researchers have mentioned the work in the scientific literature. Schellman had been the leader for Kotwal’s thesis research collaboration.

The high-energy physics community has maintained its own database of publications and citations at the Stanford Linear Accelerator Center since the 1980s. Kotwal’s thesis paper has 252 citations, to date.

His paper is now ranked number 99 among experimental high-energy physics famous papers from the last 15 years.

According to the stats, Kotwal is also co-author on five other “famous” papers and two “renowned” articles, which each have more than 500 citations. Kotwal said he hopes his thesis paper’s distinction “can provide some inspiration” for students interested in physics research.

Steve Koonin to speak March 8

By Ashley Yeager

On February 15, 2012

In Climate/Global Change, Lecture, News Release, Physics, Science Communication & Education

Official portrait of Steven E. Koonin, former Under-Secretary for Science of the United States Department of Energy. Credit: DOE.

Want to know what we should do to address America’s energy challenges?

Come hear the ideas of Steve Koonin, a former chief scientist at British Petroleum and more recently the Under Secretary for Science at the Department of Energy. He’ll speak at Duke at 5:15 p.m. on March 8, 2012. The lecture will be held in room 2231 of the French Family Science Center.

Koonin, an MIT-minted theoretical physicist and currently a researcher at the Institute for Defense Analyses in Washington D.C., will talk about strategies to incorporate alternative and renewable energy sources into our energy profile. The lecture is free and open to the public.

The talk is part of the university-hosted Symposium on Electroweak Nuclear Physics, a two-day science conference to explore the latest experiments and ideas on matter and how it behaves at ordinary temperatures — quite the opposite of what’s being studied at the Large Hadron Collider and other high-energy particle accelerators.

The symposium is being held in honor of Jefferson Lab deputy director for science R. D. McKeown’s sixtieth birthday.

Quarks make their world turn

By Ashley Yeager

On February 3, 2012

In Physics

By Ashley Yeager

This cartoon shows the axis rotation and the intrisic spin, from mass or charge, of the protons and neutrons in a He-3 atom. Credit: Yi Qiang, Jefferson Lab.

It’s good that things spin.

If the Earth didn’t, we wouldn’t have night and day. If wheels didn’t, we wouldn’t have quick ways to get around. And, if the protons and neutrons in atoms didn’t, well, it’s not clear what would happen, but we definitely wouldn’t have medical tests like MRIs.

Even though spinning particles play a large role in our everyday lives, physicists aren’t sure where the rotation comes from. They certainly have some ideas, but actually observing the origin of protons’ and neutrons’ spin has been challenging.

Now, experiments led by physicist Haiyan Gao and her colleagues are providing a more detailed picture of what makes sub-atomic particles turn. The team is using high-energy electrons and a rare form of helium at the Jefferson Lab to look at how quarks, the particles within protons and neutrons, spin.

The experiment seems simple – slam the electrons into helium-3, or He-3, atoms. But, there’s a bit more complexity. The scientists have to carefully manipulate the rotation of all of the particles involved. The neutrons of He-3, for example, must turn perpendicular to the direction of the incoming electrons. And, the electrons have to turn either in the same direction as they are moving or in the exact opposite direction.

The physicists manipulate the direction the particles spin using polarized lasers.

Getting these spins correct is critical to figuring out if the quarks within protons and neutrons spin, and if so, in what direction. In the experiment, the incoming high-energy electrons slam into the cores of the helium-3 atoms and penetrate deep into their neutrons. The electrons strike the quarks inside, knocking them loose.

The physicists found that the struck quarks turn on imaginary axes just like Earth does. And, they turn in the same direction as their parent particle. This is the first successful experiment to measure the alignment between the spin of a quark and the direction its neutron is moving, a discovery that gives scientists hints about where the rotations of neutrons and protons originate, Gao says.

This cartoon shows the rotation of an incoming electron compared to the spin of a helium-3 neutron and the ejected down quark. Credit: Jin Huang, LANL.

Past experiments have shown that the quarks’ intrinsic rotation (from mass or charge) makes up about a third of a proton’s or neutron’s overall spin. The results of the new experiment, which appear in the Feb. 3 Physical Review Letters, suggest that the remaining two-thirds of a parent particle’s rotation comes from orbital motion of the particle’s quarks.

The conclusion, however, is far from certain, Gao cautions. This new experiment is like a snapshot of how the quarks turn. Physicists do not yet have the full picture of the orbital motions of these particles, she says.

To get a more complete picture, she and her team are working on a more sensitive detector and other upgrades to the Jefferson Lab electron beam that they will use to study even more carefully how quarks spin.

