What is simplest way to join particles into a single mesh and modify during animation? I would like to modify the mesh from a particle system during animation. Without some way to join all of the particle object meshes together, modifiers like smooth do not work as needed.

What is the simplest way to create a single mesh from a particle system at each frame in an animation so that other modifiers can be applied like Smoothing?
A single mesh can be created from a particle system by using modifiers.


Create a particle system. For this example, also create a container to keep the particles in a volume.
Add a cube which fully encloses the particle system and its container. After some simulation, the geometry will look like this:





Add a sphere which will be used to display the particle system. Any manifold object can be used. If non-manifold objects are used, this solution will not work.
Add a modifier to make this sphere a particle system instance. At this point, each sphere is a separate mesh. Therefore, filtering modifiers operate on each sphere, not the combined mesh. 


 



Add a modifier to perform an intersection with the particle system and the largest cube. This will create a single mesh from all of the spheres.
Add a Laplacian Smooth modifier. The mesh will be smoothed eliminating the appearance of intersecting spheres.


 



Now other operations like Booleans can be applied.