Oodles of noodles, string and cello tape.

The mere mention of those two common household binders, string and cello tape always makes me think of Moving to black water by Reuben. Such a quality song and one close o my heart. Well all of Reuben’s work is actually since it evokes such strong memories of friendship. It’s good to hold on to fond memories like that. I must admit I’m starting to get a little homesick, especially with how crazy busy I am at the moment, I can’t believe I’ve been here three months already.

Anyway enough of my moaning that's not what you want to read about is it. This week we have had yet another slot of beamtime and we’re currently four days in. I decided to take the night shift this time around in the hopes I could easily get in touch with people from home. Alas it was not to be as most of the time has been spent working. What has made things worse is that I’m still struggling to get something delivered back to the UK, so I’ve had to work extra hours since the admin staff are only in work 9-5:30.

The reason beamtime is so mental is because it is very precious. With only 50 experimental hutches and millions of prospective users world wide, experiment time at a synchrotron is very precious. As such we try and make the most of any time we are assigned and this means performing experiments around the clock. Straight off the bat I won’t lie, it’s not fun, it does awful things to your body, but it is very interesting.

For this series of experiments I’ve not been working on my own project but helping the experiments of other members of my group, development of a Coherent diffraction-imaging (CDI) chamber. This has again meant long hours stuck inside the controlled atmosphere and artificial lighting of the ring. Fortunately the weather outside has been rubbish so I’ve not been missing too much.

Now I’ve talked about the theory of CDI before but here is a little refresher. Essentially you are using a very fine X-ray beam to probe the structure of small biological samples, usually a few microns (0.001cm). When the beam interacts with the sample it is scattered. The various types of scattering give different information. The small angles give information about the overall shape and size of the sample, whilst the higher angles will give you an impression of areas of electron density, and from this you can infer internal or surface structures.

Now of course this is just the theory and what I’ll discuss now are the practicalities. Firstly you have to make your X-ray beam coherent. Coherence describes light in which all the photons are travelling in-phase, or parallel, to each other. Picture a 4-lane motorway with four cars that are all driving side by side, then imagine that their paths bend to the left and right rather than being a straight line, but the cars remain side by side. This is kind of what coherent light would look like.

The problem is that when X-ray photons are emitted it is not coherent but in random bunches. To make it coherent we must filter out the unwanted photons and retain just those travelling in the direction we want them to, in the previous sample this would be the restricted lane of the motorway. This is achieved by placing a series of mirrors and slits in the path of the beam to filter the unwanted photons giving us a single beam. This is then reduced in size by passing it through a small aperture called a pinhole. Typically we reduce the beam size from 1mm to about 10 microns.

The crucial part is that all these focusing elements must be precisely aligned, as x-rays will scatter when they interact with any matter. This will give us a lot of ‘noise’ when the final beam eventually reaches the detector. The way we’ve gotten around this problem is to have each element mounted to a very fine motor stage all held within one chamber. Using computer software and a photodiode to detect the x-rays, the various optics components are aligned one by one.

This process is very time consuming and actually took up the first two days of our experiment. This is again why it is so important to make full use of the 24 hours we are given. We were in fact slowed down at one point. A new component we’d purchased for the chamber had not been designed quite right. It was too heavy and under the high vacuum the chamber is maintained at it cracked the Perspex hutch of the chamber. Nightmare. The group made some quick blue-peter style repairs and fortunately the equipment has been working fine since. Who said science needed to be high tech ey.

The next step is to mount samples and fire X-rays at them. The first stage, actually finding the sample also takes some time. A stepwise movement of the motor stage the sample mount is  mounted on allows the beam to scan its entire surface and the resulting patterns are recorded. Usually a signal from a sample will jump out but it requires a bit of focus and experience to be certain that what you are looking at is what you expect to see.

The main issue is that the image recorded does not look like your sample generally. The X-ray detector simply records the position and intensity of a diffracted photon. The trouble is that X-rays can interfere with each other and where there were three photons there can suddenly be one much brighter photon. The pattern produced is said to be in reciprocal space (i.e. 1/real space) and so the exact positions of electron density cannot be determined. Fortunately there are some characteristic patterns that occur due to regions of symmetry so that if you know the rough shape of your sample you can guess the kind of pattern it would produce.

