On the thermodynamics of Farts - part one

We've all been there, someone comes into the classroom, farts through the door, and leaves. 

What happenes to the room? How comes the fart can eventually even be smelt at the back of the room? Does the fart warm or cool the farter? These are all important questions that can be dealt with using thermodynamics. Today I will deal with the first part. What happens to the room.

Lets consider the room to be our system. The fart (composed of fartrogen dixoide molecules) is a fluid. Remember a fluid is either a gas or a liquid. So the fluid enters the room and with it comes the energy it contains. Energy is contained by all material (the particles whizz around at room temperature) and this is called the internal energy, U of the material, or in this case of the fart. In addition some work has been done by the farter to PUSH the fart into the room (our system). This work is the work of gas expansion, which is just the pressure times the volume of the gas, PV.

Thus the total energy added to the room is U + PV.

It turns out that this is how we define Enthalpy H so that

H = U + PV

In engineering we use enthalpy to follow the energy when fluids enter or leave systems. If there is a vent in the room, and there hopefuly is, fluids will be leaving the room and we would have to account for this when summing the energy of the system.

It turns out that under constant pressure conditions changes in enthalpy are equal to the heat (given off or supplied to)  the system, q,  i.e

ΔH = Δq

where Δ signifies a measurable change in the quantity.

This is why chemists use the term enthalpy to describe the heat of reaction, they are equivalent. We can use enthalpy to describe heat only under constant pressure conditions. Conveniently when looking at reactions in your test tube, pressure is pretty constant, it is atmospheric pressure!!

The stiffness of biomolecules - from DNA to actin

When engineers talk about the stiffness of materials they usually describe the Young's modulus, E, the ratio of stress to strain. This is constant for any geometry of that particular material. For example the Young's modulus of a particular type of steel might be 200 GPa and that of a bone might be 30 GPa.  So how would one describe the stiffness of tiny soft and floppy biomolecules? These are so puny that they are constantly being buffeted by their environment and thermal fluctuations. They can also adopt a myriad of different conformations.


We use a parameter called the PERSISTENCE LENGTH, to describe the stiffness of molecules like DNA and actin.

So what exactly is the persistence length which is often given the symbol ξ ? Essentially it is the length over which a polymer remains straight. When considering biomolecules we talk about the competition between thermal fluctuations and deterministic energy costs, Our thermal energy is KT (fluctuations) and this must be compared to the elastic energy of the polymer, that is:

here K is the famous Boltzmann's constant, T is the temperature, E is the Young's modulus, I is the geometric moment, and R is the radius  of curvature. L is the length of the polymer. Defining the persistence length to be that length for which the radius of curvature (of the bend) is equal to the length of the polymer means we can sett  L and R equal to ξ . Thus we obtain

There is a more elegant way to derive the same result using tangent correlation functions but this approach is nice and simple. So in terms of persistence length how stiff is Actin? Is DNA stiff or floppy. What about spaghetti? The values in the table below are approximate!

What do these values mean? Well spaghetti would need to be very very long for thermal fluctuations at room temperature to bend it. It turns out that DNA is very stiff for a molecule of its size. Reassuringly microtubules and actin are stiff for length scales exceeding that of the cells that they reinforce.


Messy proteins

Without proteins nothing in our body would happen.  For almost everything in our body depends on proteins, from respiration to cell division. The molecular motors responsible for cell division or carrying cargo from one part of a cell to another, to the very glue that holds tissue together. Lets just say proteins are the engines of our existence.

Proteins consist of polymer chains folded into intricate three dimensional structures. If they arent folded absolutley perfectly, then they wont work properly. Moreover every molecule of the same protein folds into exactly the same conformation! Pretty remarkable.

Protein structure reminds me of one of my favourite childhood characters, Mr Messy

What a protein does when it folds is it explores lots and lots of possible conformations. The laws of thermodynamics mean that it will adapt the lowest possible energy state, which happens to be the highest entropy state. The final state is dictated by the sequence of amino acids in each chain, which in turn affect interactions between other chains and the solvent the protein resides in.

One of the proteins I've been working on is the enzyme nitric oxide synthase, see below. At first inspection it looks pretty messy. But not everything is what it seems...



