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Despite recent market conditions and significant consolidation among photovoltaic (PV) module and cell manufacturers, the widespread deployment of PV technologies is increasingly viable. Recent advances in power electronics systems include the emergence of sub-module partial-power processing architectures based on multi-level ladder converters. This work presents a control scheme and a multiple-input, multiple-output (MIMO) maximum power point tracking (MPPT) algorithm suitable for large PV arrays controlled by series-connected modular multi-level converters. We demonstrate stability of the control system experimentally on a four-level prototype and simulation results that show convergence to global optimum conditions in less than 20 perturb-and-observe cycles for up to 300 series-connected PV substrings.