Thursday, 24 February 2011

The Quantum World of Plants and Animals.

The Quantum Revolution.

From Planck to Einstein and Bohr, the development of quantum mechanics didn’t have an easy ride. So strange and distant from our experiences in everyday life are its predictions there was a great ‘classical resistance’ to the new theory. Plack himself, the reluctant revolutionary, tried his whole life to do away with the conclusion of the quantum of energy which stemmed from his research in black body radiation. He solved the so called ‘ultraviolet catastrophe’ which apparently predicted an infinite amount of energy to be radiated from a simple heated body with the introduction of discrete packets of energy, given by Planck’s Law: E=hv. Later Einstein, whose work on the photoelectric effect that illustrated the quantisation of the electromagnetic field won him the Nobel Prize, famously said ‘God doesn’t play dice’.*

For me, Quantum Mechanics is right up there with the great modern scientific achievements alongside electrodynamics and Maxwell’s equations and Einstein’s theory of relativity. We have struggled with the physical interpretation of the theory and wrestled with the philosophical consequences in such thought experiments as Schrodinger’s Cat. At first scientists begrudgingly learnt to live with it and, after its phenomenal success, to eventually accept it. Only now in the 21st century would one would argue quantum is truly mainstream. Despite all of this, as usual, it seems nature got there first: by some billion years.

Research is suggesting that biological organisms have been utilising quantum tunnelling and superposition far before we stumbled on the idea. It is thought to be key in maximising the efficiency of photosynthesis, increasing the rate of enzyme reactions and play an important role in the smelling process of animals and humans. This fast growing field has been termed 'Quantum Biology'. Discovering the beautiful complexity of nature in this way is central to science, and there is a clear link developing between what we observe in nature and our advances in materials engineering, computing and medicine.

Quantum Tunnelling.

"I can't help the feeling,

I could go through the ceiling" Radiohead: Fake Plastic Trees

Quantum Tunnelling is pretty weird. Ivan Giaever, who shared a Nobel Prize with Josephson and Esaki for their work in electron tunnelling in solids, describes his scepticism after first hearing about the concept. The main idea is that a particle can overcome a potential barrier (whether it's a bias voltage or the repulsive force of a solid obstacle) even if it does not have enough energy to classically do so. It's kind of like not having enough petrol in your old Skoda to make it all the way up and over the hill on the way to work, and deciding to get the shovel out of the boot.. For particles that act quantum mechanically, the probability of tunnelling from one side of the barrier to the other is non zero, even if kinetic energy is less than the potential energy. The tunnelling probability is however dependant on the height and width of the barrier, making such events as a tennis ball passing straight through a tennis racket or me walking through doors very unlikely indeed. A back of the envelope calculation shows you would have to repeatedly walk into a door for far longer than the age of the universe to be successful. Ouch!

Tunnelling is a direct consequence of the wave-particle duality of matter (so in crossing the barrier, some of the waves initial amplitude is diminished). Another way to explain the phenomena is Heisenberg’s uncertainty principle which states there is a limit to how accurately we can measure the position and momentum of a particle. In other words, for small timescales and small distances, one can ‘borrow’ momentum/ energy required to jump over the barrier. These instances one finds a higher energy are cancelled out by other cases where it is found to have a lower energy than expected, hence preserving the conservation of energy. (phew!)

Fact byte: The temperature in the centre of the Sun isn't sufficient for the fusion of enough nuclei to account for the energy output: the most viable explanation is that tunnelling is playing an important role. The Sun is quantum!

Smells like tunnelling.

How do we smell? What is it about a molecule that determines how smelly it is? Clearly what we perceive as sweet or foul smells is down to the information processing of the signal from the receptors which has evolved over time depending on what is nutritious or toxic. What Physics can try and answer is how the receptors, which act like biological transducers converting information about the odorant molecule into an electrical current, interact with the molecule and by what mechanism. This interaction has been poorly understood in recent years.

