Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

Folding lattice proteins confined on minimal grids using a quantum-inspired encoding

Irbäck, Anders LU orcid ; Knuthson, Lucas LU and Mohanty, Sandipan (2025) In Physical Review E: covering statistical, nonlinear, biological, and soft matter physics 112(4).
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,... (More)
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. (Less)
Please use this url to cite or link to this publication:
author
; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Physical Review E: covering statistical, nonlinear, biological, and soft matter physics
volume
112
issue
4
article number
045302
pages
9 pages
publisher
American Physical Society
ISSN
2470-0045
DOI
10.1103/8n7p-7lh2
language
English
LU publication?
yes
id
3bdd61bd-143b-4909-801b-07beb980545c
date added to LUP
2025-10-02 10:13:25
date last changed
2025-10-02 10:48:57
@article{3bdd61bd-143b-4909-801b-07beb980545c,
  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.}},
  author       = {{Irbäck, Anders and Knuthson, Lucas and Mohanty, Sandipan}},
  issn         = {{2470-0045}},
  language     = {{eng}},
  month        = {{10}},
  number       = {{4}},
  publisher    = {{American Physical Society}},
  series       = {{Physical Review E: covering statistical, nonlinear, biological, and soft matter physics}},
  title        = {{Folding lattice proteins confined on minimal grids using a quantum-inspired encoding}},
  url          = {{http://dx.doi.org/10.1103/8n7p-7lh2}},
  doi          = {{10.1103/8n7p-7lh2}},
  volume       = {{112}},
  year         = {{2025}},
}