And that too, is a good thing, though we may not yet understand – in terms of everyday applications – why.

Citation: “Beam-Target Double-Spin Asymmetry ALT in Charged Pion Production from Deep Inelastic Scattering on a Transversely Polarized 3He Target at 1.4<Q2<2.7 GeV2.” J. Huang et al. (2012). Physical Review Letters. 108: 5.
DOI: 10.1103/PhysRevLett.108.052001

Composing music with Xbox Kinect

By Ashley Yeager

On January 27, 2012

In Computers/Technology, Faculty, Lecture, Visualization

By Ashley Yeager

Ken Stewart uses his motions and an XBox Kinect to narrate, musically, a dance by Thomas DeFrantz. Credit: Duke University Dance Program.

To watch Ken Stewart dance in front of his Xbox Kinect gives a whole new meaning to the “Dance Your Ph.D.” contest.

Stewart, a graduate student in the music department and a composer, is using the camera, along with specialized computer software, to narrate dance with sound. He demo’ed the program while walking an audience through his imnewhere, or I’m new here, composition of dance professor Tommy DeFrantz’s journey to Duke.

The Jan. 27 presentation was part of the Visualization Friday Forum and gave attendees a behind-the-scenes look at the research and mathematics behind Stewart’s new, “more expressive way” to write music.

With the Kinect, which has motion-detection technology for interacting with video games, Stewart can transform his gestures into sound, intimately controlling the loudness, pitch and rhythmic intensity of the score he creates. The system records 15 points on a controller’s body, including his head, neck, shoulders, knees and feet.

Using a library of sounds, the controller can then correlate and choreograph a composition, using the computer to calculate angles between his hands or distance between his body and the camera. These angles are converted to become the musical notes.

The work, Stewart says, gives him a way to use his ears and actions to “feel out” a song. He concedes that there are hiccups between how he moves and the sounds created, but, he says he thinks that the imprecision adds to the expressivity of the composing process.

Stewart said he and DeFrantz are still working on imnewhere. They plan to expand the piece to 15 minutes and will perform it again in Grand Rapids, Mich., Berkeley, Calif. and Belfast, UK.

Double-walled nanotubes shine, sometimes

By Ashley Yeager

On January 13, 2012

In Physics, Visualization

By Ashley Yeager

This montage shows modeled and imaged double-walled carbon nanotubes. Courtesy of: Morinobu Endo, Shinshu University.

Nanotubes are tiny, and they can give off light. Those properties make the carbon constructions promising for looking at cells inside our bodies and also making small electrons that can capture and manipulate light.

But recent research suggests that not all nanotubes shine as chemists thought, a discovery that ends a debate in the field about which type of tubes to use for applications relying on their ability to emitted light.

The debate pitted single-walled carbon nanotubes against double-walled ones. Some scientists thought only single-walled tubes could give off light and be used in light-related applications. But other scientists showed that double-walled nanotubes could also emit light and possibly replace their single-walled cousins.

Now, Sungwoo Yang, a former chemistry graduate student at Duke, and his colleagues in Jie Liu’s lab have shown that both single and double-walled carbon nanotubes shine when hit with lasers. But, in the double-walled tubes, only the inner wall emits light and only a small range of diameters of the inner tube could get their light to the outside world. The ones outside of this range gave off light, but it got doused on its way through the outer layer.

Bottom line: Some double-walled carbon nanotubes do emit light but most don’t, if you’re looking for the light outside of the tube. That discovery makes both camps in the nanotube debate correct, depending on the diameter of tube being considered.

CITATION: “Photoluminescence from Inner Walls in Double-Walled Carbon Nanotubes: Some Do, Some Do Not.” Sungwoo Yang, Ashley Parks, Stacey Saba, P. Lee Ferguson, and Jie Liu. Nano Lett., 2011, 11:10, 4405–4410
DOI: 10.1021/nl2025745

Chaos puts a path on nanoparticles

By Ashley Yeager

On January 13, 2012

In Biology, Cancer, Physics

By Ashley Yeager

Shaquille O'Neal towers over Ralph Stefanelli, the doctor who delivered him. Credit: Rich Krauss.

At just over seven feet tall, Shaquille O’Neal is easy to spot in crowd. But the individual virus structures that give him, and us, a cold aren’t so easy to see.

They’re harder to spot because they, unlike Shaq, are much smaller than the wavelengths of light we use to see them. But, physicists at Duke are now designing a technique that could give scientists a way to sense these tiny viruses and other nanoparticles and even capture their path when they’re on the go.

The team describes the new sensing system in the Dec. 16 issue of Physical Review Letters.

