Folding Lattice Proteins with Quantum Annealing

The recent publication "Folding lattice proteins with quantum annealing" by Anders Irbäck et al. (DOI: 10.1103/PhysRevResearch.4.043013) was chosen as an "Editor's suggestion" by the journal Physical Review Research. In this article, the authors – among them Sandipan Mohanty from JSC's Simulation and Data Lab Biology – explore a new way of encoding the protein folding problem for quantum computers. Using a simple HP (H = hydrophobic, P = polar) protein representation on a 2D lattice, the authors demonstrate the viability of the use of quantum annealers for bio-physical problems in the near future.

For the simple 2D HP lattice model used here, exact results are known for systems of up to 30 amino acids. This makes it an interesting test-bed for evaluating the reliability of new methods. The simulations performed on the D-Wave Advantage system JUPSI at the Jülich Supercomputing Centre show that the hybrid quantum annealer has a 100% hit rate in finding the ground state of the lattice protein model.

Crucially, the newly developed method retains its analytical simplicity as more particles are added to the system, so that larger systems can be studied with little extra effort. The authors applied the method to two systems of 48 and 64 amino acids, whose ground states were known from older classical simulations, and found that the quantum annealer identifies those ground states, once again with a 100% hit rate, costing only a small fraction of the computing time.

This study opens up exciting new possibilities regarding applications of quantum technologies in the life sciences. The authors are currently researching ways of bringing more biophysically detailed models to quantum computers.

Contact: Dr. Sandipan Mohanty

from JSC News No. 292, 2 November 2022