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An almost-tomorrow post on biological (or, as Ani likes to say, bee-ological) physics ^_^




So, on this fine Christmas night (yes, I slept all day :D), let me start by introducing myself. I am Ritwika, friend of Rahul’s (who has graciously allowed me the use of this blog), owner of two non-functional blogs (I am that lazy), final year Physics student at IISER T, consummate PhD hunter and also, aspiring writer. Additionally, I tend to write in long, rambl-y sentences with lots of brackets and dashes. Rahul, you will have to overlook that. There, that covers all the bases.

Now, when Rahul – or Poruri, as I call him – asked me whether I could blog in his absence, I thought I could get away with writing anything that came to my head, but after having read the stuff that is here, I realise that this is a predominantly science-y blog (ooh, on that note, a huuuuge shout-out to both Poruri and Shruti for their wonderful posts). So, at least for today, I will stick to tradition.

Going back to me – I am interested in theoretical biophysics, and specifically, in looking at population dynamics, evolution, collective behaviour, energy transfer processes, etc. So, I will just go ahead and talk – non-technically, mind you – about the one general theme in biophysics that I am morbidly fascinated by.

Biological systems and processes, almost as a rule, function like well-oiled machines. Energy transfer is more or less optimised (more on this later – this is my Master’s thesis work), so is information transfer (think of our own brain). The dynamics of interacting populations is a beautiful mathematical study, the most familiar example being the Lotka-Volterra model of predator-prey systems. Evolution itself works optimally, through selection, with stochastic mutations and adaptations (among other things) driving it. When you come to think of it, you realise that there is a pervasive theme of optimal operation in biology, and the prospect of understanding the physics behind this optimality is fascinating.

Now, let us zoom into one particular example of the optimal operation of biological machinery – energy transfer in photosynthetic light harvesting complexes. This process is extremely fast, and extremely efficient. Consequently, classical descriptions haven’t been able to properly elucidate the underlying mechanism. Then there is also the fact that light-matter interactions generally necessitate quantum mechanical descriptions. And, with what we know so far, the current QM understanding of photosynthetic energy transfer hinges on excitonic energy transfer.

I am going to slightly digress here, and briefly explain what an exciton is. To put it simply, an exciton is what we have when there is an excitation in the system, and in looking at the overall state, we need to represent it as a multielectron state delocalised over the system. Or, put even more elegantly, an exciton is a quanta of excitation.

Phew. Now that that is done, I am going to go back to photosynthetic energy transfer, and how there is a theory of excitonic energy transfer that is the current paradigm. But, is that all that is there?

Turns out, there is more to it than straight-forward excitonic transfer. For one, energy transfer in photosynthesis is irreversible, which means that a simple unitary evolution – which is the norm if one deals with closed systems – isn’t quite enough, as far as complete descriptions go. But, if you were to adopt an open quantum description, taking into account the effects of the environment – which, as physicists like to do, is modelled as a bath of harmonic oscillators – you would realise that the environment is, primarily, a dissipative thing. Energy from our system leaks into it, it dephases the excitonic states, and well, how would that help in optimised, quick, and efficient energy transfer?

To quote a Nature news Feature by Philip Ball (I have been doing this ever since I read that article), Nature knows a few tricks that physicists don’t. What happens is this – the structure of the light harvesting complex (my model system is the Fenna-Matthews-Olson complex found in green sulphur bacteria, chosen for the reason that it is one of the most well-studied molecules of its kind, and also because everyone uses the same model system; but for now, let us just call it FMO, pretend that it is a generic molecule, and move on, because I really don’t know much about its structure) is such that the values of relevant parameters that affect energy transfer, are optimised so as to result in a fantastically non-intuitive mechanism called the Phonon Antenna Mechanism. Let us call it PAM.

Now, PAM works such that the dephasing effect of the environment actually results in enhanced energy transfer, from the origin of excitation to the reaction center, when compared to the case of the dissipative environment not being present. That is the brighter side. On the downside is the fact that an analytical theory that elucidates this mechanism is still in the works. But rest assured, there is fantastic natural engineering at work here, which, somehow, has hit upon the configuration of the FMO complex that leads to optimised energy transfer.

And this is just one example of how there is fascinating physics at play in biology. If you are inclined to do so, there is a host of literature on energy transfer in photosynthesis. In particular – for the quantum mechanically inclined – I would suggest the work of M B Plenio and S F Huelga, on PAM, and on the general idea of dephasing assisted transport, and about a quantum mechanical heat engine picture of photosynthetic energy transfer. The literature on other biological processes is practically endless, and also, endlessly fascinating – I have come across charming articles by W Bialek, D S Fisher, M Nowak, N Goldenfeld and O Hallatschek, amongst others.

I will leave you with that, in the hopes that maybe, you would be interested enough to go check out work being done in theoretical biophysics. And tomorrow, I will be back with something less science-y, maybe something about en dashes and em dashes :D.


Ciao! Lemme get back to Christmas pizza and cake. Merry Christmas to you too.

PS: And Poruri, I am sorry the daily post has become almost-tomorrow's post! Also, I have opted for purple font :D 

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