Part 2 - a way to test the surface features
As could be seen in part 1, given sufficient velocity, you will have turbulence without any added surface features. Until you get into very high Reynolds numbers, you will also have a boundary layer against the walls with low to zero velocity.
Thus, a way to use the ink injection method to investigate the affects of surface features on wall proximity turbulence, we need to do a few things.
First, you want slower flows than you would normally have so that you are either in the laminar flow stage or close enough that you have a thick boundary layer on the walls. This is so that you can more clearly see the affects of the added surface features.
Second, you want to inject the dye/ink at a point downstream from the inlet so that the local affects associated with the inlet don't interfere. You also want the injection method to be one that causes the smallest amount of alteration to the flow.
Third, you want an area of no surface features between the ink injection point and the surface feature test area to help as a control.
Attached is a picture of one way to do this, showing the various things discussed. Note you don't have to make entire water blocks to do this, you can make simple straight channels to save time and $, and only test in a water block those surface features that look the most promising from the initial experiments. You could even take a piece of metal and put multiple seperate channels in it, with different features in each channel. (the ink inlet could be done with a hyperdermic needle, inserted through a hole drilled into the back wall of the channel)
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