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Career Outlook for New Graduates Pg. 5 • Fusion Research Pg. 8DNA Repair Pg. 11 • Web 2.0 Warriors Pg. 14

Blazing a Trail for ChipDesignersNew softwarebased on innovationsby Jacobs Schoolresearchers could revolutionize designand testing of integrated circuits.

Page 6

> dean’s column <

I

F R I E D E R S E I B L E , D E A N

Student Organizations:A Training Ground for Engineering Leaders It was with great pride that I participated in the Jacobs School’s first Order of theEngineer ring ceremony held during commencement weekend. More than 100 of our graduating engineers took an oath to practice engineering with integrity and highstandards, and placed a ring on the fifth finger of their writing hand to remind them of their oath as they sign engineering documents.

To me, the ceremony was not only a symbol of how seriously our students take theirengineering profession, but also of the incredible culture of leadership, teamwork andpride building among our student body. The ceremony was completely initiated andorganized by our Triton Engineering Student Council, and was just one of the manyexamples of our ever-increasing student activism.

This year, our students launched five new professional organization chapters. Butwhat is more amazing is how quickly they have hit the ground running. Our newInternational Association for the Exchange of Students for Technical Experience wasnamed rookie of the year, and placed third nationally for their work to arrange for 10 of our students to do internships overseas while at the same time placing 10 internsfrom other countries here in San Diego. And our Innovative Design and EngineeringApplications (IDEA) group finished their inaugural year by placing 9th in their nationalcompetition with the design of an off-road wheelchair.

We now have 17 professional organization chapters, and all of them are highly ener-gized and passionate about their mission. When I came on as dean in 2003, only ahandful of students attended the quarterly dinner with the dean meeting.Today, I’mlikely to see 60 students and more attend—all with big ideas. Naturally, we try to beresponsive to their requests and we have allocated 2,300 square feet to make room forstudent organization activities and projects.This year our students used every cent ofour $28,400 matching fund for student competitions, while at the same time raisingmore than $100,000 in outside sponsorships.

I am just amazed by the quality and maturity of our students.These forward-think-ing leaders understand that the university is their training ground and our professionalorganizations give them the opportunity to engage in community service, stretch theirtechnical knowledge, and develop commu-nications and leadership skills.

Thank you to all of our alumni andindustry partners who support our studentsas mentors and sponsors.The smallestencouragement pays off in huge dividendsas we work together to educate tomorrow’stechnology leaders.

2 www.jacobsschool.ucsd.edu/pulse UCSD Jacobs School of Engineering > Summer 2006 <

Jacobs School of Engineering

LeadershipDean: Frieder Seible

Associate Dean: Jeanne FerranteAssociate Dean: Charles Tu

Assistant Dean for Administration & Finance: Steve Ross

Executive Director of External Relations: MaryAnn F. Stewart

Academic DepartmentsBioengineering: Andrew McCulloch, chairComputer Science and Engineering (CSE):

Keith Marzullo, chairElectrical and Computer Engineering (ECE):

Paul Yu, chairMechanical and Aerospace Engineering (MAE):

Paul Linden, chairStructural Engineering: Ahmed Elgamal, chair

Council of AdvisorsChair: Andrew E. Senyei, M.D.,

General Partner & Managing Director, Enterprise Partners Venture Capital

Vice Chair: Gregory M. Papadopoulos, ’79, Executive V.P. & CTO, Sun Microsystems

Robert P. Akins, ’74, ’77, ’83, Chairman & CEO, CymerDaniel L. Alspach, ’70

Malin Burnham, Chairman, The Burnham Companies

Robert E. Englekirk, Chairman Emeritus, Englekirk Structural Engineers

Hossein Eslambolchi, ’81, ’83, ’84, Chairman, 2020 Technology Investments LLCPeter C. Farrell, Chairman & CEO, ResMed

Bernard Gordon, Chairman, NeuroLogica Corporation

Irwin M. Jacobs, Chairman, QUALCOMMPaul E. Jacobs, CEO, QUALCOMM

Brian A. Kenner, ’89, President & CEO, Learning Framework

Richard Kornfeld, ’82David M. Lederman,

Managing Director, Analytical LLCRichard Levy, Chairman, President & CEO,

Varian Medical SystemsGregory Lucier,

Chairman & CEO, InvitrogenCatherine J. Mackey, Sr. V.P., Pfizer Global Research

& Development, La Jolla LaboratoriesScott McClendon,

Chairman, Overland StorageHenry L. Nordhoff,

Chairman, President & CEO, Gen-ProbeWilliam A. Owens

Chairman & CEO, AEA Holdings ASIAAke Persson

William Rastetter, Chairman, IlluminaGene W. Ray, Managing Director, GMT Ventures

Ronald R. Taylor, Chairman, EMN8, Asteres, 3E Company

John H. Warner, Jr., Chief Administrative Officer, SAIC

Ex OfficioSteve Hart, CTO & V.P. Engineering, ViaSat

Chair, Corporate Affiliates ProgramDean Seible places the Engineer’s

Ring on a student’s finger during theOrder of the Engineer ceremony.

CONTENTS

> Summer 2006 < UCSD Jacobs School of Engineering www.jacobsschool.ucsd.edu/pulse 3

