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Scale parameter  represents the intensity of fragmentation (i.e., breaks per unit length), and—as a determinant of the mean expected fragment size—is assumed to be constant across molecules of different lengths for fragmentation protocols where the number of produced fragments depends on the molecule length. Shape parameter  reflects the geometric relation in which random fragmentation is breaking a molecule (e.g.,  corresponds to uniform fragmentation on the linear chain of nucleotides,  splits uniformly the surface, and  the volume, etc.).

The Flux Simulator employs uses a 3-step algorithm to tokenize a respective molecule; first, geometry d geometry  and the number n number  of fragments that are obtained from the molecule are determined. We found empirically that parameter d depends logarithmically on len , the length of the molecule that is fragmented d=log(len) . The number of fragments produced from a specific RNA molecule is determined by n=len/E(d_max), where E(d_max) , where  is the expectancy of the most abundant fragment size, computed from h and the gamma-function G function  of d :

E(d_max)= hG(1/d + 1) (3)