April
2005
Katherine Yelick is also a researcher with the Center for Innovative Technology Researcher in the Interest of Society (CITRIS). (Peg Skorpinski photo) |
Imagine that along with your medical records, your doctor had access to a digital doppelganger of you. The "software you" would be a 3D image-based simulation of your body. Physicians could practice minimally invasive surgery on the computer simulation long before you enter the operating room. Drugs, represented by mathematical equations, could be administered to your virtual body to identify any side effects that you may experience over the course of a real treatment. Of course, building a digital body double is a tremendous challenge for computer scientists, requiring innovative new algorithms and tremendous processing power. UC Berkeley computer science professor Katherine Yelick has put her heart into just this kind of high performance computing.
"The long term goal is to have a complete enough model of a human body that it could be specialized to a particular individual," says Yelick, a researcher with the Center for Innovative Technology Research in the Interest of Society (CITRIS) and leader of Lawrence Berkeley National Laboratory's Future Technologies Group. "In the shorter term, simulations of individual organ systems will help doctors understand the physiology of how the body works and test new prosthetic devices."
In this still image from the simulated cochlea, a sound wave can be seen caught in the middle of propagating down the membrane. |
Yelick's focus is developing software that can simulate the flow of fluid within the body, from blood through the heart to the effect of sound waves on the inner ear. Of course, scientists commonly employ computers to model fluid dynamics in mechanical systems. However, blood pumping through the heart or coagulating into clots is quite different from, say, oil flowing through an airplane engine.
"An engine is a rigid body, but skin, muscles, and arteries are not," Yelick says. "When the fluid pushes on tissue, it moves, and vice versa."
Yelick's approach to modeling these kinds of elastic structures submerged in fluids is based on an algorithm called the "Immersed Boundary Method" developed by mathematicians Charles Peskin and David McQueen at New York University . While the method is effective for modeling everything from parachutes to insect flight to the swirl of blood in the heart, simulating organs with enough resolution for many medical applications requires that the algorithm run on hundreds of computer processors working in tandem.
A visualization of the flow of blood through the heart's aortic valve, created using the immersive boundary method. |
To make medical visualizations spring to life, Peskin's former graduate student, Ed Givelberg, spent two years in Yelick's group designing a way to run the immersed boundary method on systems of massively parallel processors. That way, the difficult mathematics can be broken up into manageable chunks across the multiple machines. Peskin then built a simulation of the inner ear on top of his Immersed Boundary software.
The simulations themseles are written in Titanium, a new programming language that Yelick developed with UC Berkeley computer science professors Susan Graham and Paul Hilfinger. Titanium enables the massively parallel computer systems to be programmed with a variation of the common Java computer language. (Java was invented by Berkeley alum Bill Joy.)
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Recently, graduate student Armando Solar-Lezama used Titanium to rewrite an efficient simulation of the heart first created by Peskin and McQueen. So far, they've run the code on systems containing 128 processors. Soon, they hope to scale up to several hundred processors to generate a much finer model of the fluid dynamics.
"If you're just trying to make a heart beat, you can get by with a coarse model," Yelick says. 'But we want to understand things like how the muscle fibers contract and what happens in the vortices behind the heart valves."
While Yelick and her colleagues have tested their code on models of the heart and inner ear, the goal, she says, is to "build a generic piece of software that people could use to model multiple organs." Once simulated hearts, kidneys, brain, lungs, and other organs spring to life on the screen, they could then be linked together into more complicated biological systems. For example, electrical data from a nervous system simulation might trigger a virtual heartbeat. Then, Yelick explains, individual data from medical imaging data, laboratory tests, and medical histories could possibly be used to build a customized digital you.
"Even though most of these applications are far away, it feels good to know that what you're working on might someday save lives," Yelick says.
Hunting for Black Gold
by David Pescovitz
James Rector is an associate professor of GeoEngineering. |
In the classic Clark Gable and Spencer Tracy film Boom Town, the characters determine where to drill for oil by looking at the lay of the land. In reality, a lot of black gold was found that way. Wild catters looked for telltale topographical signs that indicated underground reservoirs. These days though, the tried-and-true technique doesn't work so well. The oil and gas reserves in this country are depleting rapidly, requiring a high-resolution view of the subsurface long before the big drills are brought in. To create these images, UC Berkeley professor James Rector applies technology more commonly seen in the doctor's office.
"To find oil and gas in the United States , we have to look for smaller and more complex reservoirs that may only be a few meters thick," says Rector, a professor of Civil and Environmental Engineering. "That requires much more sophistication in the way we collect our seismic data, process it, and then interpret what we see."
