Developing a Digital Lung
Ching-Long Lin loves his work.
The IIHR research engineer is a key player in a project to develop a digital model of the human lung. Lin, who is also a professor of mechanical and industrial engineering at the University of Iowa, has received three grants from the National Institutes of Health (NIH), including a fouryear, $1.4 million grant in 2010 to help further his study of the interactions among pulmonary airflow, lung mechanics, and cell response. Lin serves as project director for the grant, which is supporting development of a digital human airway defense system.
Lin is engaged in a productive partnership with Dr. Eric A. Hoffman, a faculty member and researcher in radiology at University of Iowa Hospitals and Clinics. “It’s turned out to be a good collaboration,” Lin says. “I’m lucky to work with Dr. Hoffman.”
Hoffman leads the Iowa Comprehensive Lung Imaging Center, which conducts computed tomography (CT) scans to study the structure and function relationship of the human lung. Scientists and physicians use CT images to evaluate distribution of air in and out of the lung for exchange with the blood. Hoffman has conducted hundreds of these scans, which Lin uses to develop a detailed geometrical model of the lung.
Lin’s computational fluid dynamic (CFD) model simulates the flow of air through the lung. Until recently, the model was restricted to the trachea and one section of the lung, due to limits on computer processing. The complexity of the task is increased by the extreme variance in scale, which ranges from the biggest trachea to the microscopic level deep in the human airway. Lin’s multiscale model can analyze more than 20 levels, or generations, of the human lung.
“It’s really challenging,” Lin says. “We are the only group that can do this.”
A new parallel high-performance computing cluster at the University of Iowa, created by a partnership of researchers and IT professionals, is playing an important role in the digital lung project. In 2008, Lin received a $473,636 Shared Instrumentation Grant (SIG) from the NIH to support cardiopulmonary computing and imaging. Lin and 11 other UI researchers pooled their funds to purchase a high-performance computing cluster—known as Helium or “He”—to provide the computational power their research requires.
A 2011 UI grant doubled Helium’s processing power. Helium harnesses the computational power of 3400 total cores, 10.6 TB of memory, and more than 500 TB of storage. Mark Wilson, director of research computing at IIHR, says researchers in many disciplines rely on Helium’s highperformance computing tools and methods. “The cluster cuts run times dramatically,” Wilson says.
Wilson credits Lin for bringing cluster computing to the university. “Ching-Long had a larger vision,” he says. “Without him, this never would have happened.” Lin, in turn, says it would have been almost impossible to build the cluster without Wilson’s expertise. “He is really good.”
The Physiome Project
Lin has also established a stereoscopic 3D visualization laboratory, enabling the analysis of large datasets on GPU-based workstations. He hopes to be able to present the results of his CFD work as 3D visualizations. “CFD scientific computation is one thing,” he says. “Presenting your result in this very fascinating way is also important.”
Before Lin joined the digital lung project, he conducted research using fluid mechanics and advanced CFD algorithms to study atmospheric boundary layer and two-phase flows. In 2004, Hoffman invited Lin to apply his knowledge of fluid mechanics and his expertise in highperformance computing to the human lung. “It is a
very interesting area,” Lin says.
The UI team’s work is part of a worldwide initiative to understand the vast scale of human biology. Known as the “Physiome Project,” Lin’s digital lung is a crucial piece of this human puzzle.
Can Work Be Fun?
For Lin, the work continues to be rewarding. “I enjoy it,” he says. And that includes interacting with students. “I am lucky to get good students,” he
says. “I try to encourage their strengths.”
Graduate student Shinjiro Miyawaki came to Iowa from Japan to study river hydrology, and found his way to Lin’s digital lung team. Miyawaki’s main role on the team is to simulate tissue motion in the lung through CFD modeling. “It’s really exciting,” Miyawaki says. He also appreciates the respectful way Lin listens to student ideas.
Lin says he tries hard to avoid putting too much pressure on his students. He hopes that they will find a profession, as he has, that keeps them motivated. “As long as they can get a job and be happy, that’s all right,” Lin says.
The digital lung project is a collaboration between the UI College of Engineering and the Roy J. and Lucille A. Carver College of Medicine. Lin’s UI colleagues include Hoffman and Dr. David A. Stoltz, professor of internal medicine.