The US government spends billions of dollars on research each year and much of it requires software development to some degree. Much of this money goes to the big guys like Boeing or Lockheed Martin, but a non-trivial portion of it is reserved for small companies as well. In any case, there are lots of programming jobs out there doing research, either directly or indirectly, for the government.
I happen to work for a small company that does contract research and software development for the gov't. We pride ourselves on writing solid, maintainable scientific software. To accomplish this goal, we need programmers and scientists, but most of all we need programmer-scientists. We are hiring (message me if you want more info), but I'm sure there are other companies out there as well.