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I have a vacuum chamber with a pressure 10-8 Torr. Then I open an Oxygen valve with a set flow of 2 sccm from a tank with a pressure of 2 bars. The pressure in the chamber decreases to 10-2 Torr. What is the partial pressure of the Oxygen in the chamber?

Is it 10-6 Torr or 10-2 Torr?

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The pressure increases, not decreases, to $10^{-2}$ Torr. As there is (almost) nothing in the chamber except oxygen, it contributes all the pressure. Note that $10^{-6}+10^{-8} \neq 10^{-2}$ The flow does not matter at all.

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