We've successfully computed the reflectance from a multilayered system of glass, organosilanes and gold nanoparticle films (SEE ATTACHED FIGURE) using the transfer matrix method, and treating the gold nanoparticles as an effective medium theory defined in this paper:

http://www.sciencedirect.com/science/article/pii/S0009261499012063

The results were actually quite good.   It's cool that the film of gold can be approximated using an effective medium theory, such that the heterogenous gold/water mixtures can be parametrized by a single complex index of refraction, n.  

I'm trying to extend this process to model films that contain gold AND silver nanoparticles (maybe of different sizes), and complex morphologies such as nanorods.  This is where my understanding is lost.  

There's a great deal of research out there on numerical analysis on exotic nanoparticles, but most of it involves the computation of single-particle properties: for example, the extinction spectrum of a nanorod.  Where I get lost is what implications does this have for the film?  I can model a film of nanospheres just fine, and I can compute the optical properties of a disperse solution of nanorods using DDA or FDTD, but how do I model a FILM of nanorods?  How could I compute the reflectance from an array of nanorods on a glass slide?  We'd expect the reflectance from nanorods to be different than nanospheres; however, how would this manifest in an effective medium theory?  In other words, can I still represent this film of nanorods with a single parameter, n?  Presumably n for nanorods would be similar to gold, but not identical.  

What is the correspondence between near-field features like particle shape, and the effect they have on the far-field properties of the film?  In other words, is it possible to predict a single index of refraction, n, that would parametrize an entire film of complex morphologies (eg rods), or multiple particle types (eg gold and silver nanospheres), similiar to how this was done for a layer of just gold sphers?  And if so, is there a theoretical prescription?  IE a cooking recipe from start to finish that would start with individual particle properties and then spit out an index of refraction approximation of the film?  Is there a way to take near-field features like aspect ratio of a nanorod, and say how this would contribute to the effective index of refraction of the film, n?

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