A central partition of molecular conformational space: I. Basic structures

On the basis of empirical evidence from molecular dynamics simulations, molecular conformational space can be described by means of a partition of central conical regions (cells) characterized by the dominance relations between cartesian coordinates. This work presents a geometric and combinatorial description of the cell arrangement which is polar to a 3x(N-1)-dimensional polytope. Conformations can be precisely located within the face hierarchy of the polytope, whose 1-skeleton provides the framework for determining paths between selected conformations.