CaDS Seminar 2022 - Nov. 15

Sandipan Mohanty (SDL Biology)

Protein folding in a 2D HP lattice model using quantum annealing

Abstract:
I will present a recent study of a very simplified version of protein folding simulations performed on JUPSI, our D-Wave Advantage quantum annealer. A protein is represented as a self avoiding chain of beads placed on a 2D square lattice, where each bead is either hydrophobic (H) or polar (P). The protein is identified by the sequence of H/P beads along the chain, e.g., HPHHPHPHHPP. The potential energy of a structure is calculated by aggregating contributions from the whole system, with a unit negative contribution for every pair of H residues occupying nearest neighbour lattice sites. The folded structure corresponds to the arrangement of the beads which minimises this energy. We formulated the problem in a manner suitable for quantum annealers, and performed simulations on JUPSI.

For the 2D HP lattice model, all sequences with unique ground states up to a chain length of 30 are known from exhaustive enumeration. We used these exact results to evaluate our quantum annealing simulations. We also performed and compared two different kinds of classical Monte Carlo (MC) simulations: methods in which the participating researchers have decades of experience. For all those sequences with up to 30 beads, the hybrid quantum annealer has a 100% success rate in finding the correct solutions, which clearly outperforms our classical simulated annealing MC runs. Two longer sequences, of lengths 48 and 64, were also studied using our quantum annealing method. Although exact results are not available for these two, these sequences have been studied in detail using extensive classical MC simulations. Our quantum annealing runs find, with a 100% hit rate, the same ground states as identified in those earlier classical MC simulations.

Our results have been recently published in the following article:
"Folding lattice proteins with quantum annealing" Anders Irbäck, Lucas Knuthson, Sandipan Mohanty, and Carsten Peterson Phys. Rev. Research 4, 043013