Category: Energy & Matter

Proton-smasher’s awaited flood of data creates big job for SMU researchers

Post author By Margaret Allen
Post date August 3, 2008
1 Comment on Proton-smasher’s awaited flood of data creates big job for SMU researchers

At 10 p.m. on a Saturday night in April, a handful of SMU scientists continue working at the European Organization for Nuclear Research, called by its acronym CERN, in Geneva, Switzerland. A scattering of lights illuminates the windows in several buildings along the Rue Einstein, where researchers from dozens of countries and hundreds of institutions are combining their expertise on the Large Hadron Collider (LHC) — the biggest physics experiment in history.

Ryszard Stroynowski, chair and professor of physics at SMU, points out each building in succession to a group of visitors. “By October, every light in every one of these windows will be on all night,” he says.

By then, the LHC is expected to be fully tested and ready to work. When the largest particle accelerator ever constructed becomes fully operational, it will hurl protons at one another with precision to a fraction of a micron and with velocities approaching the speed of light. These conditions will allow physicists to recreate and record conditions at the origin of the universe — and possibly discover the mechanisms that cause particles in space to acquire their differences in mass.

For Stroynowski, who has worked for almost 20 years to help make the experiment a reality, words seem inadequate to capture the anticipation surrounding its imminent activation.

“It is somewhat like that of a 6-year-old kid on Christmas Eve, waiting for Santa Claus,” he says. “The time stretches almost unbearably long.”

The LHC will be the site of several experiments in high-energy physics with high-profile collaborators such as Harvard and Duke and national laboratories including Argonne, Brookhaven, Lawrence Berkeley and Fermilab. None of the experiments is more imposing than ATLAS, one of two general-purpose particle detectors in the LHC array. At about 42 meters long and weighing 7,000 tons, ATLAS fills a 12-story cavern beneath the CERN facilities in Meyrin, Switzerland, just outside Geneva. It is a tight fit: ATLAS overwhelms even the vast space it occupies. A catwalk, not quite wide enough for two people to stand side by side, encircles the device and allows an occasional dizzying view into its works.

Size Matters
The detector’s scale will help to focus and release the maximum amount of energy from each subatomic collision. A series of bar codes on each of its parts ensure that the detector’s components, whether palm-sized or room-sized, are aligned and locked with the perfect precision required for operability. Scientists from 37 countries and regions and 167 institutions participated in its design and construction.

As U.S. coordinator for the literal and experimental heart of the ATLAS detector — its Liquid Argon Calorimeter — Stroynowski is helping to finalize the last details of the detector’s operation in anticipation of the extensive testing, scheduled to begin in August. He leads an SMU delegation that includes Fredrick Olness, professor, and Robert Kehoe and Jingbo Ye, assistant professors in the SMU Department of Physics in Dedman College.

SMU scientists are completing work on the computer software interfaces that will control the device, which measures energy deposited by the flying debris of smashed atoms. A cadre of University graduate students and postdoctoral fellows also is working on data processing for ATLAS’ 220,000 channels of electronic signals, an information stream larger than the Internet traffic of a small country.

An estimated 53,000 visitors crowded the CERN facilities on the organization’s “Day of Open Doors” April 6, eager for a glimpse of the work that CNN International has named one of the “Seven Wonders of the Modern World.”

At the beginning of May, the areas were sealed off in preparation for the first round of testing. Computers will remotely control the ATLAS experiment, which will not be touched by human hands because of the radiation released by the atomic collisions. Safety is the reason for the elaborate lockdown procedure involving more than 80 keys, each coded to a different individual’s biometric data. The system is designed to lock out any use of the device if even one key is unaccounted for.

“ATLAS has been built to run for at least 15 years with no direct human intervention,” Stroynowski says. “It will be as if we have shot it into space.”

Currently, the initial test run is scheduled to begin Sept. 1.

The Waiting Game
Once data start streaming in, the game of expectations management begins. The ATLAS detector will produce a staggering amount of raw information from each collision, and the most useful bits will be few and far between. Out of 40 million events per second, the researchers hope to pinpoint 10 events a year. The challenge seems a little like looking for a needle in a haystack the size of Mars.

“We may get what we’re looking for on the first try, or it may take us three years to find anything we can use,” Stroynowski says. “A big part of our job is to make sure we’re ready when we do.”

