Pulse - Fall 2009

1

T

FRIEDER SEIBLE, DEAN

Engineering Advances in Networked SystemsToday, networked systems are increasingly prevalent in every facet of our daily life. Everything from our civil infrastructure (power distribution, traffic control and telecommunications) to the appliances in our homes can now be added to a networked structure, which must be made smarter and more efficient. The Jacobs School is at the forefront of the “cyberinfrastructure revolution”

that is enabling these ever-pervasive networks. Among the challenges our faculty and students are addressing with our industry and academic partners are: how to secure sensitive data that is distributed around the world; how to increase efficiency of the new data centers that are at the heart of cloud computing; and how to incorporate the speed of optics in the smallest chips and the massive Internet backbone.Much of this work is done through three key UCSD research institutes:

our Center for Networked Systems (CNS), which focuses on fundamental advances in the security, reliability and efficiency of networks; our San Diego Supercomputer Center (SDSC), which specializes in enabling our researchers to fully exploit our cyberinfrastructure to advance research through production-level data storage, parallel computing and data analysis, and our California Institute for Telecommunications and Information Technology (Calit2), which is developing tomorrow’s infrastructure and its application of technology to areas such as medicine, transportation, and even the arts. Together, these institutes represent a research and educational platform that is unparalleled at any research university in the country. Our Center for Networked Systems, in particular, presents an ideal model

for how industry and academia can work together to advance the field. CNS was largely championed by Hossein Eslambolchi, a Jacobs School alumnus and former president and CEO of AT&T Labs. Eslambolchi believed that industry needed theoretical research to achieve the next level of advances in networks, and more importantly a partnership to translate that theory to actionable results. Under the leadership of founding director Andrew Chien (now CTO at Intel); and current director Amin Vahdat, CNS has grown from its initial three industry partners to eight members including AT&T, HP, Google, Motorola, Qualcomm, NetApp, Sun Microsystems and Cisco. Nearly 20 research faculty and 70 graduate students are currently actively engaged in the Center. Through a constant dialogue with industry partners, faculty propose cutting-edge research initiatives, and our partners vote with their financial investment on the most relevant projects. Students work side-by-side with industry engineers, both in corporations and here on campus. I invite you to learn more about the great work

of our faculty and students in this issue of Pulse, and to explore even further on our website. We welcome your partnership as we continue to push the boundaries of the new cyberinfrastructure.

Leadership Dean: Frieder Seible

Associate Dean: Jeanne FerranteAssociate Dean: Charles Tu

Associate Dean for Administration and Finance: Steve Ross

Executive Director of External Relations:Denine Hagen

Academic DepartmentsBioengineering: Shankar Subramanian, Chair

Computer Science and Engineering:Keith Marzullo, Chair

Electrical and Computer Engineering:Larry Larson, Chair

Mechanical and Aerospace Engineering:Sutanu Sarkar, Chair

NanoEngineering:Kenneth Vecchio, ChairStructural Engineering: Gilbert Hegemier, Chair

Council of AdvisorsChair: Linden S. Blue,

Vice Chairman, General AtomicsVice Chair: Claude Benchimol,

Senior Vice President, Research and Development,Genetic Systems, Life Technologies

Robert P. Akins, (B.S. ’74, M.S. ’77, Ph.D. ’83),Chairman & CEO, Cymer, Inc.Daniel L. Alspach, (Ph.D. ’70)

Malin Burnham, Chairman, The Burnham CompaniesEugenio Clariond, Chairman, Verzatec

Robert E. Englekirk, Chairman Emeritus,Englekirk Partners Consulting

Structural Engineers, Inc.Hossein Eslambolchi, (B.S. ’81, M.S. ’83, Ph.D. ’84),

Chairman & CEO, Divvio, Inc.Peter C. Farrell, Founder and Chairman, ResMed

Gordon E. ForwardJohn J. Fratamico, Jr., Sr. V.P. & General Manager

of TASBU, SAICRichard Goldberg, Vice President Corporate Quality,

Cisco Systems, Inc. Bernard M. Gordon,

Chairman, NeuroLogica CorporationSteve Hart, CTO, ViaSat, Inc.

Irwin M. Jacobs, Co-Founder, Qualcomm, Inc.Paul E. Jacobs, Chairman and CEO, Qualcomm, Inc.

Richard Kornfeld, (B.S. ’82)David M. Lederman, Managing Director,

Analytical LLCScott McClendon, Chairman, Overland Storage, Inc.

Henry Nordhoff, Chairman, Gen-ProbeBahram Nour-Omid, Senior Partner

Shelter Capital PartnersWilliam A. Owens, Chairman and CEO,

AEA Holdings ASIA, AEA HoldingsGregory M. Papadopoulos, Executive VP of Research

and Development and CTO, Sun Microsystems, Inc.Ake Persson

Gene W. Ray, Managing Director, GMT VenturesDebra L. Reed, President and CEO

SDG&E and SoCalGasDavid Schwab, Managing Director,

Sierra VenturesAndrew E. Senyei, M.D.,

General Partner and Managing Director,Enterprise Partners Venture Capital

Julie Meier Wright, President and CEO,San Diego Regional Economic

Development Corporation

Jacobs Schoolof Engineering

www.jacobsschool.ucsd.edu/pulse UCSD Jacobs School of Engineering, Fall 2009 2

> dean’s column <

On the cover: Botnet infiltrators Chris Kanich (left, computer science Ph.D. candidate) and Kirill Levchenko (right, recent computer science Ph.D. from the Jacobs School where he is now a postdoctoral researcher).

