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There is a growing interest in the applications of non-equilibrium quantum dynamics to describe biological processes (I'm not talking here about Penrose's old theories, but new stuff -- quantum coherence in light harvesting, magnetoreception etc.). What is the biologists' take on this? Is this just a whim of physicists looking for grants, or a serious part of biological research?

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Have you been listening to Bob McDonald on the CBC? ;) –  leonardo Apr 7 '12 at 23:32

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Absolutely a serious part of research - quantum mechanics defines chemical structure and reactivity. Whenever you see a headline like 'Scientists find quantum effects important in protein activity, weird huh?', read it as 'Scientists find pragmatic classical approximations inadequate in describing protein activity'.

In protein structure, for example, classical molecular dynamics/mechanics are important in generating computationally tractable problems, however they represent a tacit and streamlined parameterisation of underlying quantum mechanics. QM protein structures are usually too gnarly to compute (at least historically speaking), except in regions of interest like an active site, where a model fine-tuned for sequences of amino acids will probably fail badly anyway. As a concrete example, the group that I'm in is in part interested in computationally modelling the active site of plant photosystem II, which contains a cluster of spin-coupled manganese atoms. To glean any useful understanding of how this cluster functions via a computational model, an explicit quantum mechanical level of theory that takes into account electron exchange and correlation must be used. This requirement can probably be extended to any metalloenzyme.

And this isn't touching upon the resonance hole transfer that oxidises the active site, the Davydov solitons that manifest in protein alpha helices, or indeed the quantum electrodynamical origins of the Van der Waals interaction that causes everything to tend to stick to everything else.

Hope this is interesting :D

(note: I am not involved with PetaChem, I just think it's freaking awesome.)

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Extremely interesting! Can you provide some links to papers about the Mn clusters? –  quant_dev Apr 2 '12 at 7:10
@quant_dev - unfortunately there's very little that isn't behind a paywall, but if you don't have an institutional subscription and are happy reading abstracts, this is a decent start. IIRC the authors looked at the active site and proximate protein environment of PSII using a QM simulation (spin-unrestricted density functional theory) embedded in a molecular mechanics simulation. This paper indicates that elements of PSII WOC kinetics are affected by the Jahn-Teller activity of Mn sites. –  Richard Terrett Apr 2 '12 at 12:09
Do you know about some out-of-equilibrium stuff as well? –  quant_dev Apr 2 '12 at 12:18
@quant_dev - please elaborate on what you mean –  Richard Terrett Apr 2 '12 at 14:58
@quant_dev - That link from petachem shows the time evolution of a protein at an ab initio level of theory. I'm not well acquainted with the state of the art, but Car-Parinello molecular dynamics is a type of density functional theory that can handle potentially large molecules. –  Richard Terrett Apr 3 '12 at 9:26

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