Corporate Affiliates ProgramExecutive Board

Chair: Steve Hart, ’80 ’86, ViaSat

Vice-Chair: Bill Gang,Information Systems Laboratories

The Aerospace CorporationAT&T

ATA EngineeringBAE SYSTEMS

Booz Allen HamiltonBroadcast Microwave Services

Cisco SystemsCohu Electronics

Conexant SystemsCymer

Delta DesignEntropic Communications

ErisTechEyeSpot

Fair Isaac General Atomics

GE SecurityGen-Probe

GoogleHewlett Packard

Hughes Network SystemsIBM

IDEAL IndustriesInformation Systems Laboratories

IntuitInvitrogen

Knowledge Systems SolutionsKyocera America

Lockheed Martin ORINCON Lockheed Martin Space Systems

Luminous MedicalMITRE

NAVAIR North IslandNCR

Nokia Mobile PhonesNorthrop Grumman Integrated Systems

Northrop Grumman Defense Mission SystemsNorthrop Grumman Space Technology

Paragon Structural Design QUALCOMM

Quartus EngineeringRaytheon

Rincon ResearchSAIC

Simon Wong EngineeringSkyworks Solutions

Solar Turbines Sony Electronics

SPAWAR Systems Center - San DiegoSun MicrosystemsSYS Technologies

UnisysViaSat

Websense

Newsletter TeamDenine Hagen (editor), Rex Graham,

Doug Ramsey, Paul Laperruque

To Reply to the Editorsoecomm@soe.ucsd.edu, (858) 534-2920

9500 Gilman Drive, La Jolla, CA 92093-0403

4 AROUND THE CAMPUS

• Graduate programs rank in top 10• Recruiters get down to business on campus• Career outlook for new engineers• Students offer hope to village in El Salvador• Service learning program gains momentum

6 RESEARCH

6 Blazing a trail for chip designers7 Circuit simulation software heads to

the marketplace8 Fusion energy program heats up9 New approach to noise cancellation9 Translating bands of light10 Beyond lipids: understanding the mechanics

of atherosclerosis11 How cells survive toxic mutagenic assaults11 Stunning details illuminate nerve cell damage

12 FACULTY

• Two professors win $1 million teaching awards• Materials professor fabricates sci-fi thriller• Faculty Honors

14 ALUMNI

• Web 2.0 warriors: leading the new generationof Internet-based companies

• UCSD@Google

16 BACK COVER

• Class Notes

Visit Pulse online for more information and related links to the stories in this issue.www.jacobsschool.ucsd.edu/pulse

> around the campus <

Just months after Newsweek rated UCSD the “hottest” campus for science, U.S. News & World Report ranked three of the JacobsSchool’s Ph.D. programs in the top 10. Overall,the Jacobs School ranked 11th among 187 engi-neering schools in the annual U.S. News surveyof graduate programs released March 31.

Among the engineering specialties, theDepartment of Bioengineering ranked 2nd in thenation. The department has consistently rankedamong the top five for the past decade, and isconsidered an international model for biomedicalengineering education. UCSD also ranked 6th for its interdisciplinary bioinformatics program.

The Department of Computer Science andEngineering was ranked 9th in the nation forcomputer systems, and rose significantly in theoverall computer science ranking to 13th, aleap of seven places since computer scienceprograms were last surveyed in 2002. Over thepast several years, the department has hirednearly 30 new faculty members, establishedleadership positions in fields ranging from net-working to cryptography, and launched pro-grams in areas such as embedded systems and computer vision.

All of the Jacobs School departments hadPh.D. programs ranked among the top 20including mechanical engineering (16), aero-space engineering (19), electrical engineering(16), computer engineering (17), and civil engi-neering (17).

MAKING THE GRADE:

Bioengineering,Bioinformatics, andComputer SystemsRank in Top 10

Service LearningProgram GainsMomentumThree-year-old Matteo Mah takes a testride on a quadricycle adapted by a team of Jacobs School students for the UnitedCerebral Palsy (UCP) toy library. UCP isone of three new community clients whosigned on this year to participate in theJacobs School’s Teams in EngineeringService (TIES) program.

The Jacobs School team (l-r Stephanie Fan, Billy Ikosipentarhos, Preetam Sarma andCasey Jowers) decided to focus on a quadricycle because it is more stable than a stan-dard tricycle and can be pedaled both backwards and forwards.They replaced the cycle’shand brake with an electromagnetic braking system which can easily be activated bythe child with a large push button on the steering wheel, or by the parent with a wireless remote control.The team plans to continue to refine their proto-type this fall, before turning it over to UCP where it will be available onloan to children with disabilities throughout San Diego County.

TIES deploys multi-disciplinary teams of UCSD students tocreate technology solutions for nonprofit community partners.Launched in 2004, the program continued to gain momentumin 2005, with more than 70 students participating each quarteron eight projects. In addition to UCP, this year’s new-est TIES clients include San Diego elementary schoolsand Save Our Children’s Sight, which providesvision screening for low-income preschoolers.

4 www.jacobsschool.ucsd.edu/pulse UCSD Jacobs School of Engineering > Summer 2006 <

Students Offer Hope to Village in El Salvador

For one group of Jacobs School students,spring break meant traveling to northern El Salvador’s El Portrero, a poor communitywith no indoor plumbing or electricity.Thevillage is accessible only via a dirt road whichcrosses the La Joya River, and is subject toflash floods.The students were conducting a site visit as part of their project to designand construct a bridge for the village.

“During the rainy season from Maythrough November, the people of El Portrero are cut off from the outside world, and thechildren cannot attend school,” says Fatema Eshaq (senior, structural engineering), wholaunched the Jacobs School’s newest student organization chapter—Engineers WithoutBorders.The organization builds sustainable engineering systems for communities in need.

Eshaq recruited 15 colleagues to join her in 2005, and they wasted no time securingtheir first project. Now the students are on a tight timeline to complete their design,fundraise more than $30,000, and gather materials—all before winter break 2006, andthe next dry season.That’s when the team plans to return to El Salvador to constructtheir bridge.

To learn more about how you can help, contact Fatema Eshaq at feshaq@ucsd.edu.

Career Outlook for Graduating SeniorsBased on a survey completed by 390 Jacobs School undergraduates.

$For Those Going to Work Full-Time

(230 respondents)STARTING SALARY

<$35K

$36–$45K

$46–$55K

$56–$65K

>$65K

5%

8%

30%

29%

6%

%Highest PaidDisciplines

% WHOSE STARTING SALARY IS >$55K

Computer Science

Electrical Engineering

Mechanical/Aerospace

Bioengineering

Structural Engineering

75%

50%

40%

30%

14%

IMMEDIATE PLANS

Start Work 59%

Continue Education 22%

Education/Part-time Work 16%

Other 3%

GETTING DOWN TO BUSINESSIf recruiting visits to campus are any indication, the job market for Jacobs School engineering students is hotter then ever. Over 50 com-panies participated in the 2006 Disciplines of Engineering Career Fair (DECaF) in February, more than doubling last year’s participation.