Among those entrusted with that task are graduate students and postdoctoral fellows in SMU’s Physics Department, including Rozmin Daya, Kamile Dindar, Ana Firan, Daniel Goldin, Haleh Hadavand, Julia Hoffman, Yuriy Ilchenko, Renat Ishmukhametov, David Joffe, Azeddine Kasmi, Zhihua Liang, Peter Renkel, Ryan Rios and Pavel Zarzhitsky.

“I came to SMU for postdoctoral work specifically because of the department’s involvement in the ATLAS project,” says David Joffe, a native of Canada who received his Ph.D. in physics from Northwestern University. “For particle physicists, being part of this is really a once-in-a-lifetime opportunity.”

For Julia Hoffman, who received her doctorate from Soltans Institute for Nuclear Studies in her native Poland, that opportunity has meant expanding her own horizons.

“I learn new, and I mean really new, things every day,” she says. “Different programming languages, different views on physics analysis. I’m learning how it all works from the inside. I work with students and gain new responsibilities. This kind of experience means better chances to find a permanent position that will be as exciting as this one.”

The SMU group works with formulae based in Monte Carlo methods, the “probabilistic models that use repeated random sampling of vast quantities of numbers” to impose a semblance of order on the chaos created when atoms forcibly disintegrate. Results are highly detailed simulations of known physics that will help make visible the tiny deviations researchers hope to detect when ATLAS begins taking data.

These unprecedented computing challenges also have become an impetus for new SMU research initiatives. James Quick, SMU associate vice president for research and dean of graduate studies, hopes to contain ATLAS’ vast data-processing requirements with a large-capability computing center located on campus.

Quick visited CERN in April to discuss the details with Stroynowski and other key personnel. The proposed center would provide a first-priority data processing infrastructure for SMU physicists and a powerful new resource for researchers in other schools and departments. During the inevitable LHC downtime, as beams are calibrated and software is debugged, the SMU center’s computing power would be available for campus researchers in every field across engineering, the sciences and business.

“The ATLAS experiment presents an opportunity for the University to step up in a big way, and one that will benefit the entire campus,” Quick says.

He envisions a data processing farm of 1,000 central processing units, each connected to an Internet backbone to allow the fastest possible return on SMU’s ATLAS input. Speed and access are the keys, Stroynowski says, paraphrasing Winston Churchill: “The winner gets the oyster, and the runner-up gets the shell.”

Those who have made their careers in high-energy physics are well aware of the stakes involved in the LHC, he adds, and being the first to process certain data could separate a potential Nobel Prize winner from those who will make the same discovery a day late.

As a group, high-energy physicists are accustomed to taking the long view — and for SMU researchers, the long view has been especially helpful. The ghost of the Superconducting Super Collider, which would have made its home in North Texas, still shadows the recent triumphs at CERN.

The SSC brought Stroynowski to the University, and its 1993 demise through congressional defunding was the impetus for the LHC project. The questions haven’t gone away because the experiment has changed venues, Stroynowski says. Yet even now, as the first test nears, his anticipation is tempered by caution.

“I don’t think we’ll get a beam all the way around [the LHC tunnel] on the first try,” he says.

Indeed, the subject of whether scientists will achieve a beam collision during the first tests or after additional calibration has been the subject of a few lively wagers.

“I think we’ll have to wait at least a few more weeks for that milestone,” he adds. “But in this case, I’ll be more than happy to be wrong.” — Kathleen Tibbetts

SMU has an uplink facility on campus for live TV, radio or online interviews. To speak with Dr. Biehl or Dr. D’Mello or to book them in the SMU studio, call SMU News & Communications at 214-768-7650 or UT Dallas Office of Media Relations at 972-883-4321.

SMU is a private university in Dallas where nearly 11,000 students benefit from the national opportunities and international reach of SMU’s seven degree-granting schools. For more information see www.smu.edu.

Tags CERN, David Joffe, Dedman College, Fredrick Olness, James E. Quick, Jingbo Ye, Robert Kehoe, Ryszard Stroynowski, SMU Department of Physics

Energy & Matter Health & Medicine Student researchers Technology

Skeptics aside, “computing with light” will replace silicon chip

Post author By Margaret Allen
Post date June 30, 2008

Gary Evans

SMU Professor of Electrical Engineering Gary Evans recently received some good news: Journal reviewers said they thought his proposal for solving one of the most perplexing problems in the emerging field of integrated photonics sounded impossible.

