I think Harvard is going to be very tough, as I believe they have some hard cut-offs for GPA. Doesn’t mean you won’t get through the first round though. However, despite your GPA, I think you have a very compelling story and the URM hook. If you nail your essay, I think you’ll be a very strong candidate for a lot of schools.
Some questions: what’s your home state? Do you have safety schools already in mind? What are the classes that you struggled in/that contributed to the ding on your GPA? (mainly I’m wondering/hoping that your grades tell a story that your math/sciences are strong, since that’s what you want to do) Can you take the SAT IIs in some Math/Sciences in the fall? (will make you more competitive at top schools if you score well) What do you want from a school?
If you let us know some of these, we can help you come up with a well-rounded list. Admittedly, a lot of the top neuroscience schools are going to present a similar conundrum as Harvard–they’ll be extreme reaches for you based on GPA, however if you can tell the right story via your essays/grades/app, you may have a shot. But you’re going to need some really robust safeties & matches, especially financial safeties.
And if you haven’t seen it already, I recommend reading through these successful essays so you can figure out how to frame yours: http://www.nytimes.com/interactive/2015/05/20/your-money/college-essays-on-money.html?_r=1