“Electrical and computer engineering seemed to be the hottest fields, and we had a newinflux of bioengineering companies,” says DECaF chairman Jeffrey Mounzer. DECaF wasorganized by the Triton Engineering Student Council with support from the School’sCorporate Affiliates Program (CAP).

Throughout the spring, CAP companies such as Google, Sun Microsystems and NorthropGrumman increased their visibility on campus with a full recruiting Day@Jacobs, an exclusivebenefit of CAP membership.

In April, the Jacobs School’s structural engineering career fair drew 25 companies from as far away as Chicago and Honolulu.

“The job market is thriving, as bond money for public works and development filtersthough,” says Philip Yu, president of the School’s Society of Civil and Structural Engineers.

> Summer 2006 < UCSD Jacobs School of Engineering www.jacobsschool.ucsd.edu/pulse 5

16%

3%

59%22%

16%

N/A 22%

> research <

HHe’s been called ‘one of the best-knownacademic researchers in design automation.’Indeed, Jacobs School of Engineering pro-fessor Andrew Kahng has led the definitionof the technology roadmap for design ofintegrated circuits since the mid-1990s.Now the computer engineering professor can also be called anentrepreneur.When he returns full-time to UCSD in the fallafter a two-year leave of absence, Kahng will be able to offer stu-dents first-hand insights into the process of taking a technologyfrom the lab to the marketplace—and doing so successfully.

Kahng formed Blaze DFM, Inc. with former Ph.D. studentPuneet Gupta and industry veteran David Reed.The Sunnyvale,CA-based company, which now counts 20 employees, has hit all of its benchmarks since closing a $6 million initial round ofventure-capital financing in late 2004.Alpha testing of its firstproduct, Blaze MO, began in March 2005, and the product wasinstalled at a beta customer site last October.This spring, a cus-tomer obtained its first product silicon optimized with Blaze’ssoftware tools.

“Results so far with our first product have exceeded our customers’ most optimistic expectations,” says Kahng.“Nowwe want as many chip designers as possible to benefit from it.”

The “DFM” in the company’s name stands for “design formanufacturing,” the concept of designing integrated circuits in a way that improves the percentage of chips on a wafer that meetproduct specifications and therefore can be shipped. But as chipsizes drop and densities increase, improving yields on sub-100-nanometer (nm) processes becomes an even bigger problembecause of power leakage and manufacturing variability.

“DFM is the semiconductor industry’s only hope for a cost-effective continuation of Moore’s Law,” says Kahng.“It’s been myresearch focus since 1997. I felt I had to do something to helpsolve critical challenges of variability, power and cost—if only as a safety net for the industry.”

6 www.jacobsschool.ucsd.edu/pulse UCSD Jacobs School of Engineering > Summer 2006 <

Revolutionizing Design and Testing of Integrated Circuits

Blazing a Trail for Chip Designers

Prof. Andrew Kahng at his company Blaze DFM, which is seeing first sales ofdesign automation software to improve integrated circuit design and maximizethe number of sellable chips per wafer.

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LAYOUT, NETLIST, TIMING, & POWER CONSTRAINTS

B L A Z E

COMMERCIAL OPC TOOL

MASK DATA

> Summer 2006 < UCSD Jacobs School of Engineering www.jacobsschool.ucsd.edu/pulse 7

Kahng’s new technology does DFM with a twist. He calls it‘electrical’ DFM. Most of the DFM tools used today have a geo-metric mindset: they focus on whether the shapes of circuit fea-tures in silicon exactly match the layout as designed. But, arguesKahng, shape fidelity is not the same as maximizing the number of sellable chips per wafer (and therefore revenue per wafer).Tooptimize the yield of chips on a wafer, he says, designers must takeinto account electrical requirements, notably power and timing.

“Leakage power is a big part of the problem at the sub-100nmlevel,” notes Kahng.“Because of leakage currents, a fast chip mayburn too much power and be unusable in, say, a mobile applica-tion, and a slow chip may not be usable either. Electrical DFMlooks at these electrical requirements and optimizes the chipdesign so that manufactured silicon meets parametric specifica-tions while burning as little power as possible. Our products alsodirectly mitigate the manufacturing variation that is so challeng-ing at leading-edge process nodes.”

When he decided to start a company, Kahng recused himselffrom negotiations with UCSD’s Technology Transfer and IntellectualProperty Services (TechTIPS) office to avoid any conflict of interest.“Blaze DFM has been a canonical example of what technologytransfer at UCSD and TechTIPS is all about,” says Kahng.“UCSDand the Jacobs School enable faculty to take their innovations intothe marketplace, and to return to the university with a clearerunderstanding of how to innovate with real-world impact.”

Blaze obtained an exclusive license to Kahng’s technology, andUC received equity in the company and royalty interest fromfuture revenues. Adds Kahng:“If the company is a success, theuniversity, my home departments of ECE and CSE, my lab—as well as I and other inventors of the IP—will benefit.”

His co-founder Puneet Gupta (Ph.D., ’04), says of his experi-ence so far,“Working in Andrew’s lab kept me much closer toindustrial requirements than most other academic researchgroups, so the transition to a pure industry setting was not astough as I had anticipated. Moreover, DFM being a nascent field,there has been ample research activity inside Blaze itself.We hopeto bring to the semiconductor industry several radically new ideasover the next few years.”

Later this year, Blaze DFM’s second product is slated to hit themarket, but Kahng will be back at UCSD. He is looking forwardto returning to teaching and spending more time at home in SanDiego after commuting during the work week to northernCalifornia.“Every week and every day has a cost of being awayfrom home and family and students,” explains Kahng.“So I neverlose sight of the timeline and the mission, and of my scheduledreturn to UCSD when my leave expires.”

Cheng’s Full-Chip CircuitSimulation SoftwareHeads to the MarketplaceToday’s integrated circuits can contain 100 million elementspacked onto nanometer-sized chips. Simulating and verifyingthese elements are critical to chip designers, but the sheer density of the latest chips is stretching current simulation tools to their limits.

