The question is really broad, but I will answer from the experience that I had.
Javascript is not really intended for mathematical calculations, which may be required to quickly compute a large number of E&M phenomena (especially if they are not presented as a closed form solution). It really depends on how many details you want on your graphs (more steps = more calculations). You may need to do more optimizations to make up for the difference in performance.
I did some visualization of antenna arrays (they had closed forms, only simple arrays) in Flash, and everything turned out fine. Javascript will definitely not match any 3D sims you might want to make.
, Silverlight , .NET, ActionScript, ( - ).