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We investigate the reconstruction of the transmission matrix of a time-evolving atmospheric channel with an online recursive optimization routine, using wave-optics simulations. We demonstrate that this estimation technique is able to keep up with the evolution of the channel and enables a significant improvement of communication-relevant quantities such as the total power transmitted through the channel, and the coupling of the received light into a single mode fiber. Moreover, we show that this approach is robust against measurement noise, and that it notably reduces the probability and duration of power outages, even in strong turbulence.

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