This spring, San Jose, CA-based Fastrack Design (www.fastrack-design.com) saw its first sales on a new suite of soft-ware products for quick and accurate transistor level, full-chipanalysis. The technology is based on three UCSD patents by CSEprofessor C.K. Cheng who developed a new algebraic formula-tion as a solver engine. The circuit simulation technology avoidsthe high complexity and slow convergence of other tools on themarket. It is the first program to accurately analyze all elementsof a dense chip simultaneously, enabling designers to verify theinteractions between components. Fastrack plans a major product launch later this summer.

“Simulation and verification requires a lot of improvement to keep up with chip technology advancements,” says FastrackCEO Moazzem Hossain. “We believe the UCSD technology haspotential to offer significant capacity and speed improvementover existing tools for circuit simulation.”

Cheng says the relationship with Fastrack is ideal. “Fastrackkeeps us connected to the chip design industry, so that we canfocus our research on the most relevant problems. At the sametime we can see our work transferred from the lab to market forthe benefit of society.”

While Fastrack is commercializing Cheng’s technology, thecompany is also funding his continuing research. In addition toimproving circuit simulation, Cheng is working on high-speed,low-power interconnects for integrated circuits. Another recentinterest: applying simulation modeling techniques to improveanalysis of medical EKGs used to diagnose cardiac arrhythmias.

ip Designers

C.K. Cheng

8 www.jacobsschool.ucsd.edu/pulse UCSD Jacobs School of Engineering > Summer 2006 <

WWith crude oil prices at record highs and growing concerns over future energysupplies, the Jacobs School’s Center forEnergy Research is making key contribu-tions needed to demonstrate the scientificand technical feasibility of fusion power.UCSD researchers are studying two competing technologies to create theconditions needed for hydrogen atoms to fuse into helium atoms, with therelease of energy.

Jacobs School research scientist RickMoyer and post-doctoral scholar IlonJoseph, working with colleagues atGeneral Atomics, Lawrence Livermoreand Sandia National Laboratories, report-ed a surprising new finding relating tomagnetic-confinement fusion in the June2006 issue of Nature Physics.They found

that perturbing the magnetic fields containing the plasma prevented the for-mation of dangerous instabilities thatsometimes damage reactors’ containmentwalls.“It’s as if a dash of chaos actuallyhelps a fusion reactor,” says Moyer.

The new results, discovered on theDIII-D Tokamak reactor at nearbyGeneral Atomics, will be evaluated forincorporation into the design of ITER,a $6 billion experiment that will demon-strate the scientific and technical feasibili-ty of fusion power. ITER will be built atCadarache in the South of Franceby the European Union, Japan,China, India, South Korea, theRussian Federation, and the U.S.

Moyer’s work is part of theCenter for Energy Research’s

fusion energy research program, a researcheffort involving 20 Ph.D candidates,more than 25 research scientists andtechnicians, and four professors: FarhatBeg (MAE), Sergei Krasheninnikov(MAE), Farrokh Najmabadi (ECE), andGeorge Tynan (MAE).The center’sPISCES (Plasma Interaction withSurfaces and Components ExperimentalSimulator) program studies the physics of plasma-material interactions whichoccur when hot plasma contacts the walls of fusion devices.

UCSD researchersare also involved indeveloping inertial con-finement fusion, a tech-nology that involveslasers rather than mag-netic fields to compressand heat hydrogen fuelto fusion conditions.UCSD has the largestresearch team of anyU.S. university collabo-

rating in the High Average Power LaserProgram, a national effort to develop the science and technology for inertialconfinement fusion.

UCSD also manages ARIES(Advanced Reactor Innovation andEvaluation Study), a team of scientistsfrom national laboratories, universities,and industry that evaluates conceptualdesigns of future fusion reactors and helps guide the direction and priorities of future fusion research worldwide.

> research <

UCSD’s Fusion Energy Program Heats up

Rendering of the International ThermonuclearExperimental Reactor (ITER) machine.

“It’s as if a dash of chaos actuallyhelps a fusionreactor.”—Rick MoyerJacobs School Research Scientist

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> Summer 2006 < UCSD Jacobs School of Engineering www.jacobsschool.ucsd.edu/pulse 9

‘Translating’ Bands of LightMost of the data traveling through optical fiber around the world is transported on bands of light of a standardinfrared wavelength. The 1.55-micron wavelength is idealfor telecommunications because it is where glass fiber is most transparent and efficient. But other existing orplanned applications, ranging from airborne and submarinecommunications to biomedical lasers and remote sensing,operate at different wavelengths (and different colors oflight). And there’s the rub: most of the equipment for gen-erating, transporting and detecting optical signals wasdeveloped for the telecom market and cannot handle lightat wavelengths other than 1.55 microns.

But Jacobs School electrical and computer engineeringprofessor Stojan Radic has demonstrated a novel methodfor efficiently “translating” optical signals within the fiberbetween the infrared standard and other bands of light.With a team including ECE professors Shaya Fainman andJoseph Ford, Radic used a parametric process (i.e., aprocess that does no damage to the photonic crystal fiber)to change the wavelengths of modulated optical channelsby as much as 1 micron from infrared to visible light.Further, the before-and-after difference in frequency—375 terahertz—was a factor of ten greater than previouslyachieved.

Radic is now working on converting infrared to otheruseful wavelengths. “A parametric band translator meansthat mature telecom technology can be applied to anyother wavelength,” says Radic. “This will permit develop-ment of new applications at various bands without requir-ing huge investment in new infrastructure to replace whatalready exists.”

QUIET!New Approach to Noise Cancellation

If a tree falls in the forest and nobody hears the crash, it may not be news; however, whenthe noise inside an airplane cabin or in the air-handling system of a large building is signi-ficantly reduced, Raymond de Callafon cheers.

In a report in the April 4 issue of the Journalof Sound and Vibration, de Callafon, a professorof mechanical and aerospace engineering,described a new mathematical algorithm thatPh.D. candidate J. Zeng and he designed to dramatically improve noise-cancellation tech-nologies by destructive interference.

