Frustration, Farewells and Frisbee.

Uwa, what a week it has been. So much going on although sadly not too many interesting adventures to report back on. Tuesday saw the start of our second slot of beam time. Following on from the time off we’d been putting in 12-hour days, or more to make sure our equipment was in tip top condition. With the team now reduced to two the work was considerably more demanding.

Josie, I’ve now learned the nickname is derived from a basterdisation of bad girl in Japanese (Josei warui), was as always playing up. We spent a very large amount of time tinkering with various components, removing parts, refitting and cleaning. Basically I think I’m now well prepared for anything purchased from IKEA due to all the time I’ve spent with screwdriver, Allen key or spanner in hand.

Anyway somehow we did manage to get the DIT running in a way that would mean we could collect some good data by the time Tuesday rolled around and as we were already set up on the beam line alignment was fairly straightforward. We started as before with cytochrome C. The DIT was behaving itself for a change and we were getting very promising mass spectra. Unfortunately we still weren’t seeing any scattering, but as I’ve mentioned before, that was expected due to the small size of the molecule.

After a few hours sleep, we finished up around 2am the previous day, it was time to move on to thyroglobulin, a.k.a the devils protein. This is where are troubles normally started. However rather uncharacteristically Josie was on best behavior. We seemed to be trapping Ions well and so we could begin scanning. All the hard work and toil from the previous five days had paid off and we were able to solve any problem Josie threw at us. Or so we thought.

After our fourth data acquisition disaster struck. Cheung commented on a faint burning smell he’d noticed in the hutch, initially it was very faint and neither Takaaki nor myself could smell anything. Now however it had grown much stronger and the DIT was suddenly unable to perform mass scans.

A quick investigation of the equipment and we discovered the source. There appeared to be a faint glow from the underside of one of the control boards. Not good. We shut everything down and began to dismantle and low and behold one of the circuit boards was completely fried. It turned out that one or more of the transistors on the DIT’s control board had failed, dumping 2Kv of electricity into the resistor and melting it. With out the transistors the fine-tuning of current through the DIT could not be achieved and so it wouldn’t work.

Disheartened we dismantled the device and boxed it up to be shipped back to Manchester. A pretty rubbish end to what had looked to be a promising slot of beamtime. Ah Shikata ga nai. There will always be next time.

So we still had one day left. Rather than waste it we decided to act upon one of Cheung’s earlier ideas of using x-ray fluorescence to detect ions in the trap.

A bit of background. Atoms consist of multiple smaller particles. Predominantly these are protons, neutrons and electrons, there are actually even smaller particles but they aren’t relevant in this explanation. It is he electrons which where our focus. Electrons exist in orbitals or shells around the central nucleus of an atom, similar to the way our planets orbit the sun. When stable the electrons of an atom will exist in discrete shell at a given distance from the nucleus.

It is possible however, through the use of high-energy photons like x-rays, to cause the electrons to ‘jump’ to an orbital further from the nucleus, where it will have a higher energy. This is unstable and eventually the electron will move back to it’s favored orbital, a process called relaxation. When this happens it’ s extra energy is given off as a light, hence x-ray fluorescence.

It happens that all atoms fluoresce at a discrete frequency and so this process can be used to distinguish which atoms are present in a compound. For our purpose we had a protein containing an iron atom, cytochrome C, so if we could get a fluorescence signal for Iron we could determine its presence in the DIT. The intensity of the signal would also give us some indication of how much iron we had.

So how did we actually go about this? Well we got a very small sample of cytochrome C in solution (about 20μl) and put it into a sample chamber. The chamber has two 30μm thick windows allowing an x-ray beam to pass through. We then set up a detector just off the path of the direct beam so we could measure the fluorescence of the scattered x-rays, the direct beam would simply saturate the detector, as it was so powerful.

And so the result? Nothing, zilch, nada. Unfortunately our protein sample would be too dilute to give a strong enough signal with the equipment we had available. Still it wouldn’t be called research if you didn’t repeatedly search for something right. It was interesting to set up a new experiment at any rate.

Ok that's the boring science stuff out the way anyway. As I may have mentioned I’ve been working crazy hours at the moment, not finishing till maybe 1 or 2 am most nights and I haven’t been able to take any time off since golden week. Now like 90% of the western world I’m concerned about my weight, although not in the same way as most.