4 AROUND CAMPUS• SpaceToileTReSeaRchinZeRoG• ScavenGeRhunTbyplane

• JacobSSchoolofRock

5 hybRidpoweR:enGineeRinGSTudenTSdRiveinToThefuTuRe

• SocialMedia

• MaRconiScholaR

6 RESEARCH6infilTRaTeboTneTS

7lockThevoTe

7 cenTeRfoRneTwoRkedSySTeMS7niMbleandThRifydaTacenTeRS

8haRneSSinGTheSiGnal:enGineeRSduplicaTewaveSand bReakSiGnalpRoceSSinGRecoRdS

9SleepTalkinGpcSSaveeneRGyandMoney

9chipSandliGhT9undeRwaTeRSenSoRneTSfoRenviRonMenTalMoniToRinG

10nanobioloGy:ReSeaRchbReedSfuTuRelow-coST ‘GReen’TechnoloGieS

10diSSecTinGdnawiThnanoTechnoloGy

11lifeSTickS

11STRucTuRalenGineeRSTeSTfiRSTcoMpoSiTelandinG GeaRbRaceSfoRaiRcRafT

11 SolaRShadeS

12 eaRThquakeSafeTyandTheSanfRanciSco- oaklandbaybRidGe

13 FACULTY 13newfaculTy

14 ALUMNI 14 ReplicaTinGThehuManMind

14 baTTlealienSandcheaTeRSwiTh3diphoneGaMe

15 claSSnoTeS

16 BACK COVER• upcoMinGevenTS

7voting security

5electric car

DNA breakthrough10

Corporate Affiliates ProgramExecutive Board

Chair: Daniel Brown,Cymer

Chair: A nton Monk,Entropic Communications, Inc.

ATA Engineering, Inc.BAE Systems

Booz Allen HamiltonBecton Dickinson

Broadcast Microwave Services, Inc.Cisco Systems, Inc.Cohu Electronics

Cymer, Inc.Delta Design

DirecTVEnterprise Informatics

Entropic Communications, Inc.ESET

General AtomicsGen-Probe

GoogleHilti Corporation

Hughes Network SystemsIDEAL Industries

Information Systems Laboratories, Inc.Intercasting Corporation

IntuitKratos Defense

KuityKyocera America, Inc.

Life TechnologiesLockheed Martin MS2

NAVAIRNavy Nuclear Power & Civil Engineering Programs

NG Space & Mission SystemsNG Integrated Systems

QualcommQuartus Engineering Incorporated

RaytheonRincon Research Corporation

SAICSiliken Renewable EnergySimonWong EngineeringSkyworks Solutions, Inc.

Solar Turbines IncorporatedSSC Pacific

Staccato CommunicationsSun Microsystems

SyncronessTeradata Corporation

ViaSat, Inc.Wavestream

Yahoo!

Newsletter TeamCheryl Harris (editor)

John Cozen, Denine Hagen, Daniel Kane, Andrea Siedsma

To Reply to the [email protected], (858) 822-7656

9500 Gilman Drive, La Jolla, CA 92093-0403

CONTENTS

cybersecurity6

www.jacobsschool.ucsd.edu/pulse Fall 2009, UCSD Jacobs School of Engineering 3

signal processing8

Space Toilet Research in Zero G

Jacobs School of Rock...

Scavenger Hunt by PlaneExactly how, when

and where do fluid streams that resemble urine—in terms of both flow rate and stream diameter—break up into droplets in zero gravity? Jacobs School undergraduates spent their spring break at NASA’s Johnson Space Center finding out. With the goal of

designing a better urinal for female and male astronauts, the students boarded an airplane that made a

series of steep inclines and drops in order to create the near-zero gravity conditions that astronauts experience in space. In these short windows of microgravity, the students performed research. They fired urine-like streams of water into a water-tight observation box that looks like a 25-gallon fish tank. A pair of cameras collected data on how, when and where the streams broke up into droplets.This fall, the Jacobs School team plans to move from data analysis to prototyping.

Undergraduate Tim Havard described one promising design idea to Science magazine journalist Jackie Grom. He envisions “a receptacle filled with a honeycomb network that harnesses surface tension and the velocity of the fluid to capture the urine with minimal splash-back.”

Despite the in-flight fire caused by a faulty speed controller, an unmanned airplane designed and built by Jacobs School undergraduates won second place at an international scavenger hunt. The plane has a 10-foot wing span and a body of composite fiber that encases an autopilot and an object-recognition system. The competition resembles a scavenger hunt except that the students and their target-finding airplanes are not

told exactly what they are looking for. The autopilot charts the

course

while the object-recognition system searches the ground, more than 200 feet below, for potential targets. The plane that identifies the most targets—without any human assistance—wins. This academic year, the Jacobs School undergrads plan to design their own target recognition system using algorithms developed at UCSD. The Association for Unmanned Vehicle Systems International organizes the annual event.

...is Always in SessionEngineering and art are deeply intertwined at the Jacobs School, and the annual music jam—called The Jacobs School of Rock—is just one example. The concert fills Porter’s Pub with energy at the end of every spring quarter, but you don’t have to wait until next June to soak up the Jacobs School’s music scene. A number of

its bands, including SO3 and Juna, regularly perform in San Diego. Check out the Jacobs School of Rock website for links to band websites with concert schedules and the latest downloads: http://jsor.ucsd.edu The bands thank Yahoo! for their support in 2009.Jacobs School bands also appear on soundtracks for promotional videos. The

video about undergrads studying space pee (see above) features a track by Juna whose vocalist, Carolina Galleguillos, is a computer science Ph.D. student advised by computer science professor Serge Belongie, the frontman for SO3. http://tinyurl.com/spacepee

Christie Carlile (above) majored in aerospace engineering, graduated in June, and accepted a full-time position at NASA’s Johnson Space Center.

The Jacobs School undergrads (above) designed and built this unmanned surveillance plane. The students thank all their supporters, especially General Atomics.


