The fractional dynamics has been appearing in many phenomena such as the movement of protein in the cytoplasm. The Fractional calculus used to describe it.
Xuru's Website
Introductory Notes on Fractional Calculus
http://www.xuru.org/fc/toc.asp
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I has some class notes for free:
"Courses taught by Richard Fitzpatrick at UT Austin"
http://farside.ph.utexas.edu/teaching.html
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http://pkbiophys.blogspot.com/
Statistical Physics:Course material with JAVA applets
http://homepage.univie.ac.at/franz.vesely/sp_english/sp/sp.html
and for more books:
http://pkbiophys.blogspot.com/
In SBML family has the MesoRD program. This program used to solve reaction diffusion eq. in linear and non-linear equations(deterministic and Stochastic problem). This program simple to modify...
http://pkbiophys.blogspot.com/