Dr Administrator

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Sep 29 2009

An introduction to the big and shiny

So off to university I skipped, with paternal instructions to “blossom”. I did BSc Chemical Physics at Bristol University. This is a fine course for the indecisive, such as myself who couldn’t decide whether they were chemists or physicists. There were only 16 students in my year, we could all fit in one lift in the physics building. The chemical physics degree involves most of the first year chemistry and physics courses, but in later years you drop organic chemistry, particle physics and astrophysics to make space to do courses in the rest of chemistry and physics. This training means I’m less bemused by molecules than the majority of physicists.

It was at Bristol that I was introduced to big, shiny machines for doing science: for my final year project I worked on Extended X-ray Absorption Fine Structure (EXAFS) at the Daresbury Synchrotron Radiation Source (SRS).

I was using EXAFS to discover something about the structure of molecules in solution, and the arrangement of a glass around metal ions. This is typical of the sorts of study done at synchrotron sources: finding exactly where the atoms in a particular material. Where the atoms are helps you understand the properties of the material: what reactions does it catalyse, how well does it conduct, how strong is it, and so on.

The synchrotron radiation source is a device for producing huge quantities of light all the way across the spectrum from x-rays to ultra-violet light, passing through the visible spectrum on the way. To do this you make electrons go round and round in circles really fast inside an evacuated tube, as they go around they emit electromagnetic radiation: here’s a practical application of relativity – the electrons are traveling at a substantial fraction of the speed of light, so to calculate (and control) their behaviour you need to include relativistic effects. X-rays are actually emitted when the electrons pass through the intriguingly labelled wigglers and undulators – sets of cunningly arranged magnets around the evacuated tube.

The SRS was a pretty big machine – 30 metres in diameter, it closed at the end of 2008 to be replaced by Diamond which is substantially larger. You can see SRS, along with Diamond (near Harwell) and the ESRF in Grenoble, which is even bigger still, on this Google Map. The ring shape of SRS is just about apparent, Diamond and ESRF are very obviously rings.

I’ve worked in several big science facilities (all of them either neutron or synchrotron sources), they have  some common features. Separate instruments cluster around either a ring shaped source or a central point – a beam line (usually an evacuated metal tube) runs from the source to your experiment. The instruments have been built for different consortia by a small team and then used by scientists from around the world. The instruments are scattered around warehouse-sized sheds, filled with a wide range of machinery (which generally contribute to rather high background noise). The control stations for each instrument may be in portacabins, or small corrals. For neutron and x-ray facilities there are a lot of really big concrete blocks around to block harmful radiation.

The deal with working on these instruments is that they run 24 hours a day, and you apply for time on them. If your application is successful then you get to use the apparatus for a block of time, typically a couple of days or so. Some users are lucky: their experiments take days or hours to run, so they can pop off to the pub between runs. I’ve always been stuck doing experiments which last 20-30 minutes per shot. Normally you try to get a team of three or four people to work in shifts, through the night you survive on machine coffee, cantankerous vending machines and possibly loud music. You try to do data analysis as you go, to make sure nothing is going wrong and to help pick which samples to run next. These are one-off research machines, so the data analysis process may be a bit convoluted, and not very user-friendly.

It turns out I have some pictures from my visits to Daresbury (as part of my small obsessive streak I digitized my old photo collection a few years ago)

This is me looking really very boyish at the control station for the EXAFS machine, that’s the back of Sue’s head. Sue was a PhD student working in the same lab as me.

I’m pretty sure this is the EXAFS station I worked on, John is pointing at a polysytrene vessel containing liquid nitrogen (not quite sure why). John was another member of the research group.

This isn’t the equipment I was using but see how shiny it is, how many bolts hold it together and how many unexplained protruberances it has. Who can but fall in love with such things?

All in all it was a rather exciting introduction to the world of research science. My rather small contribution to the measurement of cobalt ions in glasses (which were subtle shades of blue and pink) led to my first paper[1] in the scientific literature!

Reference
1. Harrison, C.C., X.C. Li, I. Hopkinson, S.E. Stratford, and A.G. Orpen, Ultraviolet-Visible-Near-Infrared and EXAFS Study of Co-Ii Coordination Chemistry in Post-Doped Silica Sol-Gel Glasses. Journal of the Chemical Society-Faraday Transactions, 1993. 89(22): p. 4115-4122.

Sep 27 2009

The Mock Magnetic Resonance Imaging Machine

One of the images above shows a real magnetic resonance imager (MRI) and one is a mock one – can you tell which is which?*…. I’ve been visiting another lab where they do medical imaging, I’m not a medical physicist myself but a few years ago I did some work using a magnetic resonance imaging technique called STRAFI[1,2] – so I’ve had some contact with the nuclear magnetic resonance tribe.

(Nuclear) magnetic resonance imaging is used for non-invasively looking at a person’s giblets and as such is really useful for doctors. Unlike x-ray imaging it is best for looking at squishy bits, x-rays are best used on bones.

The core of the technique is to put your subject in a VERY BIG magnet. The magnets used for medical imaging are typically 1.5Tesla or 3.0Tesla, this is hundreds of times the strength of a little bar magnet and approaching 100,000 times the strength of the earth’s magnetic field. A big nmr spectrometer will have a field of up to about 20T.

