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@ARTICLE{Irbck:910247,
      author       = {Irbäck, Anders and Knuthson, Lucas and Mohanty, Sandipan
                      and Peterson, Carsten},
      title        = {{F}olding lattice proteins with quantum annealing},
      journal      = {Physical review research},
      volume       = {4},
      number       = {4},
      issn         = {2643-1564},
      address      = {College Park, MD},
      publisher    = {APS},
      reportid     = {FZJ-2022-03708},
      pages        = {043013},
      year         = {2022},
      abstract     = {Quantum annealing is a promising approach for obtaining
                      good approximate solutions to difficult optimization
                      problems. Folding a protein sequence into its minimum-energy
                      structure represents such a problem. For testing new
                      algorithms and technologies for this task, the minimal
                      lattice-based [hydrophobic (H) or polar (P) beads] HP model
                      is well suited, as it represents a considerable challenge
                      despite its simplicity. The HP model has favorable
                      interactions between adjacent, not directly bound
                      hydrophobic residues. Here, we develop a novel spin
                      representation for lattice protein folding tailored for
                      quantum annealing. With a distributed encoding onto the
                      lattice, it differs from earlier attempts to fold lattice
                      proteins on quantum annealers, which were based upon chain
                      growth techniques. With our encoding, the Hamiltonian by
                      design has the quadratic structure required for calculations
                      on an Ising-type annealer, without having to introduce any
                      auxiliary spin variables. This property greatly facilitates
                      the study of long chains. The approach is robust to changes
                      in the parameters required to constrain the spin system to
                      chainlike configurations, and performs very well in terms of
                      solution quality. The results are evaluated against existing
                      exact results for HP chains with up to N=30 beads with
                      $100\%$ hit rate, thereby also outperforming classical
                      simulated annealing. In addition, the method allows us to
                      recover the lowest known energies for N=48 and N=64 HP
                      chains, with similar hit rates. These results are obtained
                      by the commonly used hybrid quantum-classical approach. For
                      pure quantum annealing, our method successfully folds an
                      N=14 HP chain. The calculations were performed on a D-Wave
                      Advantage quantum annealer.},
      cin          = {JSC},
      ddc          = {530},
      cid          = {I:(DE-Juel1)JSC-20090406},
      pnm          = {5111 - Domain-Specific Simulation $\&$ Data Life Cycle Labs
                      (SDLs) and Research Groups (POF4-511)},
      pid          = {G:(DE-HGF)POF4-5111},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000881432000009},
      doi          = {10.1103/PhysRevResearch.4.043013},
      url          = {https://juser.fz-juelich.de/record/910247},
}