“To me, that’s extremely promising when the reviewers don’t think it’s possible,” Evans said. “When that’s happened, it’s been fun showing the reviewers that the conventional wisdom is incorrect.”

Photonics is the science of processing or transmitting information using light. Fiber-optic systems — perhaps the field’s best known application — transform telephone conversations into laser-generated signals that travel through thin glass wires to machines that decode the signals at the other end.

A photon is a light quantum, the smallest measurable unit of light. Integrated photonics researchers seek to create circuits that use photons to do what electrons do in electric integrated semiconductor circuits.

Evans and Jerome Butler, university distinguished professor of electrical engineering, think they have hit on a solution to the problem of integrating an optical isolator with other components in a photonic circuit. In electric semiconductor circuits, diodes act as isolators by letting electrons flow in only one direction.

“Isolation is crucial when you put about 1 billion devices on a single chip of silicon,” Evans says. The two researchers want to integrate an optical isolator with a tiny semiconductor laser that would let light travel in one direction within a photonic semiconductor circuit and keep it from reflecting back into the laser, where it could create instabilities in the laser’s output.

It is understandable that their peers might be skeptical, Evans says. Researchers around the world have been trying to create integrated photonic isolators since the 1970s and no one has overcome the problem of reflection in photonic circuits.

Evans had a similar experience when he worked with lasers at RCA Labs in Princeton, N.J., before joining SMU. In 1984 all semiconductor lasers were edge-emitting, meaning they generated light from the edge of the chip rather than the surface. Evans and his team proposed a surface-emitting laser to the U.S. Air Force.

“Their reviewers said we could never get light out, much less create a laser,” he recalls, adding that his team wrote a proposal and nevertheless received funding from the Air Force starting in 1985.

In only seven years, Evans’ group got light out of the system and demonstrated surface-emitting lasers with performance efficiencies as good as edge-emitting lasers. When he came to SMU in 1992, the Air Force continued to fund Evans’ work, which resulted in a spin-off company, Photodigm in Richardson, Texas.

Photodigm conducts research for the government and manufactures a range of lasers, most of them edge-emitting lasers that have been improved using processes developed for surface-emitting ones, says Evans. He is Photodigm’s co-founder, vice president and chief technology officer. Another co-founder is Jay Kirk, the Electrical Engineering Department’s lab manager and Evan’s former colleague at RCA. Electrical Engineering Chair and Associate Professor Marc P. Christensen is on the company’s technical advisory board, as is Butler, who worked closely with Evans when he was at RCA and helped lure him to SMU.

Evans has since expanded into medical photonics, working with SMU and Drexel University colleagues on a photodynamic therapy system to treat cancer of the esophagus.

Marc Christensen

Similar laser-based systems are used commercially, but they are large and water-cooled. The team hopes to create a machine that’s portable and cheap enough for use in every doctor’s office. Their design uses arrays of semiconductor lasers, each no bigger than a grain of sand, inserted into the esophagus via a balloon catheter. The patient is given a photosensitive drug that kills cancer cells during a chemical reaction triggered by the lasers.

Christensen says SMU’s photonics researchers — who include faculty members in electrical engineering, mathematics and physics, plus their graduate students — come together periodically for interdisciplinary meetings because so many fields are involved in creating and understanding photonic devices.

Christensen’s Photonic Architectures Laboratory has received more than $2 million in grants from the Defense Advanced Research Projects Agency, DARPA, for a project to make unmanned aerial vehicles, UAVs, stealthier.

“Today we think of a Predator UAV as flying at 30,000 feet carrying a really nice camera with a long lens that can zoom into an area on the ground and look at it very carefully,” Christensen says. Ideally, the device would be tiny with a flat lens, like a cell phone camera; however, those cameras do not produce images of adequate resolution.

Christensen’s interdisciplinary team has devised a multi-step solution that starts with an array of hundreds of tiny, flat, square cameras and equally tiny, square mirrors placed in a grid pattern that can be mounted on the underside of an aircraft as small as a model airplane. Each camera will provide slightly different information about the subject because each takes a photograph from a slightly different angle.

