A constrained variational model of biomolecular solvation and its numerical implementation

Variational based solvation models of biomolecules with smooth interface have drawn attentions in the past decade since they been developed as an efficient and reliable representation solute-solvent interfaces framework implicit solvent models. This work aims at providing solid mathematical supports for a promising geometric flow computational model (GFBSS) its involved treatments. For this purpose, we improve GFBSS by explicitly including two physical constraints: (1) novel experimental domain decomposition, (2) two-sided obstacle characteristic function describing optimal diffuse boundary. It is shown that resulting constrained mathematically well-posed. Further, to overcome challenges arising from these constraints, propose family generalized energy functionals whose variations satisfy q-Laplacian type equation nonpolar molecules. The free energies predicted converge proposed one. Most importantly, numerical difference between previous unconstrained negligible. implies newly one are equivalent each other terms calculation prediction. Our validation, implementation, convergence demonstrated using several common biomolecular modeling tasks.