Fifteen years ago, oil companies began using ultrasound systems--similar to the devices physicians use to visualize a fetus in the womb or monitor blood flow through the heart--for three-dimensional seismic imaging. At a possible drilling site, companies use "thumper trucks" outfitted with huge vibrating mechanisms to generate seismic waves that travel deep into the Earth.
"It's much more advanced than medical ultrasound," Rector explains. "The body is essentially a fluid except for the bones. But the earth is a much more complex media that we have to propagate through."
As the wave moves downward, it's reflected differently depending on the kinds of rock it encounters. The reflected waves are then detected and measured by a sensor back on the surface. That data can is finally combined into a 3D image that reveals the boundaries of the rock formations below the surface.
The problem, Rector says, is that these aboveground methods often do not provide the fidelity necessary to find the small reservoirs and understand their structure. His approach is to put the ultrasound system closer to the action, as much as 38,000 feet underground.
This cross-section of the earth was obtained using seismic reflection techniques. The colors represent formation impedance, a production of density and velocity. That impedance, combined with the structure of the area, may indicate where gas or oil may be trapped and recoverable. (courtesy the researcher) [View larger image] |
The first step though is for companies to get comfortable with the technique--called borehole seismic surveying--by using it to help calibrate and understand their aboveground 3D images. According to Rector, dropping either the receiver or ultrasound source into a borehole can increase the resolution of the image by a factor of two. One reason for the improvement is that the seismic wave doesn't need to travel all the way down into the Earth and back out before it's detected.
"Eventually, the entire survey could be moved underground," Rector says.
If the source and receiver are properly positioned and tuned, this approach--called a "crosswell survey" because the waves travel from well to well--could improve the resolution of the 3D images by a hundredfold, Rector says. Besides painting a better picture of the subsurface, borehole seismic surveys may also cause less disruption to the area under study.
In March, the US Senate voted to allow drilling in Alaska 's Arctic National Wildlife Refuge (ANWAR). If the ecologically-sensitive area is to be tapped for oil, Rector believes that borehole seismic surveys could reduce damage while the reservoirs are sought out.
"Drilling for borehole seismic surveys in a very limited area deep under the permafrost would have very little environmental impact," he says.
Currently, Rector and his research group are identifying the ideal depth and placement of the ultrasound and receiver to get the most bang for the survey buck. Another challenge is taking essentially a geometric image of the subsurface and trying to suss out the composition of the material between the layers. Ultimately, Rector says, the aim is to actually detect the oil and gas directly rather than surmising its existence.
"That's what gets me up in the morning," Rector says. "I love the chase."
Ashok Gadgil is currently developing a simple water filter made of ash coated with a compound that attracts arsenic. (courtesy Berkeley Lab) |
Every day, those of us who live in the United States use on average a couple hundred gallons of clean water per person. According to the World Health Organization though, 1.1 billion people around the world lack access to safe water. Dirty drinking water is to blame for approximately 240 child deaths every hour, almost all of them occurring in developing nations. In the next few months though, technology developed by Berkeley Lab scientist Ashok Gadgil will bring clean, low-cost water to 25,000 residents of 10 Indian villages, demonstrating one way that this massive health problem might be addressed worldwide. Just don't call it charity.
"The only way this kind of thing can be sustainable is if it makes financial sense for everyone involved," says Gadgil, a member of the lab's Environmental Energy Technologies Division.
Water taps at one of the new Andhra Pradesh water stores. (courtesy WHI) |
Several years ago, Gadgil developed a novel water purification system that kills disease-causing microorganisms using ultraviolet light. The University of California licensed the technology to WaterHealth International, a southern California-based company that markets the systems around the globe. Already, the product, called UV Waterworks, is used to prepare water for sale by local entrepreneurs at urban stores in the Philippines . And in February, the first water store opened in a rural village in the Andhra Pradesh state on the eastern coast of India.
"It was amazing when I saw the first photos of these villagers carrying four gallon jugs of disinfected water that they bought for two cents," Gadgil says. "They can now demand quality because they're paying for it."
Over the next few months, WaterHealth International's community water systems will be installed in villages that have agreed to pay for the treated water as part of a pilot project. A local non-profit organization, the Naandi Foundation, will train local technicians and educate the public on the need for safe water and good sanitation.
"We team up with local organizations because they understand the language and the culture," Gadgil says. "People in the villages trust them."
WaterHealth International's UV Waterworks system. (Photo by Robert Couto, CSO) |
Pathogens that thrive in drinking water cause debilitating and potentially deadly diseases like cholera, dysentery, and diarrhea. In the Andhra Pradesh region, diarrhea alone causes about 70,000 deaths each year. Gadgil's system kills the microbes by channeling the contaminated water under an ultraviolet light source suspended in a reflective dome. If traditional electrical power is not available, the low-power UV Waterworks system can draw its juice from car batteries or solar panels.