The prevalent model in the last 20 years or so is that individual receptors are designed to detect molecules of a specific shape and size. There would be a multitude of receptors in the nose, each with the function of sending off a signal when it sees its target molecule. This ‘lock and key’ approach is common in biology (enzymes for instance). However it cannot explain why similar, indeed identically, shaped molecules (with identical molecular structure but made of different elements or isotopes of the original element) can result in very different smells. Also it is known that there are only a dozen or so olfactory receptors which have been shown to distinguish between thousands of different odorant molecules. Hence although size and shape are clearly significant, the receptors must be able to use another property of the molecules to tell them apart.

In an attempt to address this problem in the mid 90s Luca Turin at University College London proposed a hypothesis whereby the molecule itself provides a ‘bridge’ for an electron to tunnel across a gap from a donor molecule to the acceptor (receptor). The phonons (quanta of thermal vibrations) of the molecule in the gap then effectively assist the tunnelling by tuning the energy barrier and hence the tunnelling probability depends on the vibrational modes of the bonds in the odorant molecule. This would suggest that humans and animals perform molecular spectroscopy every day!

While not wildly controversial, Turin's theory was largely ignored at the time. However there has been more recent research by the ‘London Centre of Nanotechnology’ group in 2007 which tested Turin’s hypothesis. They tested the biological validity of a tunnelling mechanism for smell, calculated that time-scales are in agreement with observations (micro-milliseconds) and showed that a vibrational spectrum is indeed related to odour.** Turin's theory has received some attention recently including an article in last month's New Scientist which is well worth a read.

Green machines.

There has been a great amount of research done recently investigating photosynthesis. What is quite amazing about this process is the remarkable efficiency with which a plant can convert sunlight into the energy to produce carbohydrates and sugars. Theses efficiencies can be as high as 95%. It’s not surprising that this has attracted interest from research groups, in a race to be the first to successfully copy photosynthesis for a new generation of biological solar cells. The process takes place in incredibly small time scales (one million billionths of a second). This appears key to the plant’s party trick, capturing the energy before it has much chance to dissipate into the surroundings. New research is indicating that in fact quantum effects such as coherence and tunnelling could aid the process.

The light is absorbed by proteins in neighbouring pigment molecules which excites the electrons from the ground state to excited state. The energy is then relayed into the reaction centre. These reaction centres are the cells in plants that convert the energy received from excited electrons into useful energy. The advantage of this is that the reaction centre or ‘solar cell’ component can receive the energy from many electron excitations in quick succession. Elisabetta Collini, Gregg Scholes et al at the University of Toronto have been observing the response of the light harvesting proteins in algae, a relatively humble life-form by all accounts, to laser pulse stimulation of various frequencies. Their aim is to figure out exactly why this energy transfer from the pigment cells to the reaction centre is so phenomenally efficient.

The group found the detected emission frequency spectrum did not match that of the initial laser pulses: leading them to the conclusion that there was a superposition of states in the pigment molecules. Their findings suggest that the excited states of the excited pigment molecules display quantum coherence. That is to say the information in the wave-functions of the electrons can be shared between neighbouring molecules. In quantum information science such a superposition of quantum states are the building blocks for qubits in a quantum computer!

The excited states oscillate between neighbouring molecules, and it is the time length of these oscillations which give the strength of quantum coherence in the system. Another way of thinking about this superposition is imagining that the energy transfer from excited electrons passing from molecule to molecule through the maze-like network can effectively explore a number of paths at the same time rather than exploring a path at random until it reaches a reaction centre. This is much like the behaviour observed in the famous double-slit experiment as explained wonderfully here by "Dr Quantum". These effects correlate with the work being done by Flemming et al at the University of Berkley, UCLA. They observed quantum coherence in plant cells in 2007 *** However their experiment had been performed very low temperatures of 77K where the environmental interference (thermal vibrations) can diminish the coherence. The group has recently reported a reproduction of their results at room temperature.


*I recommend ‘QUANTUM: Eisntein, Bohr and the great debate about the nature of reality’ by Manjit Kumar as an excellent history on the development of quantum mechanics and its pioneers.

