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ANY computer program affects the hardware. Running software is what computer hardware is designed for. If by "affect" you mean "damage", it's very unlikely that an application program may harm the hardware except for very rare cases in which running a software could "stress" the hardware up to damaging it; but this would only occur with poorly designed or defective hardware anyway. Poorly designed low level software such as firmware or device driver might damage to their devices as well, but this is something beyond the average user's control and is related to bad design or implementation as well.

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