Our examinations of the methodical implementation of the multiple time-stepping algorithms on the Stampede supercomputer reveal a speedup factor of 23 over single time-stepping algorithm, for the same problem, with the combined algorithmic and hardware accelerations. More specifically, the MTS algorithm is 11.5 times faster than the STS algorithm; the GPU-enabled system performs 2 times faster than the CPU-only system. Combining these speedups and using MTS algorithm on 16 GPU nodes on Stampede, we can simulate 1-multi-scale phenomena of flowing platelets in blood vessels can be completed within approximate 37 days, enabling practical modeling of millisecond-scale biological phenomena with spatial resolutions at the nanoscales. The mathematical algorithms and the advances of computer hardware such as the Stampede supercomputer that can be leveraged allow us to explore the new frontiers of cutting-edge applications in medical and life sciences.