Introduction to single molecule analysis and computation: the FOCUS Project

The FP7 project FOCUS “Single-molecule activation and detection” belongs to the FET Proactive 7 Programme: “Molecular Scale Devices and Systems” and is aimed at investigating and developing molecular devices (MD) where single molecules become computing elements. X-ray diffraction and NMR spectroscopy provides information on the structure of molecules with an atomic resolution, but the generated data are averaged over millions of molecules. Single-molecule analysis, in contrast, investigates properties of individual molecules not averaged over a large ensemble of similar molecules. The great majority of these properties, and of the related measurements, refers to nonequilibrium conditions. In order to obtain classical thermodynamic quantities such as changes of the free energy ΔF, special methods of statistical mechanics, such as those introduced by Jarzinski [5, 6] can be used. Single molecule experiments provide a direct view of molecular events in action and offer the possibility to verify basic notions of chemical reactions such as Kramers theory and Eyring’s transition state theory. Indeed, it is possible to characterize very precisely Kramers diffusion coefficient and free-energy barrier by measuring the temperature and viscosity dependence of the transition path time for protein folding [2