I’m not going to try explaining magnetic resonance imaging or nuclear magnetic resonance, the linked wikipedia articles look pretty good. It’s worth noting that you can make a good guess that someone is explaining nmr to a neophyte by the distinctive waving of their arms. nmr scientists seem inordinately fond of acronyms (DANTE, ADEQUATE, INADEQUATE, WEFT, NOESY, GRASE…) and I have the sneaking suspicion that they spend more time inventing their acronym than designing their experiment.

The idea with the mock magnet is that patients find the fairly confined space of the MRI machine a bit claustrophobic, but you can get them used to the idea using the mock magnet. Also if you’re doing experiments in the machine you can check your bits and pieces are going to fit in offline.

I enjoyed my time with the high field magnet, they’re clad in a shiny cryostat and they’re fond of ferromagnetic materials (like steel), this means they tend to stand alone in the middle of the lab. You can make the owner of a high field magnet very nervous by casually waving a screwdriver around in the presence of his “precious”. Even at a distance of 3metres a reasonable size magnet exerts a very noticeable pull. Once you’ve got the screwdriver stuck to the magnet it’s rather difficult to remove. Have a look on YouTube for a whole pile of videos on introducing metal objects to MRI machines.

Magnetic resonance imaging is a development of chemical shift nuclear magnetic resonance (nmr) spectroscopy, which has been keeping chemists happy for years. People are inordinately scared of the word “nuclear”, so for presentational reasons the “nuclear” is dropped from the name of the imaging technique.

An exciting aspect of nuclear magnetic resonance (and other areas involving big magnets) is the “magnet quench” phenomena, this is the problem that has caused so much trouble at CERN recently. High field magnets work by putting a large current (tens of amps) into a superconducting coil (or solenoid). The superconductors used in magnets have to be cooled by a combination of liquid helium (really cold) and liquid nitrogen (not quite so cold, but cheaper). Whilst superconducting, everything is fine – the current can flow for ever producing a magnetic field. However, if by accident or design, the superconductor stops superconducting then it heats up it’s liquid gas jacket, which vapourises potentially very rapidly. Here’s another video of  a controlled magnet quench, featuring a pretty, shiny magnet. The first minute is best, the venting helium sounds like a strange musical instrument.

I’m idly wondering whether a magnetic resonance imager embodies the most Nobel Prizes of any device you’re likely to meet in everyday life. Heike Kamerlingh Onnes won the 1913 physics prize “for his investigations on the properties of matter at low temperatures which led, inter alia, to the production of liquid helium”. Bardeen, Cooper and Schrieffer got the 1972 prize for their theoretical work on superconductors. Lauterbur and Mansfield received the 2003 prize for medicine for the development magnetic resonance imaging. There’s a whole bunch of other nuclear magnetic resonance prizes, arguably you could include Marconi for his development of “wireless telegraphy”.

*Actually, they’re both the same – I couldn’t take pictures of the machines I saw.

References

1.    Hopkinson, I., R.A.L. Jones, P.J. McDonald, B. Newling, A. Lecat, and S. Livings, Water ingress into starch and sucrose:starch systems. Polymer, 2001. 42(11): p. 4947-4956.
2.    Hopkinson, I., R.A.L. Jones, S. Black, D.M. Lane, and P.J. McDonald, Fickian and Case II diffusion of water into amylose: a stray field NMR study. Carbohydrate Polymers, 1997. 34(1-2): p. 39-47.

Sep 24 2009

The Dorothy Hopkinson Memorial Solar Panel

This post is in memory of my paternal grandmother: Dorothy Hopkinson. This isn’t going to be a maudlin post: granny died about 18 months ago at a fair old age. I remember her for her cheery smile, ultra-competitive playing of cards and Scrabble (whilst simultaneously claiming to be unconcerned by the outcome), her white drop-handlebar bike which she rode into her sixties, spectacles at a jaunty angle as she slept: snoring in front of the TV, icecream made from evaporated milk in battered aluminium dishes and nettle soup. When she died she left some money which I used to buy a direct water heating solar panel which I have christened “The Dorothy Hopkinson Memorial Solar Panel”.

So to the panel: bought from Solartwin it cost about £3000, it comprises a single panel about 6ft by 4ft which is on our roof. Installation was in September 2008, took about four hours and is minimally invasive. The panel takes cold water as it is heading towards the hot water tank, circulates it around the panel (as long as it’s sunny) heating it as it goes, then feeds it back into the top of the hot water tank. Our roof isn’t ideally oriented, it faces west rather than south, so it catches the afternoon sun. There’s only two of us in the house, we use gas for heating, hot water and cooking – so the solar panel is replacing some of that water heating. Our gas bills are already pretty low (~£360 per year). At the same time that we had the solar panel installed we added to our loft insulation and also significantly improved the insulation on the hot water tank (previously it had a flimsy red jacket, worn off the shoulder). As a side note, I found the rolls of loft insulation from B&Q to be rather huggable ;-)

I have, of course, been recording my gas and electric readings every Saturday morning for the last couple of years. Okay, I appreciate most people don’t consider this “natural” but it isn’t hurting anyone and it does give me some nice numbers to play with. Obsessive data collection has a fine track record in science: Tycho Brahe for example spent years collecting data on planetary orbits, Nevil Maskelyne collected data for determining the longitude from the location of the moon, J.D. Bernal’s poor lab technician spent what must have been an incredible amount of time fishing balls out of a bag, recording their exact location as he went (that’s more data collection by proxy) (these are just the ones I can remember off the top of my head). Of course computers and electronics have meant that a lot of data collection can be automated but there’s still a place for a bit of tedious manual data collection in the modern lab (or home). Feel free to add to tales of heroic data collection in the comments.

