We introduce the concept of Potential of Mean Force, PMF, as a way to implement upscaling modeling from the nano-scale to micron-scale. A PMF is a free energy function representing in an effective way the interactions between objects (cement hydrates, clay platelets, etc.) at thermodynamics conditions. The PMF is therefore the key piece of information allowing to coarse-grained Physical-Chemistry information in a meso-scale model formulation. The use of PMF offers a huge computational advantage as it allows a straight up-scaling to the meso-scale while keeping essential interactions information that are the hallmark of Physical-Chemistry processes. Such a coarse-grained modeling integrates atomistic response into inter-particle potentials that fully propagate molecular scale information all the way to the meso-scale.