“Noise cancellation is a hidden technology that most consumersaren’t aware of, but vehicles made by BMW, Mercedes, Honda, andother companies are now using it,” says de Callafon.“Our new tech-nique should greatly expand the potential of active noise-cancellationtechnologies.”

Basic “feedforward” active noise-cancellation is composed of a micro-phone that measures incoming noise, a computer processor that convertsthat information into anti-noise instructions, and an audio speaker thatbroadcasts sound waves that are exactly 180 degrees out of phase withthe unwanted signal and of the same magnitude. Unfortunately, feed-forward noise cancellation is plagued by noisy acoustic feedback.

“We’ve developed a totally new approach that works by generatingthe feedforward noise cancellation signals and adaptively changing themin the presence of acoustic coupling,” de Callafon says.“This has been a complicated problem to solve and we think the approach we’ve takenwill have a significant impact on the field.”

A technique invented by Raymond de Callafon improves the ability to achievedestructive interference of an electronic chirp (left) and white noise (right) emitted by a commercial air-handling system. (purple signal, unfiltered sound;green signal, after noise cancellation)

Raymond de Callafon

> research <

10 www.jacobsschool.ucsd.edu/pulse UCSD Jacobs School of Engineering > Summer 2006 <

Beyond Lipids: Understanding the Mechanics of Atherosclerosis

Atherosclerosis, the collection of deposits such as choles-terol along artery walls, accounts for nearly 75 percentof deaths from cardiovascular disease. Most drugs to treatatherosclerosis influence the levels of cholesterol andother blood lipids, but a group of UCSD researchers ledby bioengineering professor Shu Chien is investigatingthe mechanical forces acting on blood vessels as a wayto design better approaches to treatment.

Narrowing and hardening of coronary arteries typically appear first at vessel branches, and a study by Chien and his collaborators published in theOctober issue of Cellular Signalling shows that thetype of mechanical stretching found at those branchesactivates a cellular protein known to damage cells.Thereport is the first to link mechanical forces with struc-tural and biochemical changes in blood vessel cellsthat could explain why atherosclerotic lesions form at the branches of coronary arteries.

The cellular protein in question is called JNK,short for c-jun N-terminal kinase. It is a key barom-eter of outside stresses on a variety of cell types.Researchers are examining the role of JNK in manydiseases because it regulates the expression of genesinvolved in programmed cell death, tumor genesis,and other stress responses.

“We’ve known for decades that atheroscleroticlesions develop preferentially at vessel branches ratherthan along unbranched vessels, but we’ve not beenable to identify the biochemical events that triggerformation of the lesions,” said Chien, director of the

Whitaker Institute of Biomedical Engineering atUCSD.“We now have identified a possible smokinggun: activation of JNK, which is dependent on thedirectionality of blood vessel stretching.”

Chien, along with research scientist ShunichiUsami and post-doctoral fellow Roland Kaunas,stretched endothelial cells 10 percent of their length60 times per minute to simulate the rhythmic flexingof an artery in response to heart beats.

Cells that were stretched back and forth along oneaxis exhibited a healthy response: the level of JNKrose and quickly returned to basal levels as the cellsalso produced well-aligned intracellular actin fibersthat were aligned perpendicular to the axis of stretch.When the researchers stretched cells in two directionssimultaneously they noted an unhealthy response:actin fibers oriented randomly and JNK concentra-tions rose to higher levels and remained elevated.

“The actin cytoskeleton of endothelial cells issomehow playing a key role in activating and deacti-vating JNK,” said Chien.“Our new understanding ofhow mechanical forces affect JNK will eventually helpus gain better understanding of the mechanism under-lying the focal localization of atherosclerotic lesionsand design better approaches to treat this importantdisease state.”

New research by Shu Chien helps

explain why athero-sclerotic lesions form

at the branches ofcoronary arteries, work

that could lead to newavenues of treatment

for heart disease.

STRETCH EFFECT: UCSD bioengineers have found a link betweenparallel alignment of “stress fibers” in blood vessel cells and

healthy levels in those cells of a protein called JNK.

10 micrometers (10 Ìm)

Cells must continually repair dam-age to their DNA inflicted by avariety of assaults. Hoping to gain abetter understanding of that naturalrepair process, a group of researchersled by bioengineering professorTrey Ideker exposed cells to a powerful chemical mutagen anddiscovered a web of inter-relatedresponses that cells use to avoidbecoming diseased or cancerous.

Reporting in the May 19 issueof Science, Ideker’s team described a model of DNA repair that alsohelps modulate genes involved incell growth and division, proteindegradation, responses to stress, andother metabolic functions.Theresults may demystify the long-standing question of why DNAdamage influences the expression ofhundreds of genes that are not actu-ally involved in the repair process.

“With this model now in hand,we’d like to take a much closer lookat the cell’s response to environ-

mental toxins,” said Ideker.“We’d also like to understand whatgoes wrong in certain congenital diseases involving DNA repair,and how the model plays a role in various cancers.”

Ideker Group Discovers How CellsSurvive Toxic Mutagenic Assaults

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> Summer 2006 < UCSD Jacobs School of Engineering www.jacobsschool.ucsd.edu/pulse 11

Stunning Details Illuminate Nerve Cell DamageIn most types of neurological injury, cells called astrocytes create scar tissue which forms in part asastrocytes send out tendrils filled with a fibrous protein called GFAP. This response to injury, which is called reactive gliosis, plays a major role in the permanent loss of nerve transmissions through theinjured area. Bioengineering professor Gabriel Silva would like to reverse the effects of reactive glio-sis, and is visualizing the process in stunning detail with the help of nanometer-sized semiconductorfluorescent quantum dots that bind to GFAP (glial fibrillary acidic protein). Unlike standard fluorescentdyes that have broad emission spectra, Silva’s quantum dots fluoresce over a much narrower range.“This unique feature of quantum dots has permitted us to resolve these glial filaments in much greaterdetail, and we’ve realized that there are a lot more of these spidery processes between cells than weever thought possible,” says Silva. “This finding is enabling us to investigate this new form of intercel-lular communication.”