> around the campus <

Hybrid Power: Engineering Students Drive Into the Future

Engineering students at UC San Diego are fine-tuning their hand-built hybrid-electric car to compete against other universities across the nation next year. The students, who are members of the UC San Diego Society of Automotive Engineers (SAE) built their first Formula Hybrid car last year using a $15,000 grant from Plug In America, a nonprofit organization that works to accelerate the shift to plug-in vehicles powered by clean, affordable, domestic electricity. The team, which competed against 30 other universities, placed 9th out of 21 teams overall in the Formula Hybrid International Competition held in new Hampshire in Spring 2009. Next year’s competition will also be in late Spring. A Formula Hybrid vehicle must

use at least 15 percent less gasoline than a comparable standard Formula SAE racecar operated under the same

conditions. And, unlike the traditional Formula SAE gas-powered car, Formula Hybrid teams are encouraged to incorporate used racecar parts rather than build everything from scratch. Next year’s UCSD SAE car will be a full hybrid with an on board generator. “We decided to build an electric car

because of the support and push from industry,” said Jerry Curiel, former president of the UC San Diego SAE who graduated from the Jacobs School in the Spring with a degree mechanical engineering. “It also reflects the goals of UCSD to become the ‘greenest’ university in the United States. More importantly, it’s a great opportunity to make green technologies fun and exciting in the eyes of our fellow students.”

Stay Connected with Us!

Connect with the Jacobs School across social media networks. See:http://www.jacobsschool.ucsd.edu/connect for details.

Blogger

Twitter

Video & iTunes

LinkedIn

Facebook

Flash Memory Student Named Marconi Scholar

Electrical engineering Ph.D. candidate Eitan Yaakobi won a 2009 Young Scholar Award from the Marconi Society. The Marconi Society

at Columbia University recognizes and encourages scientific contributions in the fields of communications science and the Internet. The society is best known for its Marconi Prize, which goes to individuals whose scope of work and influence carry on the legacy of Guglielmo Marconi, recipient of the 1909 Nobel Prize for his pioneering achievements in wireless technology. Yaakobi was named a Marconi Scholar in recognition of his research achievements in algebraic error-correction coding, coding theory, and their applications for digital data storage, and in particular for flash memories. He works closely with the Center for Magnetic Recording Research and with electrical engineering professors Paul Siegel, Jack Wolf and Alexander Vardy.

Eitan Yaakobi


UC San Diego Society of Automotive Engineers (SAE) and their first Formula Hybrid car

Jacobs School computer scientists infiltrated the Storm botnet—an infamous spam-sending network of infected and remotely

controlled computers. To reach just one person willing to buy black-market pharmaceuticals, Storm had to send, on average, 12 million spam emails, the researchers discovered. Sneaking into the Storm botnet and collecting spam conversion information is just part of the computer scientists’ larger effort to understand online crime from a global perspective.When you think like an online criminal, you see that spam is cheap,

that getting your URLs blacklisted is not a big deal, and that software programs with “perfect security defenses” would not stop botnets.“Our work brings awareness to the fact that trying to filter spam is

not the only approach to dealing with the problem,” says Geoffrey Voelker, a computer science professor who, together with computer science professor Stefan Savage, is leading the effort to leverage the Jacobs School’s expertise in systems, networking, and security to identify cracks in the online crime world’s global façade. This project is linked to UCSD’s Center for Networked Systems.Despite the 12,000,000-to-1 spam conversion rate, a single Storm

spam campaign yielded between $7,000 and $9,000 per day in 2008, estimated the Jacobs School researchers who performed this work in collaboration with Vern Paxson and Christian Kreibich from the International Computer Science Institute at UC Berkeley.“I have a long list of reasons why we are not going to win on

the technical side of spam, e-crime or identity theft,” said Savage. “Almost everything about the landscape favors the bad guys, and it is very easy for them to change. You put in a huge investment to secure one aspect and they change. It costs them almost nothing.”Instead, computer science professors, students and researchers—

including Chris Kanich and Kirill Levchenko (on the cover of this issue)—are following the money.“What surprised me is how sophisticated these operations are.

Making money in spam requires not only a way to send spam, but also Web hosting companies and DNS registrars that ignore abuse complaints, online pharmacy operators, and so on. These all point to a sophisticated criminal ecosystem,” said Kirill Levchenko, who recently earned his computer science Ph.D. at the Jacobs School, where he is now a postdoctoral researcher.Infiltrating Storm enabled the computer scientists to intercept

outgoing commands and adjust them so that the botnet generated spam with links to dummy sites run by the researchers. “Collecting data for the spam conversion study was the most

exciting part so far,” said Ph.D. student Chris Kanich. “We were working on this botnet that we didn’t control. The botmaster could change the way things work, or find out that we’d infiltrated their botnet at any time.”One of the next steps for the computer scientists is to investigate

the relationships between the various players in online crime, including the illegal pharmaceutical Web sites that pay spammers a commission for directing buyers to their sites, the credit card processors, the product fulfillment groups, and the drug manufacturers. “We are trying to come up with empirical means to draw a CSI-

like picture of how it all works,” said Savage.A new $7 million grant from the Office of Naval Research will

help to fund the computer scientists’ efforts to better understand the underlying technical issues that revolve around botnet measurement and infiltration.


> research <

Infiltrate Botnets

Voting Machine Succumbs to New Programming Technique In 2007, computer science professor Hovav Shacham first described a powerful new programming approach that generates malicious behavior by combining short snippets of good code already present in the computer. Now, Shacham and his team demonstrated that criminals could use this “return-oriented programming” approach to force an electronic voting machine to use its good code to steal votes.

Unlike most previous voting security research, the computer scientists had no access to the machine’s source code—or any other proprietary information—when designing the demonstration attack. They reverse engineered the voting machine’s hardware and software and then used return-oriented programming to take over the machine and change vote totals.

“Based on our understanding of security and computer technology, it looks like using fast optical scanners that read paper ballots is the way to go. These systems are amenable to statistical audits, which is something the election security research community is shifting to,” said Shacham. He and computer science Ph.D. student Stephen Checkoway collaborated with researchers from Princeton University and the University of Michigan on this project.

