On 5/17/2013 1:21 PM, John Clark wrote:
On Fri, May 17, 2013 at 2:24 PM, meekerdb <meeke...@verizon.net <mailto:meeke...@verizon.net>> wrote:

> This is what makes one think the D-wave may just be a special purpose machine,

There is no "may be" about it, as I said D-wave's chip is a special purpose machine, but if it can solve the protein folding problem that's one hell of a special purpose.

But as I understand the problems its solve quickly, they are like Ising and satisfiability problems - they are essentially minimization over a set of binary choices. I don't think protein folding can be put in that form because the folds can be at different angles, not just fold/not-fold.

    > For example if you wanted to find the EM field that minimizes the energy 
for a
    give configuration of charges that's a had problem for a general purpose 
    using the best digital algorithm, but it's a trivial problem for a special 
computer that just puts charges in those places and measures the field.

Yes then you could forget about calculation and just measure the electric field at any point you were interested in, but what if you were given the complicated shape of the electric field and wanted to know the configuration of positive and negative charges that would produce it? More practically how do you arrange the 20 amino acids, some of which attract each other while others repel, so that they have the least energy; that is to say, if I want to form a given shape what linear sequence of amino acids do I need so that they all fold up into that given shape? Solving this problem would have huge implications for medicine and for the development of advanced Nanotechnology, but it's a problem too big for conventional computers but perhaps not for a adiabatic quantum computer of D-Wave's sort if it had a few thousand qubits or so.

Yes, I'm aware that protein folding is the holy grail of quantum computing - along with breaking everybody's security codes.

    > I'd like to see a paper on its theory of operation.

To my knowledge such a paper does not yet exist, at least not a detailed definitive one. The paper I gave a link to was about the results of it's operation, it was empirical not theoretical. They have some general hunches but even the people who made it don't claim to know exactly how D-Wave's machine works.

That's another thing that makes me suspicious. It's something you hear from inventors of perpetual motion machines: We can't explain exactly how it works, we just know that it does.

There are even some who say that it doesn't even calculate using quantum mechanical principles, although the number of people saying that is much smaller now than it was a year ago. And however it works there is now little doubt that it does.

It works on some problems, but whether it works better than a special purpose computer designed for that class of problems is still doubtful.


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