This presentation discusses recent numerical methods to calculate the
free energy as a function of a reaction coordinate for bio-molecules.
Free energy is often called potential of mean force and represents the
effective potential experienced by a generalized coordinate for a
bio-molecular system. Examples of coordinates are distance between
molecules, orientation of a protein, dihedral angles along the
backbone of a protein... The mathematical theory that forms the
background of these techniques is discussed along with some numerical
examples with ion channels and small peptides.

Prof. Darve got his PhD in 1999 in the Jacques-Louis Lions laboratory
in the Universite Pierre et Marie Curie, France. His PhD was in
computational mathematics and numerical analysis (topic: fast
multipole method for acoustics and electromagnetics; advisor: O.
Pironneau). He was a postdoc from 1999 to 2001 at the NASA Ames
Research Center in the astrobiology group. He has since joined the
faculty at Stanford University in the Mechanical Engineering
Department. His field of research is the fast multipole method, free
energy computation methods for proteins, and programming scientific
codes on streaming processors (graphics processing units, Cell).

Researchers should cite this work as follows: