title: Derivatives of molecular surface area and volume: simple and exact analytical formulas.
abstract: The computational effort of biomolecular simulations can be significantly reduced by means of implicit solvent models in which the energy generally contains a correction depending on the surface area and/or the volume of the molecule. In this article, we present simple derivation of exact, easy-to-use analytical formulas for these quantities and their derivatives with respect to atomic coordinates. In addition, we provide an efficient, linear-scaling algorithm for the construction of the power diagram required for practical implementation of these formulas. Our approach is implemented in a C++ header-only template library.
authors.affiliation: Steinbuch Center for Computing, Karlsruhe Institute of Technology, Karlsruhe, Germany.
authors.forename: Konstantin V
authors.initials: KV
authors.lastname: Klenin
authors.forename: Frank
authors.initials: F
authors.lastname: Tristram
authors.forename: Timo
authors.initials: T
authors.lastname: Strunk
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Wenzel
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D008958:Models, Molecular; D008968:Molecular Conformation; D012997:Solvents / Q000737:chemistry*
chemical_list: D012997:Solvents