Weight is something I struggle with, I don’t want to let it define me as it has done in the past and so I am trying to break the habit of worrying about it or analyzing it. Still I’m well aware that all this work will be taking it’s toll on my body and o I’ve been making an effort to try some more Japanese snack foods so here is a quick list of some of my recent encounters:

Kuri Shigure: Although the name would suggest they contain chestnuts (kuri) these are actually little cakes made of rice flour mixed with white bean paste and sugar. They are very soft and pretty sweet. They kind of have a muffin like texture and the bean paste isn’t particularly prevalent, making them a great little pick me up.

Soba meshi: This is actually named after a real dish that combines leftover noodles with leftover rice to make a dish of fried rice and noodles. The stuff I got was like the snack version. Think a kind of Japanese Bombay mix. The Worcestershire sauce flavor was pretty heavy but gave them a nice savory kick.

Muichaimashita chestnuts: These were cooked Chinese chestnuts I grabbed on a whim. They aren’t sweetened at all and our quite smooth in texture. Not bad as a snack but I prefer other nuts, they could be good with a bit of a sugar glaze I reckon, or possibly used in cooking.

Ramune: apparently a very popular drink in the summer months of Japan. It wasn’t particularly delicious but the bottle was really pretty to look at.  The bottle has a marble in the neck so the whole drink fizzes up with each swig. It was pretty refreshing although not that tasty, it was bubblegum flavored and I’m not a fan, I’ll have to see if there are other flavors available.

Karaimo: These things were really nice actually. They are candied Japanese sweet potatoes. Think of that what you will but in essence they taste just like treacle toffee. I’m a massive fan I’ll definitely have to invest in some more I think.

Brown sugar candies: Erm does what it says on the tin. Hydrated brown sugar, closer to small chunks of muscavado but not as densely packed. Airy with a faint hint of molasses, another winner.

Ok that's pretty much it for that section. I’ve also managed to get a bit of home cooking done as well, fed up as I am of food from the cafeteria. My latest forays include making my own sushi rolls (maki) and more oden. I’d managed to get a few more traditional ingredients to o in it such as konnyaku (a kind of jelly made from a yam like root vegetable) and surimi (mashed and formed white fish think crab sticks minus the crab), and kabocha (Japanese pumpkin). I’m a big fan of oden it’s just so easy when I’m knackered and late in from work.

Anyway after the poor ending of my own beam time I’ve actually not had a proper rest. I had a Skype meeting with my supervisor and he’s requested that I join in with my new lab group in their current slot of beam time.

My new group is all Korean, I know I’ve spent all that time learning Japanese to end up in a Korean lab. They’re actually really nice but it obviously makes taking part in experiments difficult. Whilst their English is incredible they generally talk to each other in Korean so I constantly have to ask what is going on.

Frustration aside the experiments are interesting if somewhat long winded. It’s nice to see the practical side of the Coherent diffraction Imaging (CDI) that I’ve mentioned previously. It’s always good to see things set up properly and their equipment does look very impressive, though somewhat smaller than I’d imagined.

Unlike in my own experiments the most time consuming step here is the actual alignment of the x-ray beam. For the purposes of CDI the beam must be very small, somewhere in the region of 10-15μm. This is because the samples they are using are larger but they are not looking at an averaged image of many samples, but an image of just one sample.

The samples are mounted on a thin silica membrane and fixed in place and this is analyzed under a high power light microscope to determine the samples horizontal and vertical position. It will then be placed in the path of the beam and the beam adjusted until it passes through the sample. This can take hours or days of minute adjustment, so many more sleepless nights for me.

The focus of this set of experiments is not actually the sample itself but a new piece of equipment. Daewoong, a PhD student like me in our group, has been developing something known as a cry-chamber. This will cool the samples to temperatures of about -80⁰.

The reasoning behind this is to extend the time period over which a sample can be imaged. When the high energy x-rays interact with the sample some of this energy will be transferred to the electrons of the sample in the form of kinetic energy. Over the time course of an experiment the electrons will very rapidly drift apart until the sample essentially disintegrates, the process is know as a coulomb explosion.

By reducing the temperature you restrict the movement of the electrons and can therefore extend the time period over which you can obtain a reliable image. This is vitally important when the samples in question are either highly complex, or very small.

It seemed that the first few days of experiments had gone about as well as mine. With their original set up they had spent 3 days trying to align the beam correctly but just couldn’t seem to produce the right profile.  What had I said about research earlier? Anyway the problem seemed to be related to the focusing mirrors they were using. Once they were replaced they were well on their way to start imaging some interesting samples.

