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@ARTICLE{Irbck:1047045,
      author       = {Irbäck, Anders and Knuthson, Lucas and Mohanty, Sandipan},
      title        = {{F}olding lattice proteins confined on minimal grids using
                      a quantum-inspired encoding},
      journal      = {Physical review / E},
      volume       = {112},
      number       = {4},
      issn         = {2470-0045},
      address      = {Woodbury, NY},
      publisher    = {Inst.},
      reportid     = {FZJ-2025-04091},
      pages        = {045302},
      year         = {2025},
      abstract     = {Steric clashes pose a challenge when exploring dense
                      protein systems using conventional explicit-chain methods. A
                      minimal example is a single lattice protein confined on a
                      minimal grid, with no free sites. Finding its minimum energy
                      is a hard optimization problem, with similarities to
                      scheduling problems. It can be recast as a quadratic
                      unconstrained binary optimization (QUBO) problem amenable to
                      classical and quantum approaches. We show that this problem
                      in its QUBO form can be swiftly and consistently solved for
                      chain length 48, using either classical simulated annealing
                      or hybrid quantum-classical annealing on a D-Wave system. In
                      fact, the latter computations required about 10 s. We also
                      test linear and quadratic programming methods, which work
                      well for a lattice gas but struggle with chain constraints.
                      All methods are benchmarked against exact results obtained
                      from exhaustive structure enumeration, at a high
                      computational cost.},
      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},
      doi          = {10.1103/8n7p-7lh2},
      url          = {https://juser.fz-juelich.de/record/1047045},
}