  We introduce a novel concept, the minimal molecular surface (MMS), as a new
paradigm for the theoretical modeling of biomolecule-solvent interfaces. When a
less polar macromolecule is immersed in a polar environment, the surface free
energy minimization occurs naturally to stabilizes the system, and leads to an
MMS separating the macromolecule from the solvent. For a given set of atomic
constraints (as obstacles), the MMS is defined as one whose mean curvature
vanishes away from the obstacles. An iterative procedure is proposed to compute
the MMS. Extensive examples are given to validate the proposed algorithm and
illustrate the new concept. We show that the MMS provides an indication to
DNA-binding specificity. The proposed algorithm represents a major step forward
in minimal surface generation.
