C library to compute worm-like chain polymer functions, written by
- Ruggero Cortini, Université Pierre et Marie Curie, Paris, France
- Francesco Alessandro Massucci, Universitat Rovira i Virgili, Tarragona, Spain
This library provides fast routines to calculate functions related to models of a semi-flexible polymer (generally, worm-like chain models). Both a continuous model and a discrete model are considered.
New! Now includes a Python wrapper that you can install by python setup.py install with your favourite options. From within python, you can call the library functions using
import pywlc
rho = 0.1
lpb = 45.
F = pywlc.wlc_F_rho (rho, lpb)The functions in the python modules have the same names and usages as those in the C library
Depends on the Gnu Scientific Library (GSL), available at http://www.gnu.org/software/gsl/
The functions are named wlc_A_x_regime where A (x) is calculated, in the regime "regime".
Currently available:
- g: Gibbs free energy as a function of force or relative extension
- f: Helmholtz free energy as a function of relative extension
- rho: relative extension as a function of force
- F: force as a function of extension
Regimes currently available:
- variational: using the variational formulae derived by Marko and Siggia
- interpolation
- high force
- cavity
- cavity_gradient
Regime cavity and cavity_gradient solve the discrete model in F. A. Massucci et al (2014). All other regimes are inherent to the model in J. Marko & E. Siggia (1995).
Provides also a program to quickly access to function values, named "wlc"
Formulas for variational, interpolation, and high force regimes are taken from the research article:
- J. Marko, E. Siggia, "Stretching DNA", Macromolecules, 28, (1995), 26: 8759--8770 DOI: 10.1021/ma00130a008
Cavity formulas are taken from the research article:
- F. A. Massucci, I. Perez Castillo, C. J. Perez Vicente, "Cavity approach for modeling and fitting polymer stretching", Physical Review E, 90, (2014), 5: 052708 DOI: 10.1103/PhysRevE.90.052708