Volume 6, Issue 4 
Hyuck Choo and David Garmire are PhD candidates in the Department of Electrical Engineering and Computer Sciences. |
Two UC Berkeley graduate students have fabricated a tiny microscanner, a pinhead-sized machine that can rotate a miniscule mirror back and forth 24,000 times every second with great precision. The possible applications are wide ranging, from a heads-up display that paints a video image right on your eyeball to advanced endoscopy tools outfitted with onboard CT scanners for 3D medical imaging right inside the body. Compared to similar technology currently on the market, Hyuck Choo and David Garmire's device not only performs much better, it may also be ten times cheaper when produced commercially.
"Previously, microscanners have been fabricated using complex technology involving multiple steps," says Choo, a graduate student in the Department of Electrical Engineering and Computer Sciences. "Our method is very straightforward, involves only a few processing steps, and uses only tools that are conventional for processing integrated circuits."
A scanning electron micrograph image of the microscanner. |
Under the guidance of professors Richard Muller and James Demmel, Choo and Garmire designed and built their microscanner in UC Berkeley's Microfabrication Laboratory, fabrication site for the Berkeley Sensor and Actuator Center (BSAC). In 2008, BSAC will relocate to the state-of-the-art CITRIS (Center for Information Technology Research in the Interest of Society) Nanofabrication Center currently under construction.
Choo and Garmire's microscanners are quintessential examples of MEMS (micro-electromechanical systems), teensy machines with parts no bigger than the period at the end of this sentence. MEMS are mass-produced on silicon wafers through lithographically-based processes similar to those used to manufacture computer chips. Along with fabricating transistors on a wafer, the MEMS process can also build mechanical features.
A scanning electron micrograph image showing a section of the microscanner comb drive. |
In the case of the microscanner, these mechanical structures form an array of little "fingers" interlocked together. One set of the fingers is fixed to the surface of the wafer while the other, elevated slightly above the surface, can move back and forth when driven by a voltage. Due to its appearance, this type of actuator is known as a comb drive. A mirror actuated by the comb drive can be positioned with incredible accuracy to scan a digital image onto your retina from a projector embedded in a pair of sunglasses, or steer a laser during eye surgery, for example. The researchers demonstrated the latter (sans eyeball) in a laboratory experiment.
"The human eye moves as often as 2,000 times every second and our scanners are fast enough to compensate for this motion," Choo says. "And while the macroscale scanners used now in refractive eye surgery might cost $1,000 or more, ours can be provided for a few dollars are less."
MEMS microscanners are not new, Choo explains. Earlier implementations typically required the fixed and moveable combs to be processed on separate wafers and then assembled together.
"The interleaved combs are on the scale of a few microns (one centimeter = 10,000 microns) so you have to align them with the precision of one micron or less," Choo says. "And that can be very challenging."
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Another previously described method to produce microscanners incorporates an annealing step that takes place in a 900 degree Celsius furnace. If the chip already incorporates any electronic components, the high temperature can easily ruin them.
"All of these steps add cost and lower yield," Choo says. "If the end product is expensive, that defeats the purpose of the MEMS approach. Our simple method lowers the production cost by an order of magnitude and results in an even higher yield."
Right now, the researchers are using their fabrication process to build MEMS-based phase-shifting interferometers, optical phase sensors that measure transient phenomena such as the diffusion of chemicals in human blood or the growth of cells. The newly designed device can make 20 to 30 measurements every second to gather data about a variety of fast changing biological processes. Already, the researchers demonstrated that their technology is 20 to 100 times faster than conventional phase-shifting interferometers.
"Making the new interferometer just demonstrates another application area for our new, diverse, and highly-useful MEMS process," Garmire says.
Fabrizio Bisetti is a native of Italy where he earned a second Master's of Science in Engineering from Politecnico di Milano after graduating from the University of Texas. |
Combustion is the chemical reaction that keeps our cars driving, planes flying, homes heated, and electricity flowing. How can the process be improved to make our automobiles more efficient and reduce the pollution that spews out of industrial facilities? Design better combustion chambers, says Fabrizio Bisetti, a PhD candidate in UC Berkeley's Department of Mechanical Engineering. To aid in that endeavor, Bisetti and his colleagues are simulating the complexity of combustion in a computer.
"We develop physical and computational models for turbulent combustion," says Bisetti, a graduate student in the research group of UC Berkeley professor Jyh-Yuan Chen and winner of the 2006 Chevron-Berkeley Fellowship in Mechanical Engineering. "The idea is to create models that capture the physics in an accurate manner to provide tools for designers in industry."
