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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.)

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."

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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.

Kathy Yelick's home page

"Adaptive Computations for Fluids in Biological Systems" (EnVision, October-December 2000)

"Kathy Yelick Named Leader of Berkeley Lab's New Berkeley Institute for Performance Studies (BIPS)" (Berkeley Lab, 11/8/04)

Berkeley Institute for Performance Studies

Future Technologies Group at Berkeley Lab

Center for Information Technology Research in the Interest of Society (CITRIS)

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