The new detector will compliment the few existing ways to track tiny objects, says physics graduate student Seth Cohen. He says that currently detectors can sense the presence of nanoparticles and that biomedical researchers have used virus-sized objects to tag specific parts of human cells.

“Ultimately, I would like to see this new system used to map out the dynamics inside of a living cell, using nanoparticle tags on the cell’s internal structures,” he says.

That can’t be done right now because the internal structures and other nanoparticles are smaller than 100 nanometers. Our eyes see wavelengths of light between 400 to 700 nanometers, and Shaq, by comparison, is 2.16 billion nanometers. We see Shaq because he has a lot more nanometers than those found in the wavelengths of light we use to see. But, we can’t see virus or cell structures because they’re size is far below that limit.

To overcome the problem, Cohen and his colleagues based their new sensing system on two physical properties, wave chaos and nonlinear dynamics. The proposed apparatus is shaped like a stadium, where multiple reflections of radio-frequency waves fill the entire cavity and take many different paths, a form of wave chaos. The stadium-shaped cavity and multiple-path reflections also allow the physicists to suspend the information flowing through the system, forming a nonlinear delayed feedback loop.

The virus structure, shown here, that causes the common cold is only 20 nanometers across. Credit: Michael Taylor, TurboSquid.com

In initial experiments, the team used a pair of stationary broadband antennas to track a small container filled with water, which also scatters the radio waves broadcast into the cavity. Working out the geometry of the cavity, along with all of the possible reflection angles of light, the team was able to pinpoint the object in the cavity and track it as it moved. In other words, by combining wave chaos and nonlinear dynamics, the physicists could track an object that was much smaller than the wavelengths scientists used to see it.

The team is now designing a new version of the system using laser light and a microcavity, which is only a few hundred micrometers in size and can be constructed on silicon chips. The system, which will work in the visible wavelengths of light, will provide a new and simple technique for tracking small nano-scale objects, such as viruses. Cohen will report on his progress on this sensing system in May at the Experimental Chaos and Complexity Conference in Ann Arbor, Michigan.

Citation: Subwavelength Position Sensing Using Nonlinear Feedback and Wave Chaos. Seth D. Cohen, Hugo L. D. de S. Cavalcante, and Daniel J. Gauthier. Phys. Rev. Lett. 107, 254103 (2011). DOI: 10.1103/PhysRevLett.107.254103

Particles of light overcome their lack of attraction

By Ashley Yeager

On December 5, 2011

In Faculty, Nanotech, Physics, Students, Visualization

By Ashley Yeager

This waveguide shows an electric field moving from right to left. Credit: Setreset, Wikimedia Commons.

Electrons typically repulse each other. But sometimes they can actually attract each other and pair up, which is why superconductors exist. The particles that make up light, on the other hand, have no charge and rarely appeal to or repel one other.

Now, Duke theoretical physicist Harold Baranger and his collaborators think it’s possible to get these particles, called photons, to pair up, and stay that way, as they travel through space.

The new idea could help with the development of quantum communications, and possibly quantum computing in the future, Baranger says.

Particles of light do not have electric charge so they’ve got no attraction to the particles around them. That lack of attraction gives photons the ability to travel long distances without losing information, a good trait for building quantum networks.

But, the photons’ reserve has a drawback. It makes it more difficult for scientists to control each particle and retrieve the information it carries. To rein in the seemingly aloof photons, physicists have designed cavities that trap them and boost their contact with individual atoms.

In these cavities, the particles pass one by one through an atom in a phenomenon called a photon blockade. But, the cavities trap the photons for a really long time, so they pass through the cavities really slowly, which isn’t good for networking — especially in this age of instant information.

Using pencil and paper, Baranger, his student Huaixiu Zheng and colleague Daniel Gauthier, figured out that they could avoid the problems with the cavities if the photons instead went into a one-dimensional structure, called a waveguide, which also channels the photons past an atom one by one.

In the waveguide, a control atom acts as an intermediary between the incoming particles. The first photon passes through the atom and changes its state.

This diagram shows a photon blockade in a waveguide. Multiple photons (left, yellow) pass by the control atom in a one-by-one manner, ending with a train of single-photon pulses and empty pulses (gray). Courtesy of Harold Baranger, Duke.

The atom then interacts differently with the next photons, which ultimately causes the two particles of light to interact. What’s surprising, Baranger says, is that the photons are still bound to each other for a long time, even as they move away from the atom that paired them.

These bound states also end up producing a photon blockade much like in a cavity, but through a completely different mechanism, and the photons move a lot faster, he says.

The work, which appears online in Physical Review Letters, “paves the way” for experimentalists who want to try to build quantum networks without using cavities, Baranger says. He says experiments in this area may be done at Duke in the next few years.