At its simplest, combustion is a chemical reaction where a fuel such as oil, coal, wood, or natural gas is burned to release energy. The fuel, heated to its ignition point, reacts with an oxidizing gas, like oxygen, and produces heat and light. Turbulent combustion, the focus of Bisetti's work, is a bit more involved. In this case, the interaction between the oxidizing gas and the fuel is marked by a lot of commotion. The molecules behave erratically both in their speed and direction of movement. Turbulent combustion is mostly used for industrial applications because the turbulence helps mix the fuel and oxidizer for an increased burn rate.
"Understanding turbulence has been a problem for the last 100 years," Bisetti says. "Some progress has been made, but not to the point that people can really use predictive tools. Combustion adds another level of complexity to the problem."
Bisetti and his colleagues use esoteric mathematics and statistics to create numerical models that represent the reaction. The math is then used to construct computer simulations of turbulent combustion.The researchers use their own custom software to build the simulations because commercial software, Bisetti says, isn't up to the job. Finally, the simulations are run on supercomputers at the San Diego Supercomputer Center and other research facilities. As the simulations run, their accuracy is checked against real world data provided by combustion research facilities at Lawrence Livermore National Laboratory (LLNL) and Sandia National Laboratories.
"That data is an experimental benchmark for us to test our models," Bisetti says.
Recently, the researchers examined a highly-detailed turbulent combustion simulation developed by Sandia that took a month to run on a supercomputer. Using the Sandia data, Bisetti and his colleagues built their own coarse model that employed statistical techniques and approximations. Instead of modeling every bit of detail, the simulation represents just "the big picture." It also took just a few hours to compute.
"With a turnaround time of a day instead of a month, someone could consider using this for combustor design," he says.
Bisetti believes that someday designers might virtually prototype new combustors and run them in simulation before they're actually built. Today, for example, the emissions from huge gas turbines must often undergo afterburn treatment to minimize the nitrous oxides and carbon dioxide expelled into the air. New designs for combustors that eliminate the need for post-processing while also burning the fuel more efficiently would be welcomed by both industry and environmental advocates.
"Most of the energy in the world comes from burning stuff," Bisetti says. "So even just a little boost in efficiency or reduction in pollution could have enormous impact."
Ian Holmes conducted his postdoctoral research in 2000-2001 as part of the UC Berkeley Drosophila Genome Project. He joined the Department of Bioengineering in 2004. |
What does the work of famed theoretical linguist Noam Chomsky have to do with bioengineering? DNA is just another language that can be translated, says Ian Holmes, a UC Berkeley computational biologist. Holmes is applying Chomsky's theories about grammar and syntax to the piles of genetic data that's emerging from DNA sequencing efforts around the world. The professor of bioengineering's research could someday help shed light on the beginnings of evolution and even inform the development of new antiviral drugs.
"There is so much data available in computational biology today that we don't have to be satisfied with abstract hand-waving hypothesis about evolution, mutation, and selection," Holmes says. "We're trying to actually model evolution in a quantitative way to create a realistic picture of its underlying mechanisms, patterns, rates, and modes."
To do this, the researchers study how the genomes of related species of animals differ. By comparing genes, it's possible to identify the elements of a genome that evolution has conserved, sometimes for billions of years.
"That enables us to reconstruct ancient molecular history and make smarter predictions about where the genes are in the genome and what they might do," Holmes says.
The trick is aligning the sequenced genomes from various species so that they can be combed for similarities and differences. Bioinformatics tools already exist to do this, Holmes explains, but the datasets now available only contain hundreds of genes. What kinds of tools are necessary when thousands, millions, or even billions of genes are available for comparison?
Holmes and his colleagues are developing new tools built to scale up to these massive data sets. They draw freely from such seemingly disparate fields as statistical physics, machine learning, probability theory, and, yes, linguistics.
In the 1950s, Chomsky developed a method to mathematically analyze and describe the grammar of languages. The authors of computer programming languages found inspiration in Chomsky's approach and it's also commonly used in natural language computer interfaces and translation tools. For example, a simple translation system for dialects of English would automatically substitute the American word "diaper" for the British term "nappie" or replace "or" in "color" with "our." A more complex system that can parse syntax would use a "tree tranducer" to make even more advanced substitutions such as "I have already eaten" to "I already ate."
According to Holmes, these kinds of formal rules can be combined in complex ways for bioinformatics as well. While languages like English are based on sequences of letters and punctuation or utterances, the foundation of biology are sequences of nucleotides like DNA and RNA or proteins, the building blocks of all life.