D N A R E PA I R

12 www.jacobsschool.ucsd.edu/pulse UCSD Jacobs School of Engineering > Summer 2006 <

> faculty <

The Howard Hughes Medical Institute (HHMI) has awarded $1 million each over four years in unrestricted grants to Jacobs Schoolprofessors Pavel Pevzner and Robert Sah to develop innovative edu-cational programs to “ignite the scientific spark in a new generation of students” at UCSD.

Pevzner, professor of computer science and engineering, plans tointroduce computer science and computational aspects of bioinfor-matics to all biology majors on the UCSD campus.The first com-puter scientist to be named an HHMI professor, Pevzner also plans to promote collaborative research experiences for undergraduates in bioinformatics.

Bioengineering professor Robert Sah plans to bring undergraduatestudents into his tissue-engineering research program, which is aimedat growing human cartilage and bone joints as replacement parts forpatients with debilitating joint injuries and diseases.

Sah notes that while UCSD undergraduates are exposed to excel-lent teachers in lecture halls and classrooms, students also benefitgreatly from one-on-one interactions with faculty members, graduatestudents, post-doctoral fellows, and other researchers in dynamicresearch laboratories. “In my project, there is a research theme ofregeneration of knee joints, understanding how joints normally work,and trying to understand how to create them so that we can makereplacement parts,” Sah says.

Sah and Pevzner are two of the 20 professors who this year werenotified by HHMI that they will receive $1 million “to turn their own considerable creativity loose in their undergraduate classrooms.”

Some of the 2006 award winners will design programs to attractmore women and minorities to science. Others will turn large intro-ductory science courses or classes for non-science majors into engag-ing, hands-on learning experiences that challenge students to thinklike working scientists.

“The scientists whom we have selected are true pioneers—not onlyin their research, but in their creative approaches and dedication toteaching,” says Thomas R. Cech, HHMI president.“We are hopefulthat their educational experiments will energize undergraduate scienceeducation throughout the nation.”

Pevzner was selected in part as recognition of the increasingly com-putational emphasis in biological research. He advocates a new philoso-phy of teaching computer science to biologists:“There is a largealgorithmic component to biology.Today’s biologists arguably needmore algorithms and more computer-science skills than chemists, orphysicists, or even some engineers.”To remedy that situation, Pevznerhas developed a new course on algorithmic biology that will be opento all biology students in spring 2007.

Q: Who wants to be a $1-million teacher?A: Two UCSD engineering professors.

Pavel Pevzner (top) and Robert Sah(bottom right) received Howard Hughes

Medical Institute grants “to turn theirown considerable creativity loose in

their undergraduate classrooms.”

Shu Chien has been named a fellow of the American Academy of Arts andSciences. Chien directs the WhitakerInstitute of Biomedical Engineering and

is a university professor of bioengineeringand medicine.An expert on how bloodflow and pressure affect vessels, his researchhas led to the development of better diag-nostic tests and treatments for atheroscle-rosis and other diseases.

Associate dean and CSE professor JeanneFerrante was recently recognized by theAssociation for Computing Machinery forher work on the static single assignment(SSA) form, a data structure that has led to more efficient and powerful methods of transforming a programmer’s code to machine code. Ferrante shares the SIGPLAN Programming LanguagesAchievement Award with colleagues RonCytron, Barry Rosen, Mark Wegman, andKenneth Zadeck who jointly developed

SSA at IBM’s T.J.Watson Research Centerin the 1980’s. SSA is commonly used todayin production compilers.

The Alfred P. Sloan Foundation has awardedCSE professor Alin Deutsch with a presti-gious research fellowship. Deutsch is a mem-ber of CSE’s database group, and his researchfocuses on providing infrastructure for pub-lishing and consuming data on the Web.

Associate dean Charles Tu, professorECE, was recently named the 2006Outstanding Engineering Educator by theSan Diego County Engineering Council.Tu is also the recipient of the 2005 AsianHeritage Award for research and techno-logy, sponsored by ASIA,The Journal ofCulture and Commerce.

The view from materials science professor GustavoChen’s office window takes in waves breaking ona sandy La Jolla beach as surfers farther out bobon their boards like strange birds. In Mayan Mars,Chen is the fictional hero and alter ego of thebook’s author, UCSD professor of materials scienceMarc André Meyers, whose real office has a viewof a eucalyptus tree and a sand-colored masonrywall. But even professors can dream.

Meyers has written a riveting science fictiontale that includes slavery and human sacrifice inpre-Columbian Maya society. The modern tech-

nological twist in Mayan Mars includes an accidental release of a killer microbe that wasretrieved from the Red Planet by a NASA space mission. The Maya prophesy that the worldwill end in 2012 is a central element of Mayan Mars as well as Apocalypto, an action filmabout the ancient Maya that is being directed by Mel Gibson. The movie is scheduled forrelease in December 2006.

The tale Meyers wrote is based on his research of scholarly descriptions of sometimesdisturbing Mayan myths, and his frequent travels in the Brazilian hinterland where heencountered many vestiges of Maya civilization. Coincidently, Meyers became intrigued asa young man by the beaks of the Toco Toucan that he found in the same jungles. In 2005,Meyers published the first-every analysis of the beak of the fruit-eating bird in ActaMaterialia. The unique biocomposite structure is composed of a bone-like foam covered bya keratin shell. Meyers also discovered that the system is optimized for strength and light-ness. Stay tuned for Meyers’ next scientific paper and more creative writing exploits.

> Summer 2006 < UCSD Jacobs School of Engineering www.jacobsschool.ucsd.edu/pulse 13

Materials Professor Fabricates Sci-Fi Thriller

Faculty Honors

SHU CHIEN JEANNE FERRANTE

ALIN DEUTSCH CHARLES TU

Marc Meyers

> alumni <

Web 2.0 Warriors: Leading the NewGeneration of Internet-Based CompaniesIt was Summer 2002 and Ryan Sit (B.S./M.S., ’04) was visiting his mom in SanJose before beginning his UCSD master’swork. As he attempted to teach hismom—a computer novice—how to emailphotos taken with her new digital camera,Sit realized there must be a way to auto-mate the cumbersome process.That ideabecame the focus of his master’s thesis and the start of DropShots, a service thatallows family and friends to share theirphotos and video online. Sit’s beta site was the first to use Flash for convertinghome video files to play on Web browsers.DropShots now hosts more than 4 millionmedia files, and Sit says the site has becomethe number one family photo and videossharing service in the world.