Read the paper, watch relatedvideos and listen to Shacham on NPR’s

Science Friday at: https://www-cse.ucsd.edu/groups/security/avc/

Plug-and-play data center networks and new diagnostics for router delays are among the computer networking challenges UC San Diego faculty and students, and their sponsor companies, are tackling through the Center for Networked Systems (CNS).The Center, which actively engages eight corporate partners, 20 faculty and nearly 70 graduate students, aims to enhance computer scientists’ ability to build robust, secure, manageable, and open networked systems.

Both the data center networking and the router delay projects debuted recently at SIGCOMM 2009, the top conference for computer networking. One Jacobs School team developed an inexpensive solution for diagnosing delays in data center networks as short as ten millionths of second—delays that can lead to multimillion-dollar losses for investment banks running automatic stock trading systems.

A second team from the Jacobs School developed software for enabling massive data centers to logically function as single, plug-and-play networks. The software, called PortLand, is a fault-tolerant, layer 2 data center network fabric capable of scaling to 100,000 nodes or more.

Amin Vahdat, Director of the Center for Networked Systems and a computer science professor at the Jacobs School, led the PortLand project, which has garnered considerable interest from industry. “The students are getting good jobs and internships coming out of this project because they have data center networking skills. Companies are looking for this skill set,” said Vahdat, who holds the Science Applications International Corporation (SAIC) Chair at the Jacobs School of Engineering.

Computer science professor Hovav Shacham (left) and Ph.D. student Stephen Checkoway (right) highlighted voting machine vulnerabilities.

Lock the Vote


Center for Networked Systems

Data centers are big and bulky on the outside, but computer scientists at the Jacobs School are making them agile and

flexible on the inside. Tomorrow’s data centers will be able to “see” into

the future thanks to algorithms that predict future conditions based on real-time data collected by

embedded sensors. With these predictions, data centers can proactively direct incoming jobs from

one server to another, turn fans on and off, switch power management strategies, and increase cooling—

all in real time.“The big picture is that we want to find a better way to

manage data center energy costs,” said Tajana Simunic Rosing, the computer science professor leading the

projects, which are tied to UCSD’s Center for Networked Systems.

Temperature prediction algorithms, for example, reduced costly, performance-busting hot spots on servers by as much as 80 percent.

The team’s workload prediction algorithms guide power management strategies for servers that can provide energy savings of up to 70 percent.Rosing and her graduate students are

now working to integrate the temperature prediction and workload prediction systems, and to scale up their implementations from server racks to full-scale data centers. This summer, Rosing was tapped to lead

the Large-Scale Systems branch of a $3 million multi-university initiative. This project is focused on a forward-looking computing landscape in which applications run in distributed form on platforms that mesh data centers with broad classes of mobile devices that are surrounded by large swarms of sensors. This Multi-Scale Systems Center (MuSyC) is funded by the Semiconductor Research Corporation’s Focus Center Research Program.

Nimble and Thrifty Data Centers

Data centers will “see” into the future thanks to research led by computer science professor Tajana Simunic Rosing

Engineers Duplicate Waves and Break Signal Processing Records

Breaking world records for signal processing in real time is nothing new for electrical engineering professor Stojan Radic. With each new world record, Radic moves closer to eliminating a major bottleneck in today’s fiber optic networks and ushering in

new technologies for data intensive collaborative science, future generations of the Internet, and a wide range of military and communications applications.The problem is that today’s

digital signal processors, and computers more generally, process information in real time at gigahertz per second. They can not keep up with the streams of data flowing through fiber optic networks at terabits per second.To eliminate this bottleneck,

Radic and his team have invented methods for duplicating extremely fast signals travelling through fiber optic cables and then sampling each of the copies simultaneously. Instead of processing one signal ten times in a second, you can process each of ten copies of the signal once per second. “The effective signal

processing is much faster. That’s the whole point,” said Radic, who leads the Photonics

Laboratory, housed in the UCSD Division of the California Institute for Telecommunications and Information Technology (Calit2).In 2009, Radic and colleagues published work on the first real-time sampling of a 320 Gigabit per second (Gb/s) channel, setting

multiple records in the process.“The future of the Internet—especially for data-intensive collaborative science—is predicated on finding new ways to process data

on the fly, even at the highest transmission rates. The techniques invented by professor Radic and his team are a major step forward in realizing this vision,” said Larry Smarr, Director of Calit2 and a computer science professor at the Jacobs School. Radic came to UCSD from Bell Laboratories five years ago. In that time, he has built the team and facilities necessary to circumvent

fundamental limitations inherent in the fiber optic cables, limitations that many researchers believed would make his approach impossible. With research funding from DARPA, Radic has proved the skeptics wrong. He invented a method for assembling sections of fiber optic cable that are uniform enough to create “optical mixers” that exactly duplicate extremely fast signals and map them to arbitrary wavelengths.The team starts by analyzing a high confinement optical fiber and mapping the nanometer-scale variations along the cable’s core.

Armed with this map, the group determines which sections of the fiber should be selected and reassembled to create a fiber optic cable that is free of core variations—down to the nanometer scale. Core variations comparable to a single silica molecular ring can result in inefficient optical mixing and disrupt the exact replication of signals that is crucial to this approach. Next, Radic’s experimental group cuts up the original cable and assembles a shorter nearly uniform cable based on the map. Devices made of concatenated, shorter cables have the properties necessary to make a wideband optical mixer that can exactly duplicate fast signals and thus enable record-breaking real time signal processing. UCSD holds the basic patent on this technology and has started the commercialization effort.


> research <

Harnessing the Signal

Electrical engineering

professor Stojan Radic is eliminating a major bottleneck in today’s fiber optic networks.