 

Only once you have gone through all this can you start getting data. This is actually the dullest part as you simply expose the sample for a given period of time at a fixed position and combine all the patterns recorded by the detector. Of course our samples are tiny and we are trying to hit them with a tiny beam so getting to this stage takes a lot of time.

As I said I’ve been working the night shift this week alongside Daewong and Dr. Kim from my group as well as Chan, a member of Dr. Kim’s old group in Korea. Once again I’m the only a) none engineer and b) none Korean and so I have been left out of the discussion quite a lot. It’s frustrating but it can’t be helped as everyone is pushed for time and explaining things to me in English takes a while. Not that these guys don’t speak English very well but putting together complex ideas in your native tongue is hard enough, it’s about 5 times harder in another language.

Chan has actually been really awesome. He took the time out to explain in English some of the things that were going on as he could see I was feeling a bit left out. I’m starting to get a much better handle on how these experiments work now and his instruction was really helpful. Also since he’s a PhD student and learning these things himself, I hope I’ve helped further his understanding to. I think I’m going to be working alongside him again over my 2 years so it was good to get to know him a bit better.

The major thing that has sucked about working nights though has got to be the food.  I’ve been reacquainting myself to the eastern, and a personal, obsession with the instant noodle. I actually stopped eating them for a while whilst I was at my worst, god knows why “men ga daisuke desu.” (I love noodles). In fact I do remember my dad once telling me that when I was younger I was practically made of noodles I ate them so much. The same probably holds true now. There are an incredible variety of pot noodles over here because there are just so many ways to eat them.

 

So far every conbini I’ve been to has an entire section dedicated to instant noodles, we’re talking two aisles of a corner shop having nothing but noodles. There are so many types of Ramen, Soba and Udon to go for so you could theoretically live off it without getting bored. So far my firm favorites are “Kitsune udon” (Fox udon), which has strips of deep fried tofu and Korean style spicy ramen. Chan actually brought a load of cartons from Korea with him, sadly they all contained shrimp and I couldn’t try them.

Of course pot noodles are no substitute for real food, even if the quality is vastly higher than those found in the UK. I can’t wait to get to some proper Udon/Soba/Ramen-yas and try some real hand made noodles, something I’ve disgracefully not managed yet. Either way I’m feeling the effects now. Pot noodles aren’t great as their ingredients lists are massive. I hate having to scrutinize food labels, it holds bad memories for me, and when you can’t read the language it is even tougher.

This has of course meant a few allergy fails, mainly from the use of shrimp powder in the soup bases. “Onaka ga ittai” (my stomach hurts). Amazing though it is I am actually missing the cafeteria and I can’t wait till I can eat something that only contains about 4 ingredients again.

This whole experience has actually reminded me of my gaming days, throwing the old body clock to the wind and keeping the mind active at ungodly hours. Unfortunately the strange hours have disrupted my eating patterns another source of pain. I’d forgotten how sensitive I was sadly as I’d gotten into a nice rhythm. Never mind it’ll be over soon, plus it’s been fun subsisting on junk food for a bit.  

Two snacks of note, Biro no bino a kind of crisp made from pea starch instead of potato, they were interesting not crispy but not soft, an interesting place in between. The other was warabimochi a traditional Japanese sweet. This is a kind of jelly made from braken starch that you coat with “kinako” (toasted soy bean flour) and “kuromitsu” (literally meaning black honey but its actually treacle).

It is helping me dealing with some of my neurosis actually. For one these guys are nearly all super skinny yet I see them packing away noodles and rice cakes and so on. I know I don't actually want to be skinny, I don’t care about getting fat consciously, but unconsciously something’s still there. Either way being around Chan and Daewoong has put me a bit more at ease with food. Also I’m being forced to be flexible with my eating, something that's been a struggle. You can’t eat on the ring so it’s been a case of just having to eat when I can.

It’s nice to know I’m getting there. It would have been easy to fall into bad habits this week. It’s been stressful and disruptive and I recognize these as major triggers for myself. Instead though I’ve been able to let go and just experience and learn from these experiments. I can say one thing for sure being a Synchrotron scientist sets me up for being a great globetrotter, I’m going to be able to switch up my body clock on demand soon.

“Dewa ijou desu” (well that's it). Not so many exciting travels or cool pics but hope you enjoyed reading all the same. Oh also I spent some of my birthday money purchasing some rather swank new T-shirts from some web comics I’ve been reading. “Chou Kakokii ne.”

Ja ne.