The theoretical FDC computed in Sec. 3.4.1 requires the knowledge of several (theoretical and empirical) parameters. The equations that determine the total extension (Eq. 3.23) and the total energy (Eq. 3.22) implicitly depend on:
An extra energy parameter is required to take into account the effect of the end loop. It basically increases or decreases the height of the last rip of the FDC.
In order to obtain an estimation of the NNBP, all the other parameters must be fixed. The stiffness of the optical trap and the elastic properties of the handles can be determined easily. However, some experiments must be carried out in order to determine the elastic properties of the ssDNA. Apart from this, there are two more issues that have to be addressed before proceeding with the fit of the NNBP. The following sections deal with them.