** paper reference http://arxiv.org/PS_cache/physics/pdf/0611/0611205v1.pdf

*** Scientific American article http://www.scientificamerican.com/article.cfm?id=when-it-comes-to-photosynthesis-plants-perform-quantum-computation

Friday, 18 February 2011

Life in the Slow Lane: Low Reynolds Number and Laminar Flow.


"How to swim"

This was chalked on the board by Prof Olmsted in yesterday's Biophysics lecture. Our hopes of a trip to the swimming pool were quickly dashed. In fact the topic was about the motion of cells and micro-organisms in biology. In particular, if you happen to be such a micro-organism how do you get around in order to seek out nutrients to sustain yourself? With just a simple set of physical apparatus - how would you do it?

It turns out on the micro-scale life isn't as simple as the local swimming baths. If I wanted to do some lengths, I might well choose the breaststroke.It works like jet propulsion, with each stroke I push water backwards giving myself a kick in the right direction. After each kick I will glide under my own inertia, gradually slowing down due to the drag force. There is a balance between inertial and viscous forces. What if I took a swim a bath of gloopy treacle? The viscous forces would be so great that with each kick I wouldn't glide at all. The force from my kick would move me forwards by an arms length and then - freeze - nothing.

The Reynolds number is the ratio between the inertial force and viscous force, and also the ratio between the time it takes me to stop after my stroke and the time it takes me to travel one body's length. It is used in aerodynamics and fluid dynamics by the incredibly smart guys and gals who build our planes, formula 1 cars and submarines. The maths shows that the Reynolds number (Re) is given by the density of the stuff you're swimming in times your velocity times your characteristic length divided by the viscosity (gloopiness) of the stuff you're swimming in. So a low Reynolds number means you're in a thick liquid, or can't travel fast enough to successfully get anywhere (not being a strong swimmer I can relate to the latter).

A consequence of viscous forces dominating over inertial ones is the time reversal of your motion from reversible applied forces, or reciprocal swimming strokes. If you are in the low Reynolds number domain, and do a stroke forwards, and repeat your motion in reverse, you will end up at the same position you started. This seems an obvious statement but check out the jaw dropping demonstration in the YouTube clip. It was done in the 70s by a guy called Geoffrey Taylor. Ignoring the fact he had trouble counting to 5, it's a wonderful clip.

Cellular scales produce an incredibly small Re due to the short length scales and low velocities achievable. So small in fact that it is effectively zero. This is the situation I mentioned with the treacle: turns out bacteria can't do the breaststroke. How do they get around it? Thankfully it turns out cells are pretty smart, and thanks to evolution they aren't ones to shirk a challenge. The solution is a non reciprocal method of swimming. (your stroke forward has different dynamics to the stroke back, or recovery stroke).

One solution that has evolved is the Asymmetric Cilia. They are small whip like appendages which can generate net thrust. The cilia sweeps from left to right like an arm, then bends by an angle for the recovery stroke. Many cells use this method to get from A to B in order to eat nutrients which otherwise diffuse out of reach. Other stationary cells use the cilia as a sort of arm to channel food and liquid into their path.

Another is the perhaps more well known rotary flagellum. It's an amazing piece of biological nanotechnology which consists of a helical rod (imagine like a curly pigs tail) which is rotated about its axis by a motor and results in a net force along the axis of the helix proportional to the radius and angular frequency of rotation. This is how the tail of the sperm cell propels it around, although I think most people imagine the tail to work like that of a tadpole flapping from side to side. The fact is this just wouldn't work! (reciprocal motion) It is truly wonderful how evolution has tackled an apparently huge problem with such ingenuity that any modern day engineer would be proud.

Into the great unknown

So, I figured after about 4 years of undergraduate Physics and with commencing my PhD next year I'd start an amateur science blog. The intention will be to talk about new papers in current research, summarise science news that grabs my eye and just give some examples of why science is *awesome* to the average reader.

While I'm no professional writer, nor a scientific genius, I love the subject and hope that I can impart what little knowledge and insight I have to people who don't have the time or desire to trawl through journals like Nature or Science! So sit back, relax and let the nerdiness flow.

I have found starting with a joke often helps. So how about the classic..

"Entropy: it's not what it used to be"