DropShots is one of a new generation oflean and smart Web 2.0 companies that are

flourishing as broadband access becomes com-monplace and everyone from kindergardnersto grandmothers embrace the Internet.

“We were determined to spend onlywhat we made, which gave us a hugeincentive to create something valuable that people would pay to use,” says Sit.

His objective was to create an onlinedestination where family members couldshare life’s joys and stay in touch, so hefocused on making Dropshots easy for evennon-technical users. In addition to the one-step drag and drop system that automatescompressing, transcoding, uploading, organ-izing and publishing media files, Sit’s teamcreated an interface that allows the photog-rapher and viewers to share experiences by posting comments about the images.

Sit’s plan paid off. By the time he grad-uated from UCSD, his test group of 10

users had organically grown to 5,000.Having launched its subscription-basedservice in November 2005, DropShotsbecame profitable this March.

Taner Halicioglu (B.S., ’96), employee #4at Facebook, the popular social networkingsite for college students, says being first tomarket is key for Web 2.0 companies.

“Hardware and processing power ischeap, and free software is readily available,which is why Facebook was able to get off the ground so quickly,” says Halicioglu.“With the barrier to entry so low, it’s

important to get in early and build a criti-cal mass of users who will remain loyal, solong as you provide substantive features.”

Halicioglu should know.As the senioroperations engineer for the seventh most-trafficked website in the U.S., his job is to ensure that the Facebook network andall its features runs smoothly. He saysFacebook has become a way of life formany college students (including 22,000subscribers at UCSD), and roughly 50% oftheir users return to the website everyday

“Anyone who has been throughthe Web 1.0 bubble of the 1990s,knows we are in a new bubble. As with all rapid innovations phases, not all companies will survive.” —Munjal Shah

DropShots founder and CTO Ryan Sit (front) with (l-r) CEO Darren Hardy and COO Brian Pond (M.S.,‘01). DropShots is a subscription service that allowsusers to effortlessly share photos and video onlinewith an invited circle of family and friends.

SPECIAL TO PULSE READERS:Drop Shots is pleased to offer a free 90-day Star User Account. Go to: www.DropShots.com/join.phpFree Referral Code: CTOgift

14 UCSD Jacobs School of Engineering > Summer 2006 <

1983 Wayne InmanB.A., BIOENGINEERING

Inman is deployed in support of Operation IraqiFreedom as the chief medical officer of the fieldhospital supporting U.S. and coalition forces in the Kuwait area of operation. Inman expects toreturn to Oceanside, CA in Fall 2006 to resume his orthopedic surgery practice at the NavalHospital, Camp Pendleton.

1990 Young ChoB.A., COMPUTER SCIENCE

Cho has been working at QUALCOMM for the lastthree years. His oldest daughter, Karis, is in firstgrade and younger, Caleb, is an energetic 2-year-old.

1990 Duke HongB.S., COMPUTER ENGINEERING

Hong continued his education at UC Irvine earninga Ph.D. focused on high speed computer networks.He is currently directing Internet performanceanalysis at Akamai Technologies and back at theUCSD Rady School of Business.

1993 Michael AlstonPH.D. ELECTRICAL ENGINEERING

1995 Christine AlstonB.S. ANIMAL PHYSIOLOGY

Michael is a principal engineer in the SiliconTechnology Group of ARM Physical IP, Inc. He isalso an instructor, and member of the curriculumcommittee for the professional certificate programin semiconductor engineering at UCSD Extension.Christine is a scientific homemaker who volunteersat University City High School (UCHS) and leads abook club. Daughter, Liana, is a junior and a stu-dent leader at UC Riverside. Son, Tyler, is a UCHSjunior and nationally-ranked fencer meticulouslyplotting his escape from the nest.

1992 William M. BruinP.E., B.S., STRUCTURAL ENGINEERING

Bruin and his wife (Moire), Moire (daughter, age 7),Ted (son, age 5) are proud to announce the latestmember to their family. Michael James Bruin wasborn on Dec. 6, 2005 and is a healthy and happyaddition to the family.

Class Notes

What’s New With You? Jacobs School alumni, we want to hear from you!Please send us updates on your professional activities and personal achievements. Your information will be included in the nextnewsletter and posted on ouralumni website. While supplieslast, we’ll send you a JacobsSchool alumni baseball capwhen you submit an update.

Email:soecomm@soe.ucsd.eduOn the Web:www.jacobsschool.ucsd.edu/alumni/update_form

to chat with their friends and connect withnew people.

Veteran Web-entrepreneur Munjal Shah(B.S.,’95) says the recent trend in Internetusage is why Web 2.0 companies can pur-sue highly targeted markets: “In 1999, therewere only 50 million Internet users.Today,there are a billion people on the Internet,so you need only capture a small percent-age of the market to be successful.”

Shah was the co-founder of Andale, anonline market research service for E-baymerchants. His latest venture is Riya, thefirst photo search site to use face recog-nition and text recognition technology.“Once you train the system, you can find a picture, say of your daughter and wifetogether, even though you’ve never manu-ally tagged the photo,” says Shah.

Although Shah raised $19 million for hisventure, he hasn’t spent a dime on advertis-ing or PR. Instead, his team kept a runningblog as they developed the product, tellingthe story of their trials and tribulations.With the exposure from major bloggerssuch as TechCrunch, Riya’s story was cov-ered by nearly every major newspaper inthe country.The unique face recognitionconcept was so well received, that morethan one million photos were uploaded tothe site on March 26, 2006, the day Riya’sbeta site was publicly launched.

