Using the wormlike chain calculator
This online tool calculates end-to-end statistics of a wormlike chain polymer. These statistics determine the likely conformations of the polymer, and can be used to predict such properties as the looping frequency of DNA within a cell.
The wormlike chain model
A 'wormlike chain' is a continuous polymer model in which the resistance to bending is linear. In the real-world, thermal fluctuations cause the polymer to bend and twist over 'persistence' length scales determined by the temperature and the stiffness of the polymer. The basic statistical property of a polymer is the probability distribution for finding two ends of a given segment at a given relative position and orientation to one another. This distribution depends on the persistence lengths as well as the length of intervening polymer between the two segments -- the additional stretches of polymer on either side turn out not to matter. This program calculates these distribution functions using a variety of methods.
Using this web calculator
To compute the end-to-end statistics, the user must enter the basic parameters of the polymer, such as its persistence length, etc., and specify the length and relative positions and orientations of the two ends of the segment we are looking at. The user then chooses the type of calculation to perform and clicks the "Calculate" button. The output is a probability density: i.e. a probability per some unit range of parameters about the given configuration. (We cannot give a direct probability, since the likelihood of finding the polymer in the exact configuration is zero.)
The following pages describe the different fields that the user can modify.
The command-line calculator
This web-based program is based on a command line tool which can be downloaded from the links below. The command-line version is not graphical and is somewhat more technical to use. However, it is more flexible and there are several reasons that it might be the better option:
- Long calculations may not finish before the web server times out.
- More flexibility: one can, for example, generate N-dimensional tables, save data, etc.
- The Monte Carlo method can calculate chains that are non-linear in bending and twist responses, but only in the command line calculator.
The command-line calculator is accessed via the Terminal utility on the Macintosh, or the DOS prompt on a Windows machine.