“Sleep talking” is an energy and money saving mode for personal computers invented by computer scientists at the Jacobs School and Microsoft Research. Normally PCs alternate between awake mode—where they consume significant power even when idle—and sleep mode—where they save substantial power but are essentially unavailable and unresponsive to network traffic. “Sleep talking” offers a tantalizing mix of the two traditional modes.“Many people keep their PCs in awake mode just because they want to stay connected

to an internal network or the Internet,” said Yuvraj Agarwal, the inventor of “sleep talking” who recently earned his computer science Ph.D. from the Jacobs School. “I realized that most of the tasks that people keep their computers on for—like ensuring remote access, file sharing and downloading, and maintaining presence on instant messaging and voice-over-IP networks—can be achieved at much lower power-use levels than regular awake mode.” Agarwal presented his plug-and-play hardware

prototype for personal computers in April, and the story continues to percolate across the Web.

A Technology Review story in August even triggered a second appearance on Slashdot.Agarwal recently accepted a research scientist

position at UC San Diego in the lab of Rajesh Gupta, his Ph.D. advisor. Agarwal aims to implement his sleep talking technology across networks that scale to enterprises and datacenters.

Computer science Ph.D. Yuvraj Agarwal (above) invented “sleep talking”and designed a number of energy saving prototypes for PCs (below).


Sleep Talking PCs Save Energy and Money

For a large and diverse array of` Jacobs School engineers working in the areas of optics, photonics

and networking, where the light meets the chip is where the rubber meets the road. More than 30 Jacobs School faculty, students and researchers are involved in the Center for Integrated Access Networks (CIAN), a 10-university $18.5 million project funded by the National Science Foundation. Electrical engineering professor Shaya Fainman serves as Deputy Director of CIAN, which is focused on developing optoelectronic technologies—where light and electronics interact—for high-bandwidth, low-cost, widespread access networks. Stojan Radic and George Papen, also electrical engineering professors, are the co-leads for CIAN’s UC San Diego test bed, housed in Calit2. The test bed enables collaborative research among CIAN participants and with the wider research and industrial community. Electrical engineering professor Joseph Ford and computer science professor Amin Vahdat are also on the CIAN leadership team. Check out the new CIAN Web site and newsletter at: http://www.cian-erc.org/

Chips and Light

Computer scientists are developing networks of underwater sensors for real time environmental monitoring of marine ecosystems.

While the Navy has long used sonar for underwater communications, scientists need inexpensive and power-thrifty underwater sensor technologies for capturing and transmitting environmental data back to land in real time, explained computer science Ph.D. student Bridget Benson.

Last spring, Benson and computer science professor Ryan Kastner presented a paper highlighting the energy conservation benefits of using reconfigurable hardware rather than competing hardware platforms for their experimental underwater sensor nets.

Computer science Ph.D. student Bridget Benson builds underwater sensor networks. She also monitors marine ecosystems the old fashioned way.

Underwater Sensor Netsfor Environmental Monitoring

Outside of school, Benson works for the nonprofit Reef Check, where she trains veteran divers to survey the fish, animal and plants living in reefs from Santa Barbara to San Diego.

“I have the field experience, and I see the need for the inexpensive sensor networks we are working on,” said Benson, who envisions volunteers and autonomous robots working together to monitor the health and species richness of reefs and other underwater ecosystems.

Research Breeds Future Low-Cost‘Green’ TechnologiesIn her lab at the Jacobs School, NanoEngineering professor Jennifer Cha is employing biology to engineer

the synthesis and assembly of nanoscale materials that will one day be applied to medicine, electronics, and energy.

“Bio-nanotechnology is a growing area,” said Cha, who joined the NanoEngineering Department

in 2008. “Within this area is a science that uses biology to assemble or make functional or technologically important materials for electronics, sensors, photovoltaics, fuel cells, batteries, and medical therapies.” Due to their unique electronic, optical, and

mechanical properties, nanoscale materials have been heavily explored for various applications. However, devices fabricated

from these materials have typically required expensive and environmentally unfriendly

processes. Cha and her colleagues are trying to figure out cost-effective and green chemistry strategies for nanoengineering.“For nanoscience to become technologically

viable, societal and economic impact must always be considered. We’re hoping that biomolecular systems will not only solve some technical challenges but will also

allow us to fabricate functional materials from nanoscale systems at low cost and using benign chemistries,” said Cha, who came to UC San Diego after a four-year stint as a research scientist at IBM. One of the projects Cha is working on is for the Office of Naval Research to

look for methods to engineer large-scale arrays of sub-10 nanometer materials for electronic devices. The National Science Foundation has funded another project for Cha’s lab to develop flexible, cost-effective high throughput sensors.“Nanoengineering is perfect for this kind of research,” said Cha, who was awarded

a Defense Advanced Research Projects Agency (DARPA) Young Faculty Award this year. “We hope we can make an impact on society with the help of biology.”

NanobiologyNanoEngineering professor Gaurav Arya is using innovative approaches to deduce the internal structure of chromatin, a key player in DNA regulation, a breakthrough that could unlock the mystery behind the origin of many diseases such as cancer. This new discovery reconciles a

longstanding controversy among scientists and biologist alike. The structure of chromatin has been a subject of many

controversies during the last 30 years, with two different models being the focus of debate. The new findings by Arya and his colleagues from Penn State University, the University of Massachusetts, and New York University, suggest that the structure of chromatin is actually a combination of both of these models. The function of chromatin is to package DNA into a smaller volume to fit in the cell. Chromatin also plays an important role in the regulation of genetic processes like DNA replication, transcription, recombination, and repair because all these processes depend critically on the

accessibility of the DNA, which is directly controlled by chromatin. Many diseases, including cancer, are directly linked to abnormal regulation of chromatin.

Arya and his team, for the first time, have developed a very sophisticated model of chromatin that is computationally accessible yet detailed enough to provide insights into its structure and dynamics. “This research emphasizes how engineering tools can provide new insights into biology,” Arya says.The next step for Arya and his team is to study the mechanisms by which chromatin is regulated, and how those lead

to genes being switched “on” and “off,” genes being repaired in response to mutations, and genes being replicated during cell division. Arya believes that a molecular-level understanding of such mechanisms could lead to the development of better drugs that will directly target the chromatin

around abnormally regulated genes to correct their activity.

NanoEngineering professor Gaurav Arya

the recently discoveredstructure of chromatin

NanoEngineering professor Jennifer Cha


> research <

Dissecting DNA withNanotechnology

Bacteria, fungi, sponges, nematodes and humans all rely on the stickiness of their cells for survival. There is something inherent in the task of cells sticking to cells (and of cells responding to forces) that causes common form and function to emerge across the tree of life. Bioengineering professor Adam Engler and his colleagues highlight this idea in a paper recently published in the prestigious journal Science. The capacity to form complex

multilayer organisms by way of cells sticking to cells is likely based, in part, on the evolutionary advantage enjoyed by cells that can adhere to new environments. Sticky—it seems— is good.

Life Sticks

Environmental engineering professor Jan Kleissl and MAE graduate student Anthony Dominguez

Individual cells are represented by lavender rectangles. Cells sticking to cells—a phenomenon found all across the tree of life—leads to multilayer organisms.


Dissecting DNA withNanotechnology

Solar Shades

Cool CompositesFrench Aerospace company Messier-Dowty tapped into the expertise of structural engineering professor Hyonny Kim this year to test the strength and durability of the first-ever composite landing gear braces for the commercial aircraft industry.

It was the first time Jacobs School engineers performed tests on landing gear components for the aerospace industry. Led by Hyonny Kim, a structural engineering professor at the Jacobs School, the researchers performed six months of rigorous Federal Aviation Administration tests on the landing gear braces, which were designed and built for Boeing’s new 787 aircraft. The purpose of the full-scale tests – which were performed at UCSD’s unique

Caltrans Seismic Response Modification Device (SRMD) test facility – was to prove the strength and capability of these major structural components. Kim said the recent partnership with Messier-Dowty will help open the door for future aerospace projects for the SRMD facility, part of the Jacobs School’s Powell Structural Research Labs.

Structural Engineers Test First Composite Landing Gear Braces for Aircraft

While solar panels are used for electricity generation and water heating applications,

their shading and cooling effect on buildings has been ignored. Until now. Jacobs School environmental engineering professor Jan Kleissl and a group of his mechanical and aerospace engineering (MAE) students say solar panels are not only a source of “green” power but they also impact the heat balance of roofs due to absorption of solar radiation and shading of the roof surface. Using a thermal camera, wireless sensors and computer modeling, the group of engineers found that the ceiling of a building is cooler below the actual solar panels on the roof. The experiment – the first comprehensive one of its kind – was conducted on the Jacobs School’s Powell Labs north building on the UC San Diego campus. Kleissl’s goal is to create an online calculator for homeowners and business owners to use to determine how much cooling and energy savings they will actually have by installing and using solar panels. He says this new-found discovery could give the solar industry a big boost. “We want to demonstrate the additional energy conservation potential of solar panels that may provide an incentive for their future use,” Kleissl says.


> research <

Caltrans recently completed an unprecedented aerial engineering

feat. During the 2009 Labor Day weekend, the San Francisco-Oakland Bay Bridge was closed to traffic while Caltrans cut away a 300-foot long double deck section of the existing bridge at Yerba Buena Island, and connected a temporary half-mile detour. The entire operation was performed 150 feet in the air. Rerouting the bridge that serves more than 280,000 vehicles per day is just one of the many structural engineering milestones achieved in the nation’s most ambitious bridge project to date—

building the new San Francisco-Oakland Bay Bridge east span.“The Bay

Bridge east span will be

the largest Single Tower Self-Anchored

Suspension Bridge ever built,” says UC San Diego

Jacobs School of Engineering Dean Frieder Seible. Seible is a member of

the Seismic Safety Peer Review Panel, a group of experts convened by Caltrans to provide advice on the seismic integrity of the Bay Bridge after its partial collapse

during the 1989 Loma Prieta Earthquake. “We found that three-quarters of the

existing members of the bridge needed to be replaced, and that was going to be virtually impossible to do under full traffic,” says Seible. With that recommendation, the State embarked on the design and construction of the new Bay Bridge, a project which is described as the single largest public works project in California’s history. Caltrans turned to the Jacobs School’s

Structural Engineering Department to complete all of the testing required to verify new structural systems for the seismic safety of the Bay Bridge. Indeed, several of the new systems built into the bridge were first envisioned by the structural engineering faculty at UCSD. “One of the key innovations in the

Bay Bridge which has come out of UCSD is the concept for the single 525 ft.-tall tower that supports the self-anchored suspension bridge,” says Seible. This main tower is comprised of four

separate legs connected by shear link beams. “The links are designed to be sacrificial. They will absorb the energy of the earthquake, preventing damage to the tower legs, and can easily be replaced without disrupting traffic,”

says Seible. “However, if one of the legs is damaged, the other three can still keep the bridge standing.” Testing of the shear-links was done under the direction of Seible and Professor Chia-Ming Uang. The new Bay Bridge will eventually replace

the current structure, first opened to the public in 1936. It is designed to withstand potential seismic threats from both the nearby San Andreas and Hayward faults, which could be of even greater force than the Loma Prieta quake. Construction is expected to be complete by 2013.

