1. j-factor calculation for homogenous wormlike chain model

The program calculates j-factor values for DNA fragments up to 500 bp in length. It is based on Shimada & Yamakawa formula for short wormlike chain. The programs asks to introduce 4 parameters:

1. DNA torsional rigidity, in 10e-19 erg·cm. It is normally between 2.2 and 2.6;

2. DNA persistence length, in nm;

3. DNA helical repeat, normally close to 10.5;

4. Minimal DNA length for which the calculation will be performed, in bp.

The program performs calculations for 16 consecutive lengths. The program, j-factor.exe, can be started from Command Prompt window or simply by double click on its icon. The result appears in the window and in the file "results.txt". The file can be transferred to a plotting program.

The program code is in the file j-factor.f

Reference:
Shimada, J. and Yamakawa, H. (1984) Ring-closure probabilities for twisted wormlike chains. Application to DNA. Macromolecules,
17, 689-698.

2. j-factor calculation for the general model

The program for the j-factor calculation, jfm2full.c, allows arbitrary specification of chain geometry and rigidity in its data file, jfm2full.data. It can be run as follows: