D-Wave quantum computer solves protein folding problem

[ScienceRocks]

D-Wave quantum computer solves protein folding problem

17 Aug 2012 | 18:26 BST | Posted by Geoffrey Brumfiel | Category: Uncategorized

A quantum computer form the private company D-Wave 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 Harvard group further backs up D-waves 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 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. The fact that it worked at all, though, 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.

Nature News Blog: D-Wave quantum computer solves protein folding problem : Nature News Blog

Another link http://www.sacbee.com/2012/08/14/4723560/harvard-researchers-use-d-wave.html

Can't be too hard on it as this is like a normal computer in the 1940's.

 

[ScienceRocks]

D-Wave uses quantum method to solve protein folding problem
August 21, 2012
by Lisa Zyga Enlarge 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.

Read more at: http://phys.org/news/2012-08-d-wave-quantum-method-protein-problem.html#jCp

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