Well in ST they used navigational deflector shields to protect the ships from radiation, light debris, micrometeorites and other annoying particles.
It would seem the best appoach for a mission to Mars would be to assemble the vehicle in orbit. That way you don't have to launch one large massive vessle in one shot. Of course this delays any chances of hitting Mars for a while, but that is already to be expected.
I wonder how much of the radiation is from solar activity, flares and ect. Also I wonder how strong an electromagnetic field would have to be to deflect some of them.
And just to show off what a geek I am, Heisenberg compensators in ST were used in transporters to overcome a problem that exists in modern quantum mechanics, the Heisenberg Uncertainty Princible. In modern quantum mechanics, you can accurately determain the course or the momentum of a sub-atomic particle but not both at the same time. This makes it extremely difficult to accurately track motions of sub-atomic particles. In ST, the Heisenberg compensators (I would assume) magically overcome this dilemma and allows transporters to accurately determain both speed and course of sub-atomic particles (a miracle in itself required to accurately dissassemble and reassemble matter).
Werner Karl Heisenberg (1901-1976) I feel bad, how many teenagers did you know that read Stephen Hawking's books? I started reading them when I was 13. I got to post my picture sometime soon to refute my geekiness, but darn, I am overdue for a haircut and haven't had the time to see my barber (I only trust one person on Earth to touch my hair).