Safe from HarmEarthquake Safety and the San Francisco-Oakland Bay Bridge Im

age

cour

tesy

of T

.Y.L

in In

t’l

Bay Bridge cross section UCSD Near Youin San Francisco

October 29, 2009

“Earthquake Safety and the San Francisco-Oakland Bay Bridge”

Presented by:Frieder Seible

Dean, UCSD JacobsSchool of Engineering

For more information and to register visit:

www.jacobsschool.ucsd.edu/r/UCSDNearYou

Patrick Fox Professor, Structural EngineeringGeotechnical and geoenvironmental engineering. His work includes flow through porous media, consolidation, geosynthetics, geotechnical earthquake engineering, foundation engineering, retaining structures, and slope stability. Dr. Fox is also the incoming Editor-in-Chief of the ASCE Geotechnical Journal, and recently won both the 2008 IGS Award (International Geosynthetics Society) and the 2009 ASCE Thomas Middlebrooks Award. Ph.D., 1992, University of Wisconsin-Madison Most recently: Professor, Ohio State University

Ying Shirley Meng Assistant Professor, NanoEngineeringEnergy storage and conversion materials: nano structured electrodes for advanced rechargeable batteries, dye-sensitized solar cells and thermoelectric conversion; charge ordering, structure stability, processing/structure/property - performance relation in functional ceramics. Ph.D., 2005, National University of Singapore, Singapore-MIT AllianceMost recently: Assistant Professor, University of Florida

Andrea Tao Assistant Professor NanoEngineeringFunctional nanostructured materials, including nanowires, nanophotonics, and biomimetic materials. She works in nanophotonics and optics at the nanoscale, in the synthesis and assembly of platonic nanocrystals, and in developing nanowires for sensing applications. Ph.D., 2007, UC BerkeleyMost recently: UC President Postdoctoral Fellow, UC Santa Barbara

Donald Sirbuly Assistant Professor, NanoEngineeringNanoscale sensors and energy-harvesting nanotechnologies. His research includes work in sub-wavelength waveguides and nanophotonics, use of nanophotonics for biological sensing and imaging, and synthesis of optimized nanostructured nanowires. Ph.D., 2003, UC Santa BarbaraMost recently: Graboske Fellow, Lawrence Livermore National Laboratory

Jie XiangAssistant Professor Electrical and Computer EngineeringNanostructured semiconductor materials, spanning fundamental electronic transport, nanoelectromechanical properties as well as applications in high performance nanoelectronics, energy conversion and biosensing. Fabrication of ultrasmall contact metallization for nanowires. Nanoelectromechanical (NEMS) systems based on semiconductor nanowires. Ph.D., 2007, Harvard University. Most recently: Kevali Nanoscience Institute Postdoctoral Fellow, California Institute of Technology

Gert CauwenberghsProfessor, BioengineeringAnalog and digital VLSI microsystems for adaptive neural computation and sensory information processing, from neuromorphic systems engineering and kernel-based learning machines to micropower implantable neural interfaces, acoustic microarrays, adaptive optics and biometric identification. Ph.D., 1994, California Institute of TechnologyMost recently: Professor, Biological Sciences, UC San Diego

Renkun Chen Assistant Professor, Mechanical and Aerospace EngineeringFundamentals of heat transfer in semiconductor nanostructures; Phonon physics. Ph.D., 2008, UC Berkeley Most recently: Postdoctoral Research, Lawrence Berkeley National Laboratory

Pedro Cabrales Assistant Professor, BioengineeringGas transport physiology and bioengineering design for development of next generation blood substitutes; Bioengineering microcirculation; The effect of blood substitutes on oxygen transport to tissue. Ph.D., 2003, University of Los Andes, Bogota, ColombiaMost recently: Assistant Professor and Research Scientist, La Jolla Bioengineering Institute


> new faculty <

(L-R, back row first) Jacobs School professors Robert Hecht-Nielsen, Kenneth Kreutz-Delgado

and Elias Masry enjoyed a recent visit from Jacobs School alumnus Dharmendra S. Modha

(Electrical engineering Ph.D. 1995, MS 1993)

Replicating the Human Mind> alumni <

The IEEE selected Jacobs School alumnus Dharmendra S. Modha as one of seven top minds to discuss how emerging technologies have the potential to change the world.As a part of this IEEE 125th Anniversary panel,

Modha discussed cognitive computing, an area of particular expertise for the electrical engineering Ph.D. (1995) who manages the cognitive computing department at the IBM Almaden Research Center in San Jose, CA. Modha is also the Principal Investigator for SyNAPSE, a large scale effort spread across IBM Research and five universities to replicate the human mind. Funded by DARPA, engineers and scientists are developing computing systems that simulate and emulate the brain’s abilities for sensation, perception, action, interaction and cognition while rivaling its low power consumption and compact size.

“I owe a great debt to UCSD, and to my many wonderful professors from the Jacobs School, especially Elias Masry and Robert Hecht-Nielsen, for their priceless gift of education,” says Modha, who recently returned to the Jacobs School for a visit.“Fundamental training persists. Professors change lives when they teach thinking, when they

teach students how to approach any problem—how to rigorously break down any problem and deal with it,” says Modha. “Now, as a proud UC San Diego alumnus, I am staying connected and working with our university

to raise the visibility of the accomplished students, faculty and alumni who add value to our degrees every day.”

Battle Aliens and Cheaters with 3D iPhone Game

The three computer scientists who created TowerMadness—a critically acclaimed 3D iPhone game—all studied at the Jacobs School. Playing TowerMadness means saving sheep from 3D aliens who have invaded your iPhone. While you battle aliens, the game’s developers work behind the scenes to make sure cheaters are kicked off the online leaderboard. The game’s cheat resistance is rooted in a unique online replay system that literally replays high-scoring games submitted to the leaderboard in order to check that players legitimately scored as many points as they claim. The full version of

TowerMadness and a free demo version are available through the iPhone App Store. Iman Mostafavi a

computer science Ph.D. student, Arash Keshmirian, a computer science BS/MS alumnus, and Volker Schönefeld, a former visiting graduate student to the computer science department developed TowerMadness. http://www.towermadness.com/


Class Notes

2003 Wing Sum CheungB.S. Mechanical and Aerospace EngineeringProject Engineer, URS Corporation Cheung and wife Brenda have a 4 year old daughter, Rachel. The family currently lives in suburban Baltimore. He joined URS Corp in 2006 and works on the design of baggage handling systems for airports.

