To get myself started, I found a paper by H. Michael Tulldahl and K. Ove Steinvall entitled: "Analytical waveform generation from small objects in lidar bathymetry," (App. Optics, v.38 n.6, 1999). The authors present a model to simulate received lidar waveforms in order to observe the influence of variously-shaped objects on the seabed. I am tweaking the modeled system parameters to match those of the systems I am working with, as well as the water-dependent parameters to match different water types. I am also not dealing with any objects on the seabed, and for now am assuming a flat bottom. I have only just started, so my model is nowhere near complete. Although this model is not the primary focus of my research, I see it as a way to help me understand not only what I am seeing in the data, but also predict features in the data that I might look for. Eventually I would like to have a user interface where I could simply select the lidar system and approximate water type (most likely based off Jerlov), and perhaps bed type and approximate roughness, and just hit "go!"
The model is currently in Matlab, though as it develops I may switch to a more object-oriented scripting language such as Python (I can hear Kurt applauding from here). The point is, models (and the more specifically, the development of models) can be a powerful learning tool. I wish that modeling itself (or at least an introduction to modeling) was taught as more of a core research tool, opposed to a special one.
Below is a snippet of some of the model output as it now stands. The top graph shows the volume backscattered power reaching the receiver. The middle graph shows the amount of power incident on the seabed (one-way travel), and the bottom graph shows the percentage of transmitted power returned to the receiver, all as a function of depth. In this case, the off-nadir angle of the laser is 0 degrees and I am looking only at the nadir beam. I am assuming pure seawater (just to make my initial attempts a little easier) and treating the water surface return of the green wavelength and the atmospheric loss as negligible.

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