Burst-wave lithotripsy is a non-invasive treatment of kidney stones using short pulses of focused ultrasound. In this talk, we present the use of input-output analysis to optimize the design and control of a multi-element array transducer to achieve optimal stone breakage. The analysis is based on a linear fluid-structure coupled system that maps the acoustic forcing from individual elements to the stress in a stone of assumed shape, size, and composition. We determine the optimal frequency and optimal distribution of the phase and amplitude across the aperture by maximizing a cost function that represents the strain energy in stone. The optimal parameters are obtained by applying a state-of-the-art, randomized singular value decomposition (SVD) to the discrete linear operator. The results show that carefully controlling the relative phase and amplitude between elements can increase the strain energy (by 2-3 times in certain cases) compared to a uniform distribution under the same input energy. This suggests that the stone fragmentation can be accelerated or performed with lower energy for safer treatment. The improvement is interpreted and validated by combining high-fidelity simulations with high-speed camera images of crack formation in model stones from in vitro- experiments. [Work supported by NIH, Grant No. P01-DK043881.]