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Ultrasonic energy can be used to control algae, the problem is the application of the ultrasound at sufficient power to a wide variety of hull compositions and water conditions.
The original researchers used 120 watts of ultrasonic power at 28 kHz and killed blue-green algae in test tubes. This is a long, long, way from killing algae around a 40 foot hull in the soup of western lake Erie on a hot day.
The propagation of the ultrasound is greatly affected by the material, thickness, and temperature of the hull. The temperature and suspended air in the water has a big effect.
The tuning (to the most efficient frequency) is critical. The cited company says their device "auto-tunes", but I'm not sure how that works - it sounds like magic to me.
If ultrasound were a sure-fire way of killing algae, nobody would ever see marine growth on the face of their depth sounder transducer - that is propagating ultrasound 100 feet or more at 50 kHz - pretty powerful - so why does algae grow right on the face (at least it does on mine). I know the sounder isn't on all the time, but in the initial research the powerful ultrasonic energy killed the algae, collapsed the algae's vacuuols, and caused to algae to detach and settle.
Oh, and about the toxic nature of bottom paint; unless it is ablative, the heavy metal doesn't enter the water.
Oh, and when you kill algae, which is what this system does (it doesn't just scare them away) the algae release iodine in significant quantities into the water. I think Iodine is toxic.
It sounds like these are expensive! If you want to make your own cheap version to try, go buy a medical cell disrupter on ebay: I got one for $150 that runs at 20kHz and 200W from 120VAC. Glue the transducer to the bottom and see what happens.
Anyhow, it's a good idea, but the practical application is the challenge.