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What is the definition of rate $(−ra)=−\frac{dCa}{dt}$ or $(−ra)=−1/V\frac{dNa}{dt}$ ? I think the general one is the second one and first one is for constant volume reaction system. Is the above written rate equation only valid to batch reactor? If not can we use this in a PFR or MFR? In PFR we know the rate comes out to be $(−ra)=−\frac{dFa}{dV}$ ,can we equate $−1/V\frac{dNa}{dt}=−\frac{dFa}{dV}$? If not then why? Is the rate equation not valid everywhere? Can we equate with CSTR as well ? eg $-\frac{dCa}{dt}=\frac{Fa_o-Fa}{V}$ (considering it a constant volume reaction system CSTR)

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You are correct in saying that reaction rate $(−ra)=−\frac{dCa}{dt}$ is for constant volume systems and that the more general form is or $(−ra)=−1/V\frac{dNa}{dt}$.

The general reaction rate equation is the basis for all the types of reactors you mentioned, see the link below for the derivation explanation.

http://www.the-seventh-dimension.com/images/textlev/LEVENSPIEL%20Chemical%20reaction%20engineering-ch4-ch5.pdf

The form of the rate equation as shown should be valid everywhere within the vessel, so long as the limits of integration used to describe the situation are correct. If for example, a vessel has a significant dead volume due to the flows not being properly directed through the vessel (i.e. the "well mixed" assumption is not being satisfied), then the ideal results generated from this equation may deviate significantly from actual data.

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