Computational imaging is then used to combine the numerous low-resolution images to create a sharper image that is akin to one taken by a high-performance camera too heavy to fit on the small aircraft.

Computational imaging: Each hexagonal
face is a micro-mirror, individually
positioned to create an overall shape.

“Wouldn’t it be great if the camera could determine from its wide shot which objects in the field are most important and be able to zero in on them?” Christensen asks.

Such a camera is under development at SMU. Called an adaptive resolution camera, it would analyze the wide view and use mathematical formulas to identify objects of interest — such as aircraft on the ground.

Instead of simple mirrors, the adaptive resolution camera uses an array of micro-electric machines, called MEMs. Each MEM looks like a mirror that is hundreds of microns across, or about the width of a few human hairs, attached to three even smaller levers. The levers would reposition the mirrors in the desired direction to improve the information collected by the camera’s next photographs to create another, better image — all faster than the blink of an eye.

The smarter camera would automatically put more pixels in the areas of interest and less in those considered unimportant, he says, adding that the resulting picture may look strange by conventional standards, but it would provide more useful information.

The team from the Department of Electrical Engineering in the SMU Bobby B. Lyle School of Engineering incorporates skills from physics, mathematics and computer science. Assistant Professor Dinesh Rajan, a specialist in information theory, finds the mathematical route to the best final image, a so-called “goodness value.” Associate Professor Scott Douglas, an adaptive algorithms expert, crafts the formulas to make the system home in on the important details within the big picture. And Professor Panos Papamichalis works on their robustness, making the system more tolerant of the adversities the camera will encounter in daily use.

Integrated circuits make the thousands of necessary computations, and “given the need for miniaturization, the best way to reduce the size of those circuits would make them fully photonic,” Christensen says. That step, however, is some time off. For semiconductor laser structures, Christensen works with Evans.

The two have just started a project, also for DARPA, in collaboration with the University of Texas at Dallas, Photodigm, Raytheon and Northrop Grumman. The goal: to develop signal processing with photons, instead of electrons; in other words, computing with light.

To achieve this they must create the photonic equivalent of a semiconductor chip. Most computer chips are made with silicon, which doesn’t emit light very well. A better choice is indium (In) phosphide (P), called a III-V semiconductor, Christensen says. The goal is to emit and control light, one photon at a time.

“At the quantum level you are literally controlling individual photons and providing gain (to amplify signals),” says Christensen. He compares the current state of photonic integrated circuits with the world’s first electronic integrated circuit, invented at Texas Instruments 50 years ago this summer by the late Jack Kilby when he linked a handful of transistors on a single silicon chip. Over the next 50 years, semiconductors evolved from a handful of components on that first chip to hundreds of millions of components on a single chip, he says.

“If you look at the state of photonics processing, it’s about 6 to 15 components,” he says. “It’s like we’re starting today where Jack Kilby was 50 years ago, and it will be interesting to see where a few decades takes the field of integrated photonics.” — Deborah Wormser

Tags Dinesh Rajan, Gary Evans, Jay Kirk, Jerome Butler, Lyle School of Engineering, Marc Christensen, Panos Papamichalis, Scott Douglas

Energy & Matter Health & Medicine Plants & Animals Student researchers

Aids, cancer targeted by biology researchers

Post author By Margaret Allen
Post date June 1, 2008

In his third-floor laboratory in Dedman Life Sciences Building, biologist Robert Harrod and his team are zeroing in on a new way to inhibit the virus that causes AIDS. They already have shown that their approach, which involves the rare genetic disorder Werner syndrome, works when the disorder’s enzyme defect is introduced into cells.

Now they are trying to find practical ways to use this pathway to inhibit the AIDS virus. The beauty of this approach is that the AIDS virus will not be able to mutate in a way that can defeat this treatment, says Harrod, associate professor in the Biological Sciences Department of Dedman College.

Harrod%2CRobert%20lab2.jpg

Down the hall from Harrod’s lab, Assistant Professor of Biological Sciences Jim Waddle is preparing to file for a patent on a tiny “worm” that is expected to be highly useful in drug-testing, producing results far more quickly than tests run on larger lab creatures.