On another rather sad note the other member of the team who came with me from Liverpool was finally leaving on Sunday. He’s been a great help both in terms of his experience as an x-ray scientist and his general practicality. He’s also been a great laugh, he has a crazy sense of humor and a tendency to say very inappropriate things.

I’d hoped to go for a meal or something to give him a good send off but alas no such luck. We in the end settled for a couple of drinks in the users lounge with Takaaki as well, I’d bought him some beer earlier to say thank-you for his hard work. I’d managed to get the day off on Sunday if I worked the night shift, so hopefully I could see Cheung off in Osaka.

Disaster. After about 3 hours of sleep I seemed to have woken up too late and missed Cheung's departure I was gutted. Still I carried on with my planned visit to Osaka. I’d arranged to meet up with Yuko again and go play some Frisbee, finally. It’d been 8 straight working days so I needed a break. I picked up a bottle of soukenbi cha. This is a type of mugicha or barley tea only it contains about 11 kinds of different grain. It; very refreshing on a hot day and my favorite kind of bottled tea, also caffeine free.

As I was leaving the station and trying to figure out where to go I heard a familiar voice. It was Cheung. It seem he’d over slept as well and had taken the same train as me. I was really happy I could see him off properly. I helped him get to his hotel and we said our goodbye, he was bound to Kyoto for the day, as his flight wasn’t till later that night.

Farewells said and it was time to explore a bit before I met Yuko at 2pm for a bit of friz. Osaka I huge as I’ve mentioned before so I couldn’t afford to go to far. I had a look around some of the massive department stores though. The one I ended up in was entirely dedicated to electronics and had 14 floors, unreal. A good browse later and it was already nearly 1, time to get some food before setting off to Nakatsu train station.

I’d wanted to try out some more proper Japanese food but the food court was mega busy and I still can’t really read the menus. In the end I settled for some onigiri from a convenience store. Admittedly they are still good quality, it’s not like corner shop food back in Britain, and they even had a little seating are where I could eat, win.

So fed I departed and headed back to the Hankyu station to catch a train, it’s literally only 2 minutes to get to Nakatsu by train but the walk is actually quite far. I met up with Yuko no problem and we set off for the pitch.

The wind was up sadly but the weather was so warm that I didn’t much care. The pitch was a grassy area alongside a load of baseball fields. Baseball is huge in Japan and there were loads of teams about, either playing matches or just training. I think there were some local Sunday league games going on or something.

Anyway it was like something straight out of an anime I'd watched called FLCL. We were playing just alongside the river next to a railway bridge and had a really nice view of the Juso district and the sky tower behind us. Members of the team slowly filtered in. They seemed to be from all over the place, and admittedly I’ve forgotten most of their names. Thankfully I wasn’t the only gaijin, although it was also nice to practice a bit more Japanese.

We played for a couple of hours. It was a good laugh and so nice to get running about again after such a long stint indoors. I just wish I hadn’t been so sleepy. I wasn’t playing that great but then it was no serious thing really. Quite a few people had never actually played before, just thrown around a bit, so I soon had my coach head on. I tried not to let my competitiveness take hold when it became turnover central, this was just for fun after all.

Sixes with no subs w still tough though, lots of running about. It came to 5 o’clock and besides being tsukareta (tired) I also needed to head off. We took a few silly pics of what was apparently the Japanese “style” of wearing a sash, I’m not convinced, and then I headed back to the station. 

Just before catching my train I swung by this awesome little japanese style bakery. There had been something I'd wanted to try since arriving in Japan but hadn't yet got round to. It was a kind of cake called a melon pan. Don't be fooled by the name it contains no melo. It is acctually a sweet bread with a cookie like topping giving it a nice crunch, the name comes from the fact it looks a bit like a melon. From the research I'd done it was apparently best to buy them fresh and not packaged as the main appeal was the crispiness of the topping. I'll not lie I don't see the appeal. It was alright not mega sweet not overly doughy but at least I've tried it.

It would have been nice to stay and chill a bit but I was determined not to get stuck in Aioi again, the outrageous price of taxi fare was not something I wanted to deal with again. Alas it was not to be. My train was delayed, I still don’t know why all the announcements were in Japanese, and so I arrived in Aioi an hour later than planned, and ten minutes after the last bus left. Yet another takai visit to Osaka.

Demo tanoshikatta desu (But it was fun).

Dewa matta