2005 Albert FongB.S. Electrical EngineeringChief Project Engineer, Albiasa Corp. After graduating from UCSD, Albert worked for 2.5 years in the semiconductor industry in San Diego. Albert returned to the Bay Area in August 2008 to act as the chief project engineer for Albiasa Corporation, subsidiary of Spanish solar developer Albiasa Solar. At Albiasa, Albert helps manage new development of utility scale solar projects in the US and specifically oversees the $1 billion dollar Albiasa Kingman 200MW concentrating solar power project in Arizona, poised to be commercially operational in 2013.

2008 Neal BloomB.S. Mechanical EngineeringEngineer, Pratt & Whitney Rocketdyne Neal took 3 months to travel through China and Europe after graduation, then joined Pratt & Whitney Rocketdyne (Canoga Park) in the Fall of 2008. He currently works on the Space Shuttle main engine, supporting test and flight operations for the U.S. Space Program, and yes, he says he loves his job!

2008 Adam MarkowitzB.S. Structural EngineeringEngineer, Materials/Structures, Pratt & Whitney, Rocketdyne Adam performs structural analysis on various rocket engine components at Pratt & Whitney Rocketdyne, including the Space Shuttle main engine’s combustion chamber and the gas generator on NASA’s new upper stage J-2X engine. The J-2X will be used in the Constellation Program aboard the Ares rockets.

2003 Doris ChunB.S. BioengineeringChemist, Hewlett-Packard

After graduating in 2003, Doris spent a year as research associate at ActivX Biosciences in La Jolla, before she began her graduate study in organic electronic

materials in the chemistry department at UCLA. In 2006, she interned at IBM Almaden Research Center to study self-assembled polymeric nanoparticles. Doris is now a Ph.D. chemist working at Hewlett Packard laboratories in Palo Alto performing ink-related research. She is engaged to Craig Chang, whom she met at UCSD.1998 Larry Faria

B.S. Structural EngineeringStructural Discipline Practice Leader, CH2M HILL

Faria (pictured in upper right) was recently appointed as the Structural Discipline Practice Leader for CH2M HILL’s Government Facilities

& Infrastructure group. Faria and his wife, Ausa, recently welcomed their second child, Madison Anne, in July 2008. She joins her 5 year old big sister, Lauren Michelle.

2008 Roman KononovB.S. Mechanical EngineeringSoftware Engineer II, Cisco Systems, Inc.

Roman joined Cisco approximately a year before graduation and he has been with the company ever since. “I love every moment of it,” he says, and is part of the

Physical Surveillance Business Unit of the Emerging Technology Group. At Cisco, he works on “bleeding-edge” technologies such as new high-definition (1080p) surveillance camera systems.

1987 Chuck EggersB.S. Mechanical and Aerospace EngineeringAssociate Patent Counsel,Qualcomm, Inc.

Chuck lives with his wife of 14 years, Sandy, and their 11 year old daughter, Remy, in Ocean Beach. Chuck began a transition into patent

work in 2002, leading eventually to a J.D. from the University of San Diego School of Law in 2007. He is currently working at Qualcomm, Inc., as an Associate Patent Counsel.

What’s new with you?Jacobs School Alumni, we want to hear from you! Send us updates on your professional activities and personal achievements. Your class note will be included in our next Pulse newsletter and posted on our alumni website. While supplies last, we’ll send you a Jacobs School cap. Send to [email protected] or visit www.jacobsschool.ucsd.edu/alumni

www.jacobsschool.ucsd.edu/pulse 15 Fall 2009, UCSD Jacobs School of Engineering

Team InternshipProgram

Upcoming Events Oct - April

UCSD Near You San Francisco The Waterfront RestaurantThursday October 29th,5:30PM - 7:30PMEarthquake Safety and the San Francisco-Oakland Bay BridgeDean Frieder SeibleRegister: www.jacobsschool.ucsd.edu/r/UCSDNearYou

Young Alumni WeekendFebruary 12-14th, 20109:30AM - 3:00 PMReconnect with classmates and explore the newest spaces on campus in a fun-filled weekend for graduates from 1999 to 2009!

DECaF: Disciplines of Engineering Career FairFriday, February 19, 2010Corporations and organizations are invited to register now to reserve a recruiting table at DECaF, the Disciplines of Engineering Career Fair. DECaF is an annual student-managed multidisciplinary career fair coordinated by TESC and 20 pre-professional engineering student organizations who work in close collaboration to maximize the attendance of UCSD’s undergraduate/graduate student engineers. Space is limited. Early registration discounts apply until October 31.More information: http://tesc.ucsd.edu/decaf

Research Expo(in conjunction with NAE regional meeting) Thursday, April 15, 20101:00PM - 6:30PMThe annual Jacobs School Research Expo features research posters by 250 M.S. and Ph.D. engineering students, technical breakouts led by Jacobs School faculty, and a reception where guests can interact with faculty and students who share their research interests. The theme of this year’s event is “Renewables and America’s Energy Future” with a keynote address by Larry Papay, CEO of PQR and co-author of the National Research Council report America’s Energy Future (2009). The Jacobs School has the privilege of hosting the regional meeting of the National Academy of Engineering (NAE) in conjunction with Research Expo 2010.More information: http://www.jacobsschool.ucsd.edu/re

University of California, San DiegoJacobs School of Engineering9500 Gilman Drive, Dept. 0403La Jolla, CA 92093-0403

Rajnesh Kirshnan, Lea Rudee Prize Winner, Research Expo 2009

Documents

Pulse - Fall 2009