Scientific Publications
Enumerating and indexing many-body intramolecular interactions: a graph theoretic approach
Journal of Mathematical Chemistry, 53(7), 1634-1648
The central idea observes a recursive mapping of n-body intramolecular interactions to (n+1)-body terms that is consistent with themolecular topology.Iterative application of the line graph transformation is identified as anatural and elegant tool to accomplish the recursion. The procedure readily generalizes to arbitrary n-body potentials. In particular, the method yields a complete characterization of 4-body interactions. The hierarchical structure of atomic index lists for each interaction order n is compactly expressed as a directed acyclic graph. A pseudo-code description of the generating algorithm is given. With suitable data structures (e.g., edge lists or adjacency matrices), automatic enumeration and indexing of n-body interactions can be implemented straightforwardly to handle large bio-molecular systems. Explicit examples are discussed, including a chemically relevant effectivepotential model of taurocholate bile salt.
Journal of Mathematical Chemistry, 53(7), 1634-1648
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