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D-Wave quantum computer solves protein folding problem

A quantum computer from the private company D-Wave, based in Burnaby, British Columbia, has solved the puzzle of how certain proteins fold.

The D-Wave One quantum computer (which bears more than a passing resemblance to the monolith) consists of 128 superconducting quantum bits or ‘qubits’. The computer works on the principle of quantum annealing. Essentially, it involves preparing some sub-group of the qubits into their lowest-possible energy state, or ‘ground state’, and then performing a series of operations to put it into a more complex ground state that can’t be easily solved using classical methods.

If it sounds complicated, it is; so much so that some scientists have questioned D-Wave’s claims in the past. More recently, however, the company has been able to prove that its computer is working as claimed.

The latest  finding from a group at Harvard University in Cambridge, Massachusetts, further backs up D-Wave’s claims of quantum-computing supremacy. The paper, by Alan Aspuru-Guzik and his colleagues, shows that the D-Wave One could predict the lowest-energy configurations of a folded protein. Proteins are very complex, and a quantum computer can, in theory, process all the possible configurations better than a classical one.

The model consisted of mathematical representations of amino acids in a lattice, connected by different interaction strengths. The D-Wave computer found the lowest configurations of amino acids and interactions, which corresponds to the most economical folding of the proteins. It worked, but not particularly well. According to the researchers, 10,000 measurements using an 81-qubit version of the experiment gave the correct answer just 13 times. This was owing, in part, to the limitations of the machine itself, and in part to thermal noise that disrupted the computation. It’s also worth pointing that conventional computers could already solve these particular protein folding problems.

I just got off the phone with Colin Williams, the director of business development at D-Wave, who I was speaking to about another story. We discussed the paper, and he admitted that the computer didn’t work perfectly for the protein problem. But the fact that it worked at all was significant, he says, and things will only get better from here: “As D-Wave goes forward we’re going to make the chips more capable,” he says.


  1. Report this comment

    Chuck Baggett said:

    In the first sentence, “A quantum computer form the private company” has “form” instead of “from”.

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    Mohsen Chitsaz said:

    This is a promising route, however there are two points I wanted to mention:

    1. The title of the news is over stating what D-wave computer has done. D-wave did not solve protein folding problem, instead it solved an extraordinarily simplified model of the problem with only 40 discrete states.

    2. The computation done by D-wave computer is not still clear that is in a quantum mechanical fashion. According to the article, less than 1% of measurements gave the ground state, so I think something that needs to be shown is that if the machine is really doing quantum computation or just computation.

    This route is extremely beautiful and promising and I don’t want to be discouraging, but also I encourage accuracy and precision in the news and reports.


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