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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:
Eric F Darve (2006), "Vector Free Energy Calculation with Adaptive Biasing Force," https://nanohub.org/resources/1589.