The Prometheus Project Books 1 and 2--Trapped and Captured, by Douglas E. Richards (DNA Press, 2006 and 2007, 135 and 160 pp, middle grade).
Ryan and his little sister Regan are not at all happy that their parents have moved to the middle of nowhere to take new jobs. But then they find out, with the help of some unintentional eavesdropping, how to break through the security systems that guard the top secret Prometheus Project their parents are working on. Soon they are plunged into an adventure involving a hidden alien city, other worlds, and a bit of computer-engineered time travel on the side....
The second book of the series finds the Prometheus Project under threat from an alien criminal mastermind. Their parents and all the other scientists inside the city are being held hostage, and Ryan and Regan are the only two good guys who haven't been captured. It will take all their intelligence and scientific knowledge to figure out how to foil the evil alien's plan.
Trapped is a book I'm happy to recommend to any geeky type kid, who loves cool machines and science facts and figuring things out (perhaps the kid who really enjoyed the Magic School Bus chapter books). There's lots of science present in the conversations that the two kids have as they try to make sense of of things, as in this example:
"So imagine the force-field surrounding the city is like our skin-- our first line of defense against invaders. The best way to avoid an infection is to not let it enter the body in the first place. Our skin helps prevent an invasion by bacteria, maybe the force-field is there to prevent invasion by...well, maybe invasion by...us."
Regan frowned. "Maybe. But if that's true, it has failed. we did get in. We cut the city's shield." (page 76)
To the adult reader, this sort of almost pedantic discussion might be an impediment to reading enjoyment, but I bet the aforementioned science-minded kid would be more appreciative.
Edited to add: my older boy has now read these, and thought they were fabulous (here's what he said over at his blog, Pickled Bananas). So my recommendation (perfect for technology minded, non-fiction-loving kid) has been vindicated!
Trapped is a well-constructed, very interesting story, qua story, and I enjoyed it. Captured did less for me, primarily because the basic plot (clever kids foil bad guy) is not exactly fresh, and the wonderful mystery of the alien city that enlivened the first book is, by the second, not news anymore. But Captured might well appeal to kids less jaded than me who are looking for an exciting adventure story.
These two books are published by a small press (DNA) that specializes in things scientific. The "small press" part shows a bit, I think, in the cover designs, but these books happily don't suffer from any inadequacies of copy editing. Edited to add again: they now have new covers--the one for Trapped is shown at right.
Here's what The Children's Book Review has to say about these, and another review from The Super Mom (with her look at the second book here).
(note: my review copies supplied by the author)