Shah credits Jacobs School computerscience professors Mohan Paturi, David

Kriegman and Serge Belongie for provid-ing initial encouragement that inspiredhim to pursue Riya. Face recognitionexperts Kriegman and Belongie continueto provide technical advice as the companydevelops.And like Sit and Halicioglu, hesays he relies on the fundamental educa-tion he received at the Jacobs School.

“The Internet is in a rapid innovationphase and not all Web 2.0 start-ups willsurvive,” says Shah.“I am a big believerthat the long-term competitive edge startswith deep technology that others cannoteasily replicate.The intensely rigorous cur-riculum at UCSD gave me exposure todifficult concepts like artificial intelligence,and is the reason I was prepared to take on a highly technical challenge like Riya.”

Riya co-founder MunjalShah. Riya’s face recog-nition software allowsusers to search theirown private photos, without manually tagging each shot.

Taner Haliciouglu atFacebook, where he isexpanding the collegesocial networking sitewith new features target-ed to the corporate community.

Google hosted a reception attended by more

than 100 Jacobs School alumni on June 1st.

It was the largest turn-out to date for a UCSD

alumni mixer outside San Diego. Guests were

treated to great food and Google gifts as well

as technical talks by CSE professor Geoff

Voelker and alumnus Paul Muret, whose web

analytics company Urchin was acquired by

Google in May 2005. With the success of this

year’s mixer, fellow Web giant Yahoo, has

volunteered to host the Bay Area regional

reception for the Jacobs School next year.

For more information, contact Kelly Briggs,

kbriggs@ucsd.edu.

> Summer 2006 < UCSD Jacobs School of Engineering www.jacobsschool.ucsd.edu/pulse 15

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1995 Jason InghamPH.D., STRUCTURAL ENGINEERING

Ingham is an associate professor of structural engi-neering in the Department of Civil and EnvironmentalEngineering at the University of Aukland in NewZealand.

1997 Eric TakeuchiB.S./M.S., ELECTRICAL ENGINEERING

After spending some time as a principal engineer,Takeuchi has shifted career focus to become sr.product manager for solid-state lasers at MellesGriot in Carlsbad, CA. He has one-year-old son,Kevin, and a 3-year-old daughter, Megan.

1998 Andrew Huffmaster B.S., BIOENGINEERING

Huffmaster worked at the neu-rovascular division of BostonScientific Corporation inFremont, CA, for 7.5 years inthe development of neuroendovascular medical devices.This March, he started a newjob at Hantel Technologies inHayward, CA, which is a con-tract development and manu-facturing company serving the

medical device industry. As if that wasn’t enoughchange, his wife Elisabeth gave birth to their firstchild, Nathaniel, on Easter Sunday! Elisabeth alsograduated from UCSD with a B.S. in Physiology andNeuroscience in 1999 and the couple was married in Oakland in 2004.

2000 Rob FahlerM.S., ELECTRICAL ENGINEERING

Fahler began working with Argon ST in November as a DSP engineer. He currently performs FPGAdesign using DSP techniques and C programming in a DSP platform.

2000 Jorge A. RiveraB.S., M.S., STRUCTURAL ENGINEERING

Rivera has worked in structural design for the pastsix years with Nabih Youssef & Assoc. in LosAngeles. He is currently pursuing a Ph.D. in earth-quake engineering at the Rose School in Pavia, Italy,where he is collaborating on research with the Univ.of Arizona, UCSD, and Lehigh Univ.

2001 James GitreB.S., ELECTRICAL ENGINEERING

Gitre is an RF design engineer for Motorola in Austin,TX, where he is working in the mobile devices divi-sion on new platforms for communications.

2001 Maria D. Martinez-RodrigoM.S., STRUCTURAL ENGINEERING

Martinez-Rodrigo is back in Spain, where she servesas an associate professor in the Mechanical Engi-neering and Construction Department of UniversitatJaume I. She is finishing her Ph.D. thesis whichdeals with the reduction of resonant vibrations inhigh speed railway bridges by means of passiveenergy dissipation devices.

2002 Brandon LeongB.S., COMPUTER SCIENCE

Leong lives in Los Altos, CA, where he is working asa systems engineer at Radiance Technologies, Inc.and beginning his career in real estate.

2002 Cole C. McDanielB.S., M.S., PH.D., STRUCTURAL ENGINEERING

McDaniel recently became an assistant professor inthe Architectural Engineering Department at Cal Poly,San Luis Obispo after spending three years as anassistant professor at Washington State University.

2003 Joshua HuB.S., AEROSPACE ENGINEERING

Hu recently moved to the El Segundo, CA area wherehe is a senior QA engineer for Raytheon.

2003 Chris StearnsB.S./M.S., STRUCTURAL ENGINEERING

Stearns works for MKA, a structural engineering firmin Seattle, WA. He designs high-rise buildings all overthe country, and makes frequent visits to San Diego.

2004 Ryan HerrellB.S., STRUCTURAL ENGINEERING

Herrell is the regional manager for the SouthernCalifornia office of Fibrwrap Construction (Fyfe Co.certified contracting arm). Fibrwrap Construction is a design build company that for concrete restora-tions/strengthening, and seismic rehabilitation.Herrell oversees all projects in Southern California,Nevada, and Arizona, from the initial development,design, contracting, construction, and conclusion.

2004 Eric KelleyB.S., M.S., STRUCTURAL ENGINEERING

Kelley has worked as a bridge design engineer inCalifornia, Oregon and Washington. Currently, histeam is beginning the design of a new basculebridge, a type of moveable bridge, in theSeattle/Tacoma area.

2005 Sao Kun Ao IeongB.S., BIOENGINEERING: BIOTECHNOLOGY

Sao Kun is a research associate at Roche Palo Altoworking on enzyme kinetics/characterization anddrug potency screening.

2005 Andrea MartinezB.S., STRUCTURAL ENGINEERING

Martinez works for DeBerry Engineering where shedesigns residential buildings.

2005 Franklin YangB.S., ELECTRICAL ENGINEERING

Yang is working for a major wireless tech companyin San Diego, and learning wireless communicationmethods and assembly language.

Class Notes continued from page 15