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A few days ago, a Russian water reclamation system took up smoking. The smoke that was produced traveled through the air ducts and was thus propagated throughout the station.

According to the article, ground controllers 'isolated' the US ventilation from the Russian system:

The ventilation system for the station's Russian segment was isolated from the U.S. Operating Segment with commands issued by NASA flight controllers.

How is this accomplished? Is a tube connecting the Russian and American side literally blocked?

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I don't know of any specific explanations of that particular issue, but in general it sounds like a fairly standard ventilation fire suppression system. This paper is one example of fire prevention in ductwork; in large buildings in the US and other countries being able to isolate sections of the buildings automatically would be required by building code. In the answer to your direct question, it is likely that the ductwork connecting the Russian and the American side is indeed literally blocked (with a damper).

This Boeing article discusses shutoff systems and other fire prevention systems, and as well discusses the separate ways the Russian and US segments add oxygen to the air mix in the Atmospheric Control and Supply section. This answers the obvious followup question "If it is blocked, how do they breathe?"; as with many things on the ISS, there are backups for the backups - in this case, independent atmospheric systems.

This paper shows some interesting cross sections of the ventilation system, and while it is focused on acoustic abatement, it is pretty easy to see how you might implement fire abatement blocks in the system.

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