Folding lattice proteins confined on minimal grids using a quantum-inspired encoding
Irbäck, Anders LU
; 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:
https://lup.lub.lu.se/record/3bdd61bd-143b-4909-801b-07beb980545c
- author
- Irbäck, Anders
LU
; Knuthson, Lucas
LU
and Mohanty, Sandipan
- organization
- publishing date
- 2025-10-01
- 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
- 2025-10-03 03:05:17
@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}},
}