Static versus Dynamic calibration
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It would seem there are two main issues to consider. For dynamic calibration techniques, the environment the cantilever is in will change the behavior. Calibration done in air will yield a different result than that done in vacuum due to the viscous damping.
The other consideration would be calibrating a cantilever with a dynamic method that you are using in contact mode for your experiment. The difference here would be the internal damping that occurs in the cantilever.
It seems the best approach is to make sure you calibrate your cantilever in as close to the same environment and same type of nominal motion (static or dynamic) as your experiment. -
Another point: all AFM's that use the laser beam reflection method (which is almost all of them) measure the slope of the end of the cantilever, not the deflection of the end of the cantilever. These are directly related to one another, but the relation is different for static end loading vs. dynamic oscillation with a free end (a factor 3/2 I believe). This is discussed in:
Calculation of thermal noise in atomic force microscopy
Butt, H.-J.; Jaschke, M. Source: Nanotechnology, v 6, n 1, p 1-7, Jan. 1995 -
Also, I shouldn't say: "AFM's ... measure the slope of the end of the cantilever". Rather, they measure the average slope of the region on which the cantilever is incident. This of course is not the same location of the tip, nor is it the end of the cantilever. This means that certain calibration methods require you to correct for the difference between the full length of the cantilever and the length to the tip, depending on what you have extracted from your calibration.
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If done correctly (see the Cook et al reference), then the dynamic methods account for the differences in boundary conditions, the deformed shape of the vibrating cantilever, viscous effects, etc..., so I don't think this would be a huge issue. I think that the bigger issue is whether the cantilever obeys the assumptions made in the calibration and whether one knows the boundary conditions for the experiment (e.g. in the actual measurement, is the beam really acting as a cantilever with zero moment on the tip?).