Meanwhile, their colleagues, Associate Professor Pia Vogel and her husband, John Wise, a lecturer in the Biological Sciences Department, are conducting work that may have implications for cancer treatment.

In university laboratories throughout the world, enormous strides have been made in biology research in recent years, including the mapping of the human genome. With young faculty members like Harrod, Waddle and Vogel working on cutting-edge conundrums, and a recent $3.6 million gift to Biological Sciences, SMU’s department is poised to play a high-profile role in biology advances in coming years, says William Orr, chair and professor of biological sciences.

The gift from philanthropist and SMU Board of Trustees member Caren Prothro and the Perkins-Prothro Foundation includes $2 million for an endowed chair, $1 million for an endowed research fund, $500,000 for a graduate fellowship fund and $100,000 for an undergraduate scholarship fund.

The endowment will enable the University to attract a biologist with a national reputation in research to join a faculty that is strong in cellular and molecular biology and biochemistry and is doing research that could have practical applications in medicine, Orr says.

For example, Vogel and Wise are looking for a way to improve the long-term efficacy of chemotherapy treatments. Wise uses a nautical metaphor to explain their work: “Picture a cancer cell as a ship on a sea and the chemotherapy being dumped into the ship, there’s a mechanism like a sump pump that will dump that chemical back overboard,” he says.

That cellular “sump pump” is important to normal cell health because it keeps toxins out.

“Of course, with cancer cells that are targeted for destruction by chemotherapeutics, you’d like to be able to turn off that mechanism,” Wise adds.

John Wise

Vogel explains that many cancer cells respond to treatment by pumping out more and more of the toxins as time goes on, so that a cancer treatment that works well initially might not work as well in later stages.

“Switching chemotherapy drugs doesn’t help because the cancer cells just pump out everything, resulting in multi-drug resistance,” she says.

Using Electron Spin Resonance Spectroscopy, a biophysical technique that obtains structural information about the cellular pump, Vogel’s research group is trying to find a way to shut off the ATP energy usage by this cellular sump pump.

“If you can knock out the pump, you can sink the cancer ship,” she says.

Harrod, who studies retroviruses that infect humans and who is focusing on transcriptional gene regulation, is working on a mechanism that might sidestep a more specific type of multidrug resistance — of the virus that causes AIDS to the conventional HAART (highly active antiretroviral treatment) drug regimen.

Pia Vogel

His approach is related to a rare genetic disorder called Werner syndrome, which causes premature aging in those who have the disease. Researchers have noted that individuals who are carriers for Werner syndrome do not develop AIDS. Harrod hypothesized that the enzyme involved in Werner syndrome is necessary for transcription of the retrovirus.

Using cells that had the Werner syndrome defect inserted into them, his lab was able to confirm this link, and last year he and co-researchers published the findings in “The Journal of Biological Chemistry.” Now his group is looking for molecules that might be used to block this transcription-necessary enzyme. Included among the researchers cited in the journal article were several biological sciences students. Both graduate and undergraduate students assisted Harrod in his lab work on retroviral transcription.

Ask Assistant Professor Jim Waddle about the contributions made by students, and he’ll talk about the weird “worm” discovered by one of his graduate students. Waddle, whose Ph.D. work was in molecular genetics, has been studying the nematode Caenorhabditis elegans as a model for food absorption in the human gut.

Fingerlike projections called microvilli, which are necessary for the absorption of nutrients, line the human gut; nematodes have microvilli on every gut cell.

As part of their research, Waddle’s lab doused the nematodes in mutation-causing chemicals and examined them via a fluorescent protein.

Ph.D. candidate Christina Paulson looked at 20,000 nematodes in this manner and came up with one that had a nematode version of diverticulosis, with outpouchings all along the gut.

Disappointingly, the mutated worm turned out to be normal in terms of lifespan, reproduction and absorption of nutrients. But, Waddle says, “we threw our heads together and thought about conditions the nematode might encounter in the wild” versus the laboratory setting. He wondered if the worm might have trouble eliminating toxins. It did.

Jim Waddle

Normal nematodes eliminate toxins too quickly for the worms to be useful in drug testing, but toxins stay in the weird worms long enough to have an effect on them. And that means the millimeter-long creature likely will be highly useful in drug-testing situations, because a nematode’s life cycle is so much shorter than that of the larger animals, such as mice, that generally are used to test drugs.