"We're using versions of these grammatical models that can translate one thing into another to make good first approximations of how you can parse a genome into its various features" and relate genes to one another, Holmes says.
Through these translations, the researchers hope to "wind present-day sequences backwards in time to make inferences about our evolutionary past." In one research project, they're exploring a controversial theory in molecular biology suggesting that all life was originally based on RNA, and that DNA and proteins evolved later.
Holmes's tools may have biomedical applications as well, identifying parts of a virus that are evolving quickly or others that have been conserved all the way back to a common ancestor. A protein coding gene that "has been sticking around for a long time might make a good target for a vaccine," Holmes explains.
"DNA is the language of life," he says. "It's a mega cliché, but the cliché hides deep mathematical truth."
Cool Alum: Yasmin Byron
The book only a daughter could write
by Patti Meagher
Yasmin Sabina (Khan) Byron (M.S.'83 CE) in the 1970s with her father, structural engineer Fazlur Khan, whose life, work and genius are the subject of her recent book, Engineering Architecture: The Vision of Fazlur R. Khan.
PHOTO COURTESY YASMIN SABINA (KHAN) BYRON |
It is a story that spans two continents and two generations, the tribute of an American-born daughter to her Bangladeshi father, Fazlur Khan, whose move to Chicago in the 1950s would forever change the field of structural design.
Yasmin Khan Byron (M.S.'83 CE) spent seven years researching and writing the book, Engineering Architecture: The Vision of Fazlur R. Khan, published by W.W. Norton in 2004. It was her first major writing effort in what had been, until 1997, a career in building design in San Francisco and Boston.
"After my father died in 1982, a couple of professors said they would like to write a book about him, but they never did," Byron says. "Then my mom died in 1995. She had been putting his papers together, and I saw how much material was available." After a friend suggested that Byron herself write a book, she realized she could provide a unique perspective.
Regarded as one of structural engineering's great visionaries, Khan is best known for his pioneering high-rise designs for Chicago's 100-story John Hancock Center and 110-story Sears Tower, two of the world's tallest buildings. But perhaps his most brilliant work is one of his last, the immense roof of the Hajj Terminal in Jeddah, Saudi Arabia. Using fabric as a structural material, Khan designed more than two hundred 150-foot-square tents for the airport that shelters the more than one million pilgrims who travel to Mecca each year.
The book's cover shows Khan's design for the Hajj Terminal in Saudi Arabia. A recent review in The Journal of Architectural Education says it is an "eloquent" and "much needed" work that reveals Khan to be "a human being of extraordinary spiritual depth. He appears as a model of what many would like to be."
PHOTO COURTESY OF W.W. NORTON |
"He became involved in tall buildings because he was in Chicago in the 1960s and he started working at Skidmore, Owings & Merrill," Byron says, referring to the prestigious architecture and engineering design firm. High-rise development was increasingly attractive, particularly in New York and Chicago, due to the baby boom, the thriving economy and the burgeoning workforce. Predominant construction styles using multiple columns throughout the floor plan were excellent for carrying gravity load, but not strong enough to resist wind at greater heights. Stiffening and reinforcement could take the building higher, but not without adding considerable expense.
Khan approached this challenge with a bold new structure, a tubular form for the building's entire perimeter. It was a completely new idea that was exceptionally efficient and made the construction of tall buildings economically feasible. He initiated the framed tube in a 43-story Chicago apartment building constructed in 1964, then introduced several variations on the theme including the trussed tube, bundled tube, and tube within a tube, devising a new system for each new building scale. All have become accepted standards for skyscraper design.
Born in 1929 in East Bengal, India (later East Pakistan, now Bangladesh), Khan received his B.S. in civil engineering at the University of Dhaka. Then, on Fulbright and government scholarships, he moved to Illinois for graduate study, unavailable at the time in Pakistan. In only three years at the University of Illinois, Urbana-Champaign, he earned two master's degrees and a Ph.D.
"Although by nature very gentle and philosophical, he was a driven man," Byron says. "I wanted to incorporate these aspects of his personality into the book because people really loved him." Her own work experience gave her the other tools she needed to craft a book that could be appreciated by engineers, architects, or anyone interested in building design. The book has earned considerable praise from architecture and engineering reviewers for its blend of technical detail and personal/historical context for Khan's achievements.
"The book is also a good example for students of how exciting and creative a career in engineering can be," Byron says. It can be found in the collection at UC Berkeley's Kresge Engineering Library.
