Yes it definitly can. Therefore you have various options using either the transport of dilluted species or the transport of concentrated species coupled with the reaction kinetics module, you can even simulate reactions between different spicies.
It really depends on what kind of processes you want to simulate and with which accuracy. If you're interested in industry-level accuracy (mostly qualitative results) and diffusion dominated mixing, COMSOL will probably be sufficient. If you're interested in highly accurate results produced mostly by advection-dominated mixing, you should consider writing you own code. That's what I've done.
Yes, the advection-diffusion equation is available in Multiphysics. I did in the past several numerical simulations of mixing processes using Multiphysics. You could download some of my papers here where these simulations are presented.
For most fluids, and in the general case where the continuum hypothesis applies, COMSOL predicts rather accurately the mixing of species. You have to be more careful in the domain of nanofluidics and when you deal with visco-elastic fluids.
Yes, you can. You can either choose diluted species module (or another equivalent, depending on your concentrations) or you can use the levelset method. The documentary help is very useful and clear in ComSol and can help you a lot with the technical details. In specific cases, you can also add equations yourself (or even use a model where you implement your own equations)
We have used it to analysis fluid flow and contaminant transport through a porous landfill. In the solution, COMSOL Multi-physics first modeled steady-state fluid flow by employing the Darcy’s Law Application Mode and then followed up with a transient solute-transport simulation by the use of Solute-Transport Application Mode from the Earth Science Module of COMSOL.
What am trying to say is that it can do it but one must have the deep knowledge of how COMSOL Multi-physics works.
Comsol, or finite element method is suitable to handle species diffusion, but it takes longer than finite volume method to solve the fluid dynamics of the problem. Your decision depends more on the fluid regimen than on the diffusion or reaction phenomena. Comsol isn't the best to deal with the turbulent phenomena required for mixing; it has to use segregated solvers that are expensive in terms of hardware. If your problem is laminar, Comsol is ok, but I would look for finite volume method to solve a turbulent problem, Openfoam or Fluent.
There is indeed a module for Chemical reaction engineering, where you can either import a kinetic mechanism input file or write the equations yourself with the rate constants and also supplementary information (type of reaction, equilibrium or not, third body interactions, enhancements etc.)
Reaction engineering associated with laminar flow, will give very often good results. Nanoflow is another story. The thermal conductivities, viscosity (and other fluid characteristics) can behave (strongly) differently from laminar flow, so that it is not that easy to model in ComSol just using the laminar flow module. You should definitely take into account these aspects (depends again on how "nano" your fluid is).
Flow can alter the mixing quality and thus the probability of molecules "getting in touch" with each other. So, yes. In nanoflow, I am not sure, since the characteristic lengths are so small (maybe even smaller than the mean free paths) that "mixing", if we may speak about that in such a way, could have less influence (keeping in mind that I am not sure whether you can simulate nanoflow by using NS equations).
As long as you specify the rate constants of each intermediate reaction and its dependence on the concentration of the intermediate species. This can be done easily in the Reaction Engineering Module.
I would agree that using moles is easier compared to mass/liter since we are going to have two inputs: one with 100% concentration and the other woth 0% concentration.
At nanoflow, we expect the flow to be laminar. We are wondering whether results will be that much different if we assume Newtonian fluid (as opposed to using non-Newtonian fluid model)?