A Variable Neighbourhood Descent Heuristic for Conformational Search Using a Quantum Annealer

By Dominic Marchand, Moslem Noori, Austin Roberts, Gili Rosenberg, Brad Woods, Ugur Yildiz, Marc Coons, David Devore, & Peter Margl

Discovering the low-energy conformations of a molecule is of great interest to computational chemists, with applications in in silico materials design and drug discovery. In this paper, we propose a variable neighbourhood search heuristic for the conformational search problem. Using the structure of a molecule, neighbourhoods are chosen to allow for efficient optimization using a binary quadratic optimizer. The method is flexible with respect to the choice of molecular force field and the number of discretization levels in the search space, and can be further generalized to take advantage of higher-order binary polynomial optimizers. It is well-suited for the use of devices such as quantum annealers. After carefully defining neighbourhoods, the method easily adapts to the size and topology of these devices, allowing for seamless scaling alongside their future improvements.

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