Sending a virus in an envelope

Some viruses are enclosed inside a lipid bilayer annexed from the infected cell. Protruding from these envelopes are glycoprotein "spikes" which are important in anchoring and fusing the virus particle to the target cell. In my lab we are very interested in these ENVELOPED viruses including HIV, Flu and Ebola.

If you are unfortunate to have a virus such as HIV, you will have gazillions of these virus particles floating around your body. Have a look at the little bugger. This one was drawn by my MEng student Penny Miles (who is now working at Ely Lilly).

                The HIV virion

At first sight you can see a beautiful symmetry, in fact you could say this is almost a perfect self-assembled structure. I use the term self-assembled lightly as obviously the particle is assembled with the help of the host cell machinery. The spikes attach the virus particle, or virion, to the immune cell surface. This then fuses and infects the target cell with its cargo, the viral RNA. Now here is the clever bit. The virus particle also contains an enzyme that turns the RNA into DNA, so that this DNA can then be incorporated into the host genome, hijacking the cellular machinery to produce tonnes more virus particles.

It turns out that this conversion from RNA to DNA is highly prone to error, which means the virus particle often mutates, rendering some treatments useless. In my lab we are interested in how the virus attaches, fuses and infects at the molecular level. If we understand this perhaps more generic drugs could be developed targeting these processes and being less susceptible to viral mutation.

Viral mutation is a real pain. Take the new flu jab. It is only 3% effective largely because of mutated viral strains. This demonstrates how fast viruses can mutate. Our next system will be Ebola. One hypothesis regarding why Ebola is so deadly is that the glycoprotein spikes "shed" when the cell is churning them out. These spikes then cause an immune response severe enough to cause organ shutdown and probable death.

HIV, Ebola...deadly but fascinating!

 

Thermal jiggling and why I married someone called KT

Cells, viruses and bacteria are organised structures of biomolecules. All of these biomolecules are constantly jiggling about due to thermal energy. Other deterministic forces, such as those driving a molecular motor from one side of the cell to another (sometimes diffusion just isn't good enough over long distances), are also at play. They are necessary to get things done and move things in a straight line!!

So whats more important for biomolecules in these systems, thermal jiggling or deterministic forces. It turns out that the thermal energy at room temperature can be calculated by the most simple of formula:

Thermal energy = KT

K is the incredible Boltzmann's constant and T is the temperature. It turns out at room temperature that 

KT = 4.1 pN nm

As molecular motors work with picoNewton forces over distances of nm there will be a constant competition between these thermal forces and tiny little motors trying to move cargo from one side of the cell to the other.

It turns out I had a fish called Boltzmann (Unfortunately he died), and I have a wife called KT. What a coincidence!!


How to keep my trifle cold

I like trifle, especially extra triple layer sherry trifle from Marks and Spencers. But how does the fridge keep my trifle cold. The cold space in the fridge needs to be kept at about 8 degrees Centigrade. To achieve this heat has to be dumped out of the cold space otherwise it would warm up and it wouldn't be cold anymore!

If we open the fridge door heat would flow into the cold space as we know from the second law of thermodynamics that heat flows from hot to cold.  That is the direction of things!!. So how do we get the heat flowing in the opposite direction?

The big trick of the fridge is that it doesn't have to make heat flow "in the wrong direction". Our lovely fridge sticks to the rules, or at least doesn't have to exert hard work pushing against the tide.

My fridge and most fridges work as vapour-compression systems.  See diagram below.  A very very cold fluid (the refrigerant), colder than the cold space in the fridge, passes the cold space, dragging out the heat from the "hotter" cold space, into the colder fluid. This satisfies  heat flowing from hot to cold. Somehow this heat stored in the refrigerant must now be dumped somewhere. To achieve this the fluid is compressed which heats it up to temperatures above that of the surroundings in my kitchen. This heat can then be dumped out the back of the fridge , which is why the back of the fridge is nice and warm.

The fluid is then cooled back down by expanding it through a valve, and then the cycle continues indefinitely, dragging heat out of the cold space, dumping it behind the fridge, and cooling the fluid through the valve.

