Using a supercomputer, a team of scientists from Los Alamos National Laboratory in New Mexico, the University of Washington and the Fred Hutchinson Cancer Research Center in Seattle, have simulated an H5N1 epidemic. The idea was to understand the spread of the virus in the continental United States and to develop possible epidemiological control methods:
“Based on the present work … we believe that a large stockpile of avian influenza-based vaccine containing potential pandemic influenza antigens, coupled with the capacity to rapidly make a better-matched vaccine based on human strains, would be the best strategy to mitigate pandemic influenza,” say the authors, Timothy Germann, Kai Kadau, Ira Longini and Catherine Macken…
“In the highly mobile U.S. population, travel restrictions alone will not be enough to stop the spread; a mixture of many mitigation strategies is more likely to be effective than a few strictly enforced ones,” said Kadau, also of Los Alamos’ Theoretical Division.
The model of disease transmission involves probabilities that any two people in a community will meet on any given day in any one of a number of settings, such as home or workplace. Thus, simulated disease transmission is more likely for two people in the same household and less likely for two people who have less in common. “So we are only computing the probability of any person becoming infected on any given day, and a roll of the dice is needed to decide whether they are infected or not,” said Germann.
Other elements of randomness modify the simulated disease course. A significant fraction of infected people (33 percent in the present model) never develop clinical symptoms, although they are themselves infectious. In addition, the durations of the incubation and infectious periods can vary and are randomly chosen from distribution functions for each individual, involving more throws of the virtual dice.
“Computer models serve as virtual laboratories where researchers can study how infectious diseases might spread and what intervention strategies may lessen the impact of a real outbreak,” said Jeremy M. Berg, director of the National Institute of General Medical Sciences. “This new work exemplifies the power of such models and could aid policymakers and health officials as they plan for a possible future pandemic.”
The pandemic simulation model has been implemented in the Laboratory’s celebrated Scalable Parallel Short-range Molecular dynamics (SPaSM) large-scale simulation platform developed for the nuclear weapons program. It runs on the Los Alamos supercomputer known as Pink, a 1,024-node (2,048 processor) LinuxBIOS/BProc “Science Appliance” running Clustermatic 3, the largest single-system image Linux cluster in the world. Pink’s nodes have dual 2.4 GHz Intel Xeon processors (Pentium 4) with 2 gigabytes of memory per node. The purchase of the Science Appliance was funded by the National Nuclear Security Administration’s Advanced Simulation and Computing program. Pink is currently a system software research platform, a science appliance cluster concept invented at Los Alamos in the Computer and Computational Science Division. Los Alamos has four science appliance clusters in use at this time for a variety of projects across the full range of Laboratory mission areas.