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Yes, the equation will still have a negative sign in front. When work is done on the system, the change in volume is negative. This negative cancels with the one in the equation, resulting in a positive value for work. This makes sense because when work is done on the system, the value should be positive.
Yes, when calculating the work always use the equation W = - (P*deltaV) and make sure to include the negative sign. If work is done on the system, then you know a compression will occur which means the volume will decrease. If the volume decreases due to compression, then the change in volume will be negative since the smaller final volume is subtracted by the larger initial volume. The negative change in volume when plugged into the equation will cancel out the negative sign in the equation, making the calculated value of the work positive.
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