If you don't believe me take a really sharp knife and poke around in the ice box of your freezer. If you poke hard enough you can perforate the plastic and release the fluid. [Warning, this will break your fridge, only suitable for  adults who have enough money to buy a new fridge]

In the diagram Qin is the heat going from the cold space into the refrigerant, evaporating it in the process. Qout is the heat being dumped out the back of the fridge, as the heat leaves the fluid, the fluid condenses. Win is the work needed to run the compressor, this is why we have to plug our fridge in!!

In the diagram Qin is the heat going from the cold space into the refrigerant, evaporating it in the process. Qout is the heat being dumped out the back of the fridge, as the heat leaves the fluid, the fluid condenses. Win is the work needed to run the compressor, this is why we have to plug our fridge in!!

Curly hair and thermodynamics

Curly hair is cool. You stretch and straighten one  in your hands, let it go, and it springs back into curly messiness. 

This always reminds me of the behaviour of an ENTROPIC SPRING. When you stretch an entropic spring, rubber molecules for example, you have to do work to stretch it. When stretched there are fewer ways to arrange the molecule than in its tangled state, thus you have decreased its entropy. The molecule wants to spring back into its messy/random state to increase its entropy (disorder) and lower its free energy.

Curly hair and entropy, curly hair and entropy...

 


What am I?

Q - What am I?

A - I am a bilaterally symmetrical, metamerically segmented, triploblastic, coelomate.

This is because we as humans  have mirror symmetry through the Saggital plane, we are constructed of a linear series of repeating parts - though not as pronounced as in an Earth worm, we have three primary tissues, and finally we have a body cavity.


The origins of life on Earth

How did life on Earth begin? That is, how was there a transition from non-living matter, the primordial soup, to systems that could grow, divide, transfer information between generations, and evolve.

 

Szostak and others have pioneered the idea of a protocell, that is a primitive ancestor of modern day cells, possessing the fundamental characteristics of life.  They are enveloped by fatty acid bilayers and contain RNA capable of both encoding information and catalysing reactions.

Szostak's model protocells are elegant but havent been fully implemented in the lab. Moreover his systems assume that the RNA polymer was there to be utilitsesd in the first place, the so-called RNA world hypothesis.

My PhD work concerned how biomolecules like RNA could come into existence in the first place. I worked on the hypothesis that the inherent order from crystals could be translated into the assembly of prebiotically available monomers. In particular I looked at the crystal directed assembly of the nucleic acid bases- adenine, thymine, guanine and cytosine. I also looked at the origin of biological chirality. Our group (my supervisor, myself and a postdoc) were successful in creating the first chiral surface from adsorbed amino acids.

Anyway here and now my group are working on the Newcastle protocell model. We want to create life in a test tube, from scratch. This will be a lifetimes work with absolutely no guarantee of  even partial success. 

The limitations of synthetic biology

Question: Is synthetic biology going to cure cancer, save the planet from global warming, and replace machines with cells capable of advanced computation?

Answer. Absolutely not.

So why are we being inundated by such predictions from both media and government agencies. Why is such hype allowed to spin out of control?

 

This is probably because scientists refuse to talk about the limits of synthetic biology. It turns out that if you try and do anything too extreme to a cell, the cell dies. This is why you may be able to squeeze a drop of biofuel out of some bacteria but to produce anything in usable quantities is near impossible. With respect to harnessing the power of cell metabolism for advanced computation, individual genetic circuits can be created, but only a few can be connected together before the cell begins to act in a chaotic manner. This isnt to say such work shouldnt be funded, some of these "toy systems" are both elegant and clever, worthy of being labelled as fantastic science.

I forsee some nice developments in drug synthesis and biosensor technology, but these developments could all be carried out by non synthetic biology routes, probably quicker and faster. Besides these advances would occur without the "synthetic biology" spin if the less sexy genetic engineering description would have been left alone.

Where synthetic biology really does come into is own is in the field of artificial life and artificial biological molecules. Combined with directed evolution, in my opinion, this is the real synthetic biology. It might not have immediate obvious applications but synthetic biology in this form can revolutionise knowledge and advance civilisation. However the time frame for such advances could be on the order of decades. We will all have to be very patient.