The idea to write this book unfolded when I more and more realized how equally frustrating and fascinating it can be to design research projects in molecular biophysics and chemical physics – frustrating for the sheer amount of inconclusive and contradicting literature, but fascinating for the mechanical precision of the complex interplay of competing interactions on various length scales and constraints in conformational transition processes of biomolecules that lead to functional geometric structures. Proteins as the “workhorses” in any biological system are the most prominent examples of such biomolecules.

The ability of a “large” molecule consisting of hundreds to tens of thousands of atoms to form stable structures spontaneously is typically called “cooperativity.” This term is not well defined and could easily be replaced by “emergence” or “synergetics” – notions that have been coined in other research fields for the same mysterious feature of macroscopic ordering effects. There is no doubt that the origin of these net effects is of “microscopic” (or better nanoscopic) quantum nature. By noting this, however, we already encounter the first major problem and the reason why heterogeneous polymers such as proteins have been almost ignored by theoretical scientists for a long time. From a theoretical physicist's point of view, proteins are virtually “no-no's.” Composed of tens to thousands of amino acids (already inherently complex chemical groups) linearly lined up, proteins reside in a complex, aqueous environment under thermal conditions. They are too large for a quantum-chemical treatment, but too small and too specific for a classical, macroscopic description. They do not at all fulfill the prerequisites of the thermodynamic limit and do not scale.