I give the gas and electricity numbers to a little program I wrote in C# (a relatively new programming language), which plots them out. I used C# as a little exercise to get me using the language – normally I use Matlab (which is a language environment more suited to scientific programming).

Making graphs with numbers comes very naturally to me, and I find it very easy to read a graph. But I observe when we go walking that I’m much happier reading an OS map than my wife who prefers words in a guide book – so I’m not sure everyone reads a graph in the way I do. Perhaps you’d like to comment?

So in the graph above, time runs along the bottom axis from left to right, the gas used in a week runs in the vertical direction. The mountainous bits are the winters, when the central heating is switched on. The relatively flat bits in between are the summers. First thing that strikes you is that the amount of gas used for central heating in the winter is huge (about ten times more) compared to the amount used just to heat water, during the summer. The solar panel was installed in September 2008 (almost a year ago),  over the winter it probably had relatively little effect, although looking at the raw numbers gas usage over Winter 2008/09 was about 20% lower than Winter 2007/8 despite this year being a colder winter. This is probably due to the improved insulation installed at the same time, we went from about 10cm thickness to about 25cm thickness. In the summer the reduction in gas usage is pretty large – down by 55%. Through this summer you can see that the gas usage drops gently to a minimum around June, this is due to the increasing height of the sun in the sky and the lengthening day.

Was the panel worth it? Well, it is quite exciting seeing your water getting heated for “free”, and during the summer months (even a relatively poor summer) we used a lot less gas. In financial terms the payback time for us is very long, although with a larger household and larger hot water tank the pay-off time would be reasonable (i.e. <10 years). Personally, I think the financial argument is missing the point, if we only change our behaviour for short term financial benefit we will all steam, gently over the next 100 years or so.

Sep 21 2009

57 varieties

At the end of the last post I said it wasn’t important what sort of scientist I was. This isn’t entirely true, once you leave school you have to make a fairly definite decision as to what you will study at university. In fact, in the UK, you narrow down your options quite significantly at the age of 16, when you chose which A-levels to do.

This is a rather timely post since across the country thousands of students will be exchanging information on A-levels as they start at university, and it’s a pretty safe topic of conversation.

For my A-levels I did chemistry, physics and a double helping of maths. To be honest it’s a very long time ago that I decided to follow this path, so some of the thinking behind this choice has left me. I like playing with numbers (and computers) which explains the maths. Chemistry was just fun: involving fire, fumes, pretty colours, fragrant solvents and other cool stuff – okay cooking peas in different salt solutions and processing cabbage to measure vitamin levels and the thing with the liver and the apple were a bit unpleasant but at least gripping – I can remember them 20 years later. I don’t remember greatly enjoying physics at school, but it seemed to have great potential (astronomy, Einstein, gadegts and so forth). I really wish I’d done biology as well, I think I was put off by the “naming of parts” and the fact that most of the specimens for dissection had gone off a bit.

Of course as time passes the broad division of science into three areas (physics, chemistry, biology) seems awfully crude and as I progressed through academia I seemed to end up in ever smaller silos – hence the 57 varieties. Back in the good old days scientists ranged freely over vast areas, nowadays it feels like we struggle to find an ever smaller niche to call our own. I don’t really want to be master of one tiny corner, I want to be a welcome visitor all over town.

Sep 20 2009

The Scientist

So I announced my scientist-ness in my profile to the right. Why did I do that?

It’s the tribe I belong to, the people I feel kinship with across the world, the badge I’m proud to wear, it’s the single word that says the most about me.

I’m told my first words were “oooo…look!”, this to my mind is the first half of the mindset of a scientist. Mark Carwardine has just illustrated this nicely on the rather wonderful TV programme “Last Chance to See“, they’re on Madagascar. He’s wandering around crying out “oooo….look”, pointing things out to Stephen Fry: a leaf-tailed gecko, a pygmy chameleon, sifaka… Okay, so he is varying his vocabulary a bit, but that’s the gist.

“Why?” is the other half of the mindset. In the case of Madagascar, it’s that way (rich in unique wildlife) because it split from the rest of Africa long ago. And in the glorious recursive way of it all those few words “…it split from the rest of Africa long ago” lead into another story of how the continents we stand on are gliding across the world (albeit very slowly).

To me it doesn’t really matter the type of scientist, it’s an artificial division. “oooo…look” and “why?” are the important things. Perhaps everyone thinks this way, but some of us have just had the fortune to get paid for it.