SRIM and TRIM are a collection of software packages which calculate many features of the transport of ions in matter. A full description of the calculation is found in the tutorial book "The Stopping and Range of Ions in Solids", by J. F. Ziegler, J. P. Biersack and U. Littmark, Pergamon Press, New York, 1985 (new edition in 2003).
IBA Data Furnance is a computer code to extract elemental depth profiles from Rutherford backscattering and related ion beam analysis spectra. One of the review publications describing the program states it is useful for the NDP application.
N.P. Barradas, C. Jeynes, Advanced physics and algorithms in the IBA DataFurnace, Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, Volume 266, Issue 8, 2008, Pages 1875-1879, ISSN 0168-583X, https://doi.org/10.1016/j.nimb.2007.10.044.
Thwaites, D. T. (1983). Bragg's Rule of Stopping Power Additivity: A Compilation, and Summary of Results. Radiation Research 95, Pages 495-518
James F. Ziegler, Jochen P. Biersack, Matthias D. Ziegler, SRIM: The Stopping and Range of Ions in Matter, Lulu Press Co.; 860 Aviation Parkway; Suite 300; Morrisville, NC, 27560 USA
Dietmar Fink, Neutron Depth Profiling, HMI-B 539 (1996) Hahn-Meitner-Institut, Berlin, Pages 311, Nr: FD/96/036 (http://d-nb.info/948247029) - Perhaps the single most comprehensive reference on the topic of NDP.