Right now, he plans to work out what happens to the photons if more than one atom sits in the waveguide. The photons will be interacting in a lot of different places, and “one can imagine that there could even be a quantum phase transition, giving rise to some new quantum state,” he says. “But, that’s just a hope at this point.”

CITATION: Cavity-Free Photon Blockade Induced by Many-Body Bound States. Zheng, H., Gauthier, D., and Baranger, H. Phys. Rev. Lett. 107, 223601 (2011).

DOI: 10.1103/PhysRevLett.107.223601

Atomic core, shaken not stirred

By Ashley Yeager

On December 5, 2011

In Physics

By Ashley Yeager

When hit right, protons and neutrons can have a distinct ring, like a hammer hitting a bell. Credit: Geo Martinez, 123rf.com.

When struck just right, protons and neutrons ring. The sub-atomic particles don’t jingle like when a hammer hits a bell. But they do jiggle in an odd dance where the protons move in one direction and the neutrons move the other way.

Studying this particular particle movement has been difficult because of other motion within an atom’s nucleus. But now, researchers using the High Intensity Gamma Ray Source, or HIGS, located on Duke’s campus, say they have gotten the best look yet at a nucleus as it starts its complex, resonant dance.

In the experiment, the researchers slammed a chunk of bismuth-209, which had 83 protons and 126 neutrons, with a polarized beam of high-energy photons.

The team then recorded all the gamma rays knocked from the nucleus after the collision. Based on the direction the gamma rays were traveling, the scientists were able to figure out the energy, width and strength of the resonance at which the particles’ rang.

The results, which appear in the Nov. 25 issue of Physical Review Letters, along with future studies on the vibrations of other nuclei planned at the HIGS facility will help theorists write a clear, accurate mathematical description of how protons and neutrons behave and also for the state of matter in black holes, neutrons stars and even in star explosions called supernovae.

CITATION: New Method for Precise Determination of the Isovector Giant Quadrupole Resonances in Nuclei. Henshaw,S., Ahmed, M., Feldman, G., Nathan, A., and Weller, H. PRL 107, 222501 (2011).

DOI: 10.1103/PhysRevLett.107.222501

A sip or quick dip could change your DNA

By Ashley Yeager

On November 15, 2011

In Animals, Biology, Cancer, Chemistry, Environment/Sustainability, Genetics/Genomics, Global Health, Lecture

By Ashley Yeager

Micronuclei in mammalian cells form when DNA undergoes stress and not all the material makes it into the two new nuclei of a dividing cell. Credit: CRIOS.

As a long-time swimmer, I was a bit disturbed when EPA scientist David DeMarini said he had scientific evidence showing that extra time in the water could damage my DNA or even raise my risk for bladder cancer.

The damage, he said, comes from leftover chemicals from the treatment process in which bromine and chlorine are used to kill E. coli and other bacteria in drinking, bath and swimming water.

There are at least 600 of these chemicals, called disinfection byproducts or DPBs, released into the water after treatment, and DeMarini has spent more than a decade identifying them and how they interact with the molecules in our bodies.

Through his research, he has shown that many of the DPBs, whether ingested, inhaled or absorbed through our skin, can change our DNA. Yet, only 11 DPBs, all from drinking water, are regulated in the U.S., and none are regulated in any of the other developed countries, DeMarini said during a Nov. 11 Integrated Toxicology & Environmental Health seminar at Duke.

No one really thought about pool water until about five years ago because “people always thought swimmers weren’t at risk for anything. They thought, ‘swimmers are healthy, so why waste our time studying them,’ ” DeMarini said.

That assumption changed in 2007. Researchers in Spain found, based on interviews, that swimmers had a 1.6-fold increase for bladder cancer. Then, in 2010, DeMarini and his colleagues showed that after a 40-minute workout, swimmers’ cells created micronuclei, suggesting damage was done to the DNA so that another nuclei formed as the cell began to divide.

Together, the teams were able to identify a specific gene that makes some individuals more susceptible to DNA damage from DPBs, further increasing their cancer risks. About 28 percent individuals in the U.S. have this gene.

That doesn’t mean we should stop swimming, bathing or drinking municipal water though, DeMarini stressed. He said that the known benefits of drinking, bathing with or swimming in chlorinated water are still much greater than the potential health risks from DPBs.

“You’re naïve, though, if you think that the environment you live in is pristine,” he said. “It’s not.”

But to keep pools a little cleaner and reduce the burden of disinfection byproducts, he suggested not peeing in the water and showering before taking a dip. Drinking pool water is not a good idea either.