According to Gadgil, a single community water system can provide a village of up to 3000 people 10 liters of safe water per person each day, adding up to an annual water bill of approximately $2 per individual. The proceeds will cover the purchase of the UV system along with pumps, tanks, valves, controllers, civil structures, and maintenance. Besides periodic cleaning and upkeep of the filters and pump, the only expected maintenance "is for someone to change the ultraviolet lightbulb once a year," Gadgil says.
The Andhra Pradesh pilot project is partially funded by GlobalGiving, an online service that's something like a matchmaking service for donors to directly help fund social, environmental, and economic development projects. The safe drinking water effort was one of five projects that split $100,000 in prize money awarded by GlobalGiving and the Global Philanthropy Forum, a project of the World Affairs Council of Northern California. On a broader scale, Gadgil's work dovetails with the College of Engineering 's efforts to harness technology for sustainable development.
"Through organizations such as Engineers for a Sustainable World, many Berkeley students are using their vacations to design and implement water purification projects in places like the slums of Bombay ," says Thomas Kalil, Special Assistant to the Chancellor for Science and Technology. "Dean Richard Newton and I are committed to providing even more Berkeley students an opportunity to participate in these kinds of high-impact projects by launching a 'Technology Peace Corps.' Ashok's work and related research by Berkeley engineering faculty are powerful examples of technology being used to improve the human condition."
Bicyclists pick up bottles of clean water to deliver to villagers. (courtesy WHI) |
Gadgil's eyes light up with excitement as he clicks through digital snapshots emailed by his WaterHealth International colleagues who spent weeks in the villages getting the system operational. One photo depicts villagers holding sheets of perforated certificates that they exchange for refills. Another shows children on bicycles toting jugs of water.
"Now a secondary industry has developed where kids will deliver your water so you don't have to carry it back from the store," he says.
As water from the Andhra Pradesh project begins to flow, Gadgil has begun development of a new kind of water filter that could help millions of Bangladeshis. Resembling a tea bag, the filter is a pouch filled with powder derived from coal ash that sifts out the poisonous arsenic tainting so many Bangladeshi water sources. Gadgil estimates that the filters would cost about 30 cents per person per year.
"I get the most satisfaction from applying the advanced science and engineering that so many of us know to help people who don't have those kinds of resources," he says. "The potential for societal impact really fires up my passion."
Cecilia Aragon (M.S. '87 CS) |
Shortly after completing her master's degree, Cecilia Aragon (M.S. '87 CS) earned her pilot's license, became an air show pilot, and was a two-time member of the U.S. Aerobatic Team. Now, she has returned to Berkeley after a 14-year hiatus from her studies to complete her doctoral degree in computer science, where her passions for flight and mathematics merge.
"It's so exciting being back in school," she says. "Berkeley is really at the forefront of this kind of work."
As a computer scientist in the computational sciences division at NASA Ames Research Center in Mountain View, Aragon's work involves the study of local wind shear and other airflow hazards in the search for ways to improve air travel safety. With more than 5,000 accident-free hours in flight, she may have a more personal investment in keeping the skies friendly.
"I have these two viewpoints that not many people have, and I want to use them to make a difference," Aragon says. "People involved in aviation tend to be very specialized. I've known 20-year veteran aircraft designers who have never been in the aircraft they were designing for."
Once painfully shy, late to ride a bike, and nervous about driving a car with a stick shift, Cecilia Aragon (M.S.'87 CS) is quite at home in her custom-built Sabre 320, which climbs at 4,500 feet per minute and has a roll rate of 420 degrees per second. |
Aragon has developed a cockpit display system that displays invisible air currents to warn pilots of impending disturbances in the air. The system was incorporated into a high-fidelity rotorcraft simulator and tested by 16 U.S. Coast Guard and Navy pilots, with dramatic results: For hazardous landing approaches in highly turbulent conditions, the hazard indicator reduced the crash rate from 19 percent to 6.3 percent.
Perhaps the most dramatic thing about Aragon, however, is that she used to be deathly afraid of heights, a fear she aggressively conquered after a flight in a private plane over the beautiful San Francisco coastline. ("I was in heaven," she recalls.) Now she fearlessly executes air tricks like multiple snap rolls and tailslides.
"Mastering my fear gave me a feeling of confidence that has carried over to other parts of my life," Aragon says. "Let's face it. Compared to pointing the nose of an airplane straight at the ground and flying vertically down at 200 miles an hour, everything else in life seems easy."
