This thesis describes searches for new particles predicted by the super symmetry (SUSY) theory, a theory extending beyond the current Standard Model of particle physics, using the ATLAS detector at the CERN Large Hadron Collider. The thesis focuses on searches for stop and sbottom squarks, the SUSY partners of the top and bottom quarks, which are expected to be lighter than the partners of the first and second generation quarks and therefore good candidates for the first evidence of SUSY. It describes novel techniques for estimating and rejecting the Standard-Model backgrounds to searches for...