The student who identified the worm is one of 18 graduate students in the Department of Biological Sciences. Nine are working on Master’s degrees, nine on Ph.Ds. With 126 undergraduates, the department enrolls the largest segment of undergraduate majors in the natural sciences at SMU. Undergraduate students who intend to go into biological research can apply for the BRITE (Biomedical Researchers in Training Experience) program, a collaboration between SMU and the University of Texas Southwestern Medical Center that leads to acceptance into a UT Southwestern Ph.D. program.

Orr believes the department is poised for a leap forward in size and stature. Administrative support to boost research has come from Provost Paul Ludden, whose background is in biochemistry. Current research projects are supported by $4.3 million from agencies that include the National Institutes of Health and the National Science Foundation.
Christina Paulson

Orr’s dream for the department is to double the current tenured and tenure-track faculty to 18 members. Of the nine, seven conduct ongoing research projects, five of which are funded by federal agencies. The department will add an assistant professor in spring 2009. Later that year, a national search will be conducted to fill the new Distinguished Chair of Biological Sciences.

Although the department is small, a synergy has developed from building a faculty that is focused on cellular and molecular biochemistry, Orr says.

Researchers can work together on projects, brainstorming ideas for new areas of investigation. More grants can be applied for, which means more grants awarded.

“We have a strong group that is focused on certain areas. By adding new faculty we will be able to boost the overall stature of the department,” Orr says. “If we increase the academic stature and the amount of research, we can provide more opportunities for graduate students and for undergraduates. It all works together.” — Cathy Frisinger

William Orr

Tags Christina Paulson, Jim Waddle, John Wise, Pia Vogel, Robert Harrod, SMU Department of Biological Sciences

Energy & Matter Health & Medicine Technology

New durable materials result from silicon polymers

Post author By Margaret Allen
Post date June 1, 2005

David Son uses some of the Earth’s most common building blocks to create complex new materials with potential wide-ranging applications.

Son conducts research on polymers containing silicon. One of the main elements in the Earth’s crust, silicon is the major ingredient in common sand, and is readily available.

“It’s fairly easy and inexpensive to transform silicon into compounds we can manipulate,” says Son, associate professor in SMU’s Department of Chemistry in Dedman College. “And because silicon is an inorganic element, it gives materials great stability against temperature changes and oxidation.”

Silicon-containing polymers might be used to create more heat-resistant and longer-lasting plastic materials than common organic polymers such as polyethylene or PVC, Son says. One example is the silicone ovenware widely available in stores. Pans made of silicon polymers are temperature-safe, naturally nonstick, and so flexible that they can be turned inside out to remove baked goods.

Most polymers are what chemists call the straight-chain type, with each molecule consisting of atoms laid more or less end-to-end. Son’s research focuses on a new class of polymers called dendrimers, also known as “arborols” for their molecular resemblance to trees with many branches.

The dendrimers’ structure gives them many advantages.

“You can dissolve them much more easily in solvents,” Son says. “Because the molecules are shaped like balls, they roll right over each other and don’t get tangled up the way straight-chain polymers do, so you can use them as lubricants.”

Other possible uses include new drugs in which medicines are encapsulated in the dendrimers’ branches, transported to targeted areas of the body, and then stimulated to release medication directly to those sites.

Most recently, Son has begun creating materials that merge metal ions with organic compounds called ligands. Ligands can be as simple as water or as complex as ethylenediaminetetraacetic acid, or EDTA, a compound commonly used as an anticoagulant in medicine.

Son is especially interested in how nitrogen- and sulfur-based ligands bond with silver, gold, palladium, and platinum, which are elements with well-established catalytic properties. He hopes to create compounds that can be used to improve everything from optics to plastics manufacturing.

Platinum and palladium compounds are used industrially to spark reactions in other materials. Creating better catalysts, Son says, could enable more efficient manufacturing processes, for example, at lower temperatures or with fewer defects.

Son received his Ph.D. degree in organic chemistry from MIT and has conducted research at the Argonne National Laboratory and the Naval Research Laboratory.

Tags David Son, Dedman College, SMU Department of Chemistry

Stroynowski with Large Hadron Collider model

Book a live interview

Related links

More SMU Research news