Harvard researchers fold proteins with D-Wave quantum computer


December 27, 2012

The D-Wave One quantum computing system (Photo: D-Wave)

The D-Wave One quantum computing system (Photo: D-Wave)

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Many were skeptical when, back in 2007, Canadian company D-Wave announced that it had built the world's first commercially viable quantum computer. Now a study published in the August issue of Nature's Scientific Reports co-authored by D-Wave and Harvard researchers proves the D-Wave One is the real deal.

"The D-Wave computer found the ground-state conformation of six-amino acid lattice protein models. This is the first time a quantum device has been used to tackle optimization problems related to the natural sciences," said Harvard professor Alán Aspuru-Guzik, the lead author of the paper.

The precise details of the protein-folding study are a bit complex, but basically they were looking for the lowest-energy configuration of folded proteins, which is believed to be the correct one since it is the most stable. In nature, proteins fold themselves correctly most of the time, but when they don't they cause diseases such as Alzheimer's. The quantum computer correctly solved 13 times out of 10,000 for four-amino-acid and six-amino-acid sequences under the Miyazawa-Jernigan model of lattice protein folding.

In the abstract, the authors seem optimistic about the computer's prospects, stating that, "the approach employed here can be extended to treat other problems in biophysics and statistical mechanics such as molecular recognition, protein design, and sequence alignment." And Google has adopted the system to train image recognition software.

What's next?

D-Wave has been working on a 512 qubit chip since 2011, but since publication lags behind current work, this study used the company's 128 qubit chip. The experiments only required between five and 81 qubits, and while the 128 qubit chip isn't as powerful as regular supercomputers (or even some desktop computers), the speed is determined mainly by the type of quantum algorithm being run.

However, one can extrapolate speeds, and in an interview with NextBigFuture, D-Wave CTO Geordie Rose said that 512 qubits would be approximately 1,000 times faster than 128 qubits, and a projected 2,048 qubit chip would be 1,000 times faster than 512 qubits.

Source: Nature via D-Wave

About the Author
Jason Falconer Jason is a freelance writer based in central Canada with a background in computer graphics. He has written about hundreds of humanoid robots on his website Plastic Pals and is an avid gamer with an unsightly collection of retro consoles, cartridges, and controllers. All articles by Jason Falconer

Yay for Quantum Computing!

Raymond Johnson

13 times it succeeded out of 10,000 tries? Hmm, makes Microsoft's windows look promising. I'll be impressed when it solves problems 9,999 times out of 10,000. i can live with a little tiny error.


Hate to be a downer, but this doesn't seem to be any improvement to current computing. And the thought that all that has to be done is increase it's computing power doesn't seem to be any different than adding power to current where will this take us in the end?

Jess Atwell

Maybe these new quantum computers will figure out a way to fold space. Then we can get on with the business of interstellar colonization.

Chuck Anziulewicz

I wonder how many times out of 10,000 tries a monkey would get it right? Just wondering if it statistically significant.


Looking forward to the D-Box gaming system!

Paul Smith

Yes Bew, what exactly is the success rate of a monkey solving six-amino-acid folding sequences under the Miyazawa-Jernigan lattice-model?

A working, commercially available quantum computer is a big deal. It is long way away from mass market but this is still a significant benchmark.

In normal computing there are two states, 0 or 1. In quantum computing there are multiple possible states or quantum bits (qbits) so it has the potential to scale exponentially.


It would have been helpful if the author had posted what a purely random approach would have yielded so we can gauge what the significance of 13/10000 is, since otherwise it looks lousy.


@Adrien the short answer is 0/10,000 but check out folding@home (, it is a distributed computing platform that uses mostly donated CPU cycles to complete protein folding.

Here is a quote from the page:

"It's amazing that not only do proteins self-assemble -- fold -- but they do so amazingly quickly: some as fast as a millionth of a second. While this time is very fast on a person's timescale, it's remarkably long for computers to simulate. In fact, it can take about a day to simulate about a hundred nanoseconds (1/1,000,000,000 of a second). Unfortunately, many proteins fold on the millisecond timescale (1,000,000 nanoseconds). Thus, it would take 10,000 CPU days to simulate folding -- i.e. it would take 30 CPU years! That's a long time to wait for one result"

If you are just adding a couple numbers in a single computation it is possible for a random result to occasionally equal the correct result but for something as incredibly complex with as many calculations required to complete a protein folding sequence the odds of a random result being correct are abysmal.


In other news: "What?!! Quantum computers are real!?!"

Ken Dawson

I think 13 out of 10,000 means the 13 correct minimum configurations out of 10,000 possible non minimum configurations. It doesn't mean 13 correct out of 10,000 correct.

Ulf Lindroth

Not all quantum computers are created equal. D-Wave's machine is a special purpose device (albeit still quite versatile) but not what is referred to as a universal gate based Quantum Computer.

I recently tried to sort this out in this blog post.


From the Nature Article : "Even though the quantum device follows a quantum annealing protocol, the odds of measuring the ground state are not necessarily high. For example, in the 81 qubit experiment, only 13 out of 10,000 measurements yielded the desired solution. We attribute these low-percentages to the analog nature of the device and to precision limitations in the real values of the local fields and couplings among the qubits in the experimental setup. "

I think what you have to remember is that quantum computing is completely different than regular computing. From what I recall (I don't have time to comprehend the article, its very advanced) You feed in the question, and the answer is given right more times than not... You collect all the answers of multiple runs and they give you something like a bell shaped curve pointing at the correct answer. Feel free to correct me on that. I'm pretty sure its not as cut and dry as "1+1 = 2" but more like 1+1 = median(1,2,2,3,2,4,2,2,1,2,2,4,4,2,1,5,2,0,2,2,2), with the more calculations performed, the higher acuracy result.

I think a better question might be how many of the 10'000 indicated a unique noncorrect solution. If it was more than 13, then theres something wrong with the computer, or just a statistical fluctuation. Don't you just love quantum mechanics?

Tony Smale

I really find this hard to believe. Has anyone taken the "Quantum computer" apart to see how it actually works? I think in a number of months, we will find out that this is a hoax or complete fraud, similar to all the "Perpetual motion" machines or "Cold fusion" devices out there.


@Satviewer2000 If you would like to go ahead and rip open the D-Wave Computer to show the world that it's merely a fraud, be my guest, but remember that Quantum Computing isn't something as black-and-white as Cold Fusion or Perpetual Motion, and also remember that if you do look at the inside of this D-Wave computer, you are likely to render it useless as all the qubit particles decouple from having been observed.

Kayvon Manian

Quantum mechanics: The Science of how the Universe works, from beginning to end! Has had a 'rough''line''wave' ride into hard science; These past few years, man's timeline, its finally arrived; Hard Core Scientist have embraced Quantum! In doing so, many non-believers, are now believers of Quantum Theory! I teach Quantum Theory of Everything! A Quantum Computer, and and will prove to be very valuable in Quantum Time Line!

Don't believe me study the Science of Quantum and believe!! Or come into my QuantumCafe'Coos, on Facebook!

Dr Gene Landrum, PhD in Quantum!!


My embedded link was dropped. Anyhow, google "Quantum Computing Taxonomy" if you want to learn more about the significant differences in Quantum Computing designs.


So now they have the 1000 times more powerful 512 bit processor - equivalent to 5 petaflops, or the 10th most powerful supercomputer. at least for the specialized problems. If they are able to keep progressing as they promise they can the 2048 bit processor will be 5000 petaflops equivalent,.... or faster the the faster supercomputer in China right now of 35 petaflops.

Nicholas Mathews Hoover
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