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Tuesday, February 07, 2023

D-Wave Quantum Annealing Solving Protein Folding

 Have mentioned our linking with D-Wave for very large search problems, recently some news about their work in other spaces we also examined:  Protein Folding.  

Quantum Annealing by D-Wave

See: https://www.youtube.com/user/dwavesystems

Also  https://www.dwavesys.com/media/exqjbloj/dwave_menten-ai_case_story_v10.pdf

Also reported on here:  https://www.youtube.com/watch?v=Z50kjnZXpXg&t=35s

D-Wave uses quantum method to solve protein folding problem    by Lisa Zyga , Phys.org

D-Wave One and CEO Geordie Rose. Image credit: D-Wave Systems, Inc.

(Phys.org) -- While there has been some skepticism as to whether the Canadian company D-Wave’s quantum computing system, the D-Wave One, truly involves quantum computing, the company is intent on proving that the system is both a quantum device as well as a useful one. In a new study, D-Wave CEO Geordie Rose and other D-Wave researchers have teamed up with Harvard quantum physicist Alán Aspuru-Guzik and post-doc Alejandro Perdomo-Ortiz to demonstrate that the D-Wave One system can solve the challenging task of finding the lowest-energy configuration of a folded protein.

The study, “Finding low-energy conformations of lattice protein models by quantum annealing,” is published in a recent issue of Nature’s Scientific Reports.

The computer used quantum annealing to find the lowest-energy protein configuration by solving for the configuration as an optimization problem, where the optimal state was the lowest-energy state. Proteins can be folded in a large number of ways because they’re made up of many chains of amino acids. Yet somehow, proteins almost always manage to fold themselves in the correct configuration (when they don’t fold correctly, they can cause misfolded-protein diseases such as Alzheimer's, Huntington's, and Parkinson's). Scientists think that proteins fold themselves correctly because the correct configuration is also the state of lowest energy, the state at which the protein becomes stable.

In quantum annealing, the system starts by randomly picking a starting state, and then selecting random neighbor states to see if they have lower energies than the starting state. If they do, the computer replaces the original state with the lower-energy state. The process is considered quantum because it involves quantum tunneling to explore the different states by traveling directly through certain barriers rather than climbing over them. In this way, quantum annealing differs from the classical version, called “simulated annealing,” which explores different states based on temperature. Previous research has shown that quantum annealing has advantages over simulated annealing in some situations. ... ' 

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