There is no health risk. The gas contains tracing particles that look like drops of perfume from an atomizer before quickly dissipating.
Detectors have been installed in more than 55 stations and some outdoor spots to see where the vapors go. The collection boxes pull air through filters and capture particles into bags for analysis. About 12,000 samples will be taken this week, federal officials said.
"We're not aware of any specific threats against the subway. We are just trying to make sure that we are prepared," he said.
Researchers also are watching for how and where the particles settle, and whether they re-disperse into the air as trains zoom by.
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The test vapors are called perfluorocarbon tracer gases and present no health or environmental hazard to the public, officials said. Gas will be released for five days at two of three major transit hubs: Grand Central, Times Square or Penn Station. About 5.6 million people ride the New York City subway on an average weekday.
"There will be a lot of information that is not being made public. I think we do want to be careful with what we do say," he said.
Similar studies have been done in Washington DC, Boston and one in New York in 2013 that focused on chemical, not biological, agents, officials said. That study was run in partnership with the city's transit agency, police department and the US Department of Energy's Brookhaven National Laboratory. There also was an airflow study in New York in 2005.