HPCwire: Connecting the Virtual Human

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March 28, 2008

Connecting the Virtual Human

by Aaron Dubrow

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Ranger helps scientists model 3-D blood flow through the arterial tree

March 26 -- George Karniadakis' conversion to computational science as a PhD student at the Massachusetts Institute of Technology was practically a matter of necessity. "After burning my eyes several times doing an arc welding experiment with very high radiation, I said, 'Forget it, I'll simulate the whole thing.' From there I started simulating all kinds of things."

Bats in flight, crashing waves, the jolt of churning pistons -- as a professor of applied mathematics at Brown University, Karniadakis has simulated all of these phenomena. But for the last decade, he has focused his attention on computational biology, developing and optimizing algorithms to model blood flow through the human body.

His research is in the spirit of the Physiome Project, a corollary to the Human Genome Project that precisely maps the workings of the body, from the molecular level to the entire system, to establish essential information about how the body works. With research teams around the world working on computer models of the heart, the kidneys, the lungs, and other physiological systems, Karniadakis focuses on the arterial tree -- the link that connects all of these systems -- to reconstruct and simulate the arteries of a virtual human with greater accuracy than ever before.

Using Ranger, currently the world's most powerful supercomputer for open science research, Karniadakis and his team will soon create the first fully three-dimensional model of the arterial tree. Integrating multiple scales of vessels throughout hundreds of connected branches, Karniadakis' study may one day help clinicians obtain quick and accurate information about how a blocked artery will affect blood pressure or how efficiently drugs are dispersed in the bloodstream.

His decision to study the arterial tree derived in part from past failures with single-system simulations. "We have seen, when we do simulations, that what happens in the carotid artery affects the entire brain, and in fact the entire body," Karniadakis said. "These are global interactions, and unless you include them in a more integrated systems approach, you will miss important interactions, especially when you have pathologies."

This insight led Karniadakis to model the vast highway of vessels that connects our vital organ and feeds our cells oxygen, energy, and other necessities. The arterial tree is composed of three systems: the macrovascular system, made up of arteries only a few millimeter in diameter but clearly visible under the skin; the mesovascular system with arterioles (100 microns in diameter) that split from the arteries like branches of a tree; and the microvascular system, made up of capillaries so narrow (5 microns in diameter) that red blood cells have to hunch to travel their length.

To simulate this three-level arterial tree, computational scientists translate clinical data about blood pressures and flow rates from a real patient into a computational grid. This grid is mapped onto the complex geometric architecture of the blood vessels using a mesh of triangles, pyramids and tetrahedrons. As the elements that represent the distinct points of blood flow travel over hundreds of time-steps -- the equivalent of dozens of cardiac cycles -- they speed or slow, or head down a capillary, based on their location and flow rate within the arterial tree.

Even with Ranger's unprecedented computational power, it is impossible to fully model these three scales of vessels. "Our body has several thousands of arteries, millions of arterioles, and billions of capillaries," Karniadakis explained. But, with thousands of processors and careful computational algorithms, Karniadakis and his team can get closer than they ever have before.

"At the macrovascular level, we know the equations and the geometry and everything is very accurate," Karniadakis said. "But at the mesoscopic and microscopic level, we cannot image the vessels, therefore we don't know their exact diameter. So we have to improvise."

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