A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it is possibl
e that so many initial configurations proceed to fold to a unique final configuration. We put energy and dynamical considerations temporarily aside and focus upon the geometry alone. We parameterize the structure of an idealized protein using the concept of a ribbon from differential geometry. The deformation of the ribbon is described by introducing a generic twisting Ansatz. The folding process in this picture entails a change in shape guided by the local amino acid geometry. The theory is reparamaterization invariant from the start, so the final shape is independent of folding time. We develop differential equations for the changing shape. For some parameter ranges, a sine-Gordon torsion soliton is found. This purely geometric waveform has properties similar to dynamical solitons. Namely: A threshold distortion of the molecule is required to initiate the soliton, after which, small additional distortions do not change the waveform. In this analysis, the soliton twists the molecule until bonds form. The analysis reveals a quantitative relationship between the geometry of the amino acids and the folded form.
In a ring of s-wave superconducting material the magnetic flux is quantized in units of $Phi_0 = frac{h}{2e}$. It is well known from the theory of Josephson junctions that if the ring is interrupted with a piece of d-wave material, then the flux is q
uantized in one-half of those units due to a additional phase shift of $pi$. We reinterpret this phenomenon in terms of geometric phase. We consider an idealized hetero-junction superconductor with pure s-wave and pure d-wave electron pairs. We find, for this idealized configuration, that the phase shift of $pi$ follows from the discontinuity in the geometric phase and is thus a fundamental consequence of quantum mechanics.
