
Quantum Entanglement Holds DNA Together, Say Physicists - Anon84
http://www.technologyreview.com/blog/arxiv/25375/?ref=rss
======
PhysicsAndYou
Wow a biophysics related article on HN. I can finally be an interesting
commenter!

First and foremost, no one is writing off quantum mechanics. There are a lot
of physical mechanisms that can't be well described by classical models:
charge transport, some examples in protein folding, optical interactions, etc.

The issue is that current computational resources are limited. We can't even
give a full MM (classical) simulation of a small virus without months of
distributed computing efforts and thats with algorithms that scale like
O(n^3).

Even DFT models that are pretty far from the theory we're looking at O(n^5).
It'll be farther into the future before we can do more.

That said QM/MM simulations of macromolecules (DNA in particular) are
extremely common though the goals may be quite different so I'm not entirely
certain where the basis for the claim that CV entanglement is needed for
stability at a physical level. They do such a simulation with 2 different
factors for the VDW interaction and note that shrinking it by a factor 10
leads to stability issues. (Rather obvious claim in context)

The authors recognize entirely that this model is not going to be accurate.
The question is, how inaccurate can you be before your results don't mean
anything?

To me their work kinda straddles the line. Issues with their simple model I
see: Lack of rotational degrees of freedom of the base-pairs, Lack of a
polarizing solution (water) !!! (Critical since the entire basis of this was
the non-trivial mechanics of non-permanent dipole moments)

And of course the very obvious issues that arise from modeling DNA as just a
plane of positive charge with a single electron orbital.

All they end up saying is that for that scaling factor at the very small value
you don't get as much of an energy increase in the molecule that leads to
instability in a "normal" QM/MM simulation. I'm certainly not convinced that
this energy difference can be directly said to be because of entanglement and
not just flaws in their model and certainly not willing to say that this small
value represents anything physical.

There were a few more confusing things in the analysis but I admit I'm only
glancing over the paper but I think the most we can take away from this is
that there may be non-trivial effects of CV entanglement. Maybe that's all
they really wanted.

~~~
dalke
O(n __3) for classical MM? Electrostatics is O(n __2) and with multipole
methods it's less than that. What's O(n __3) about MM?

~~~
PhysicsAndYou
One of many typos unfortunately.

Keeping track of everything explicitly its n^2.

Also it really, really depends on the level of theory for the scaling of
quantum regions/algorithms. To say at minimum O(n^5) is incorrect.

------
pook
I'm reminded every time I hear about QM being "weird", of Eliezer Yudkowsky's
Quantum Physics sequence.

"I am not going to tell you that quantum mechanics is weird, bizarre,
confusing, or alien. QM is counterintuitive, but that is a problem with your
intuitions, not a problem with quantum mechanics. Quantum mechanics has been
around for billions of years before the Sun coalesced from interstellar
hydrogen. Quantum mechanics was here before you were, and if you have a
problem with that, you are the one who needs to change. QM sure won't. There
are no surprising facts, only models that are surprised by facts; and if a
model is surprised by the facts, it is no credit to that model."

<http://lesswrong.com/lw/r5/the_quantum_physics_sequence/>

------
snissn
As a physicist, one can't even think about 'chemistry' without starting with
the Schrödinger equation..

~~~
niels_olson
as a physics major who went back for med school pre-reqs several years later,
including orgo, this is so true. I spent a huge amount of the class trying to
ignore the screaming oversimplifications.

------
nitrogen
It's disappointing to see the comments section of the arxiv blog being used
for spam.

