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Well, I cant say nothing about aero dynamics :3
But for eg, macs have a certain way of getting the air in, When the case is on, it will be cooler because it directs the air.
But i guess you just have a PC, Leaving the case open lets more air in, But it's not directed like it is when it's on, You should have 1-2 fans blowing air in the front, Then 1-2 fans at the back blowing air out, Then another fan blowing in on the side of the case, That's if you have fans on your side cover.
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If your GPU is over heating probly you will have to replace it, i had the same problem.... the GPU fan was fucked and it kept overheating.
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69 c is a normal temperature for a GPU
Generally leaving your box open is stupid, it was made to be closed. If your box is open your letting dust and foreign particles get into it easier, which could screw up your pc parts (I've seen this happen one to many times)
Open = bad
Closed = good
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Good case manufacturers (Antec for example) design their cases to ensure that closed case airflow keeps the important components as cool as possible, closed case is always better, because if it is open, air flows right out the case!
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The main thing a pc case + fans do is remove the hot air as fast as possible from your components and NOT bringing cold air inside so having one side of the case open helps. I don't know how some people manage to break their components and blame dust, the thing is that I've been without a side on my case for well over a year now and the last vacuum clean up I did was the day I took the side down and my computer is still up and running