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I guess if the DC DC controller is a current based controller then depending on its control strategy, with different pannels receiving different solar insolations, that may automatically result in different frequencies and duty cycles for the boost converter?
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That is definately an option, if the control is variable frequency you will get a natural variation that'll probably stop any problems. EMC and noise stuff can get a bit accedemic at the best of times, lots of things that'll help and hinder in various cases, beats are just a specific thing that
can be a problem, and worth being aware of choices that'll make eliminating it more or less easy.
I'm glad you mentioned current mode control, because, yeah, that's a bit important. I guess you may know that as you sweep from high to low current or high to low voltage from the PV source, the incrimental impedance changes a lot, and you'll need to work over quite a wide range if you're working with unknown panels. That can be a big problem for converter stability (Middlebrook criterion) and it is a big enough variation that trying to neutralise the probelm with input (as you might with a conventional voltage source having some impedance variation) isn't really practical or cost effective, so better to handing the stability problem functionally and ooptmise the filter for the EMC purposes.
For the single point that the individual converters feed, there will be some stability concerns there too. The response of each converter will be dependent on its PV source and the output voltage; the output voltage (input voltage to the inverter) is defined by the contributions of all other sources and how much power is being sucked out by the inverter. That's a bit more than I can come up with a solution in my head right now, needs a diagram, I'll check back later when I have a bit more time.