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.
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.
if you get a chance, check out a book by 'Bruce H. Lipton PhD' called 'The biology of belief', it was recommended to me by a cellular biologist friend of mine, and it delves further into this topic.
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."
9 comments
[ 2.1 ms ] story [ 31.8 ms ] threadFirst 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.
if you get a chance, check out a book by 'Bruce H. Lipton PhD' called 'The biology of belief', it was recommended to me by a cellular biologist friend of mine, and it delves further into this topic.
very interesting indeed
cheers
This thing?
I'm not for pseudo-scientific garbage.
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.
"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/