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When we calculate the excess pressure on the concave side of the meniscus of the liquid surface formed in a capillary tube, we balance the force by the atmospheric pressure, force by the pressure on the the side of the fluid , and the force due to surface tension, to derive the expression for the excess pressure on the concave side of the meniscus, but, my question is, when we balance the forces acting on a body, we balance the net external forces on a body for it to be in equilibrium, but here the surface tension force is an internal force on the surface, applied by the surface molecules themselves, then why do we include it in the equation for balancing the net external force on the meniscus?

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To the extent that surface tension acts on the sidewalls of a liquid container, it is an external force. Dangling an object in liquid with a wire, one can see the tension in the wire change when a bit of detergent is added to the liquid; that meniscus at the wire-liquid entry point was causing a tug on the wire.

Positive (concave fluid at wall) and negative (convex fluid at wall) surface tension forces are both possible.

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When you cut an infinitesimal volume across the surface and write the equilibrium of forces, you get pressure stresses on the upper and lower sides (assuming a nearly horizontal surface) of the volume and the surface tension on the lateral sides.

Everything here is a contribution of external (surface) forces w.r.t. the volume considered.

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