  We develop a theoretical approach to the protein folding problem based on
out-of-equilibrium stochastic dynamics. Within this framework, the
computational difficulties related to the existence of large time scale gaps in
the protein folding problem are removed and simulating the entire reaction in
atomistic details using existing computers becomes feasible. In addition, this
formalism provides a natural framework to investigate the relationships between
thermodynamical and kinetic aspects of the folding. For example, it is possible
to show that, in order to have a large probability to remain unchanged under
Langevin diffusion, the native state has to be characterized by a small
conformational entropy. We discuss how to determine the most probable folding
pathway, to identify configurations representative of the transition state and
to compute the most probable transition time. We perform an illustrative
application of these ideas, studying the conformational evolution of alanine
di-peptide, within an all-atom model based on the empiric GROMOS96 force field.
