My future extends brightly forward.

Ee. Konshu wa sugku itsogashi desu ne! What a week its been. Sadly I can’t report that I’ve been up to any exciting adventures, not of the physical variety anyway but I have been delving in to the depths of frontier x-ray imaging science. Ok so perhaps I’m bigging myself up a bit there but there really have been some exciting things going on out here.

First things first my supervisor from Liverpool swung by, I love how casual I make flying 6000 miles sound there, to check on the progress of my experiments. Luckily for us Josie chose that day to behave and we could show off the wonderful spectra of trapped Cytochrome C molecules. Yatta.

There was also another purpose for his visit, namely to sort out what I’ll be doing here over the next few years. This meant a day full of meetings, introduction and discussion. I met a lot of new people on Monday and I’d be lying if I said I could remember all their names. One I do remember of course is Song-san, or Changyung Song. He is a scientist from Korea and head of a group here known as the Song initiative, and also my new supervisor (The guy with glasses whom I'm standing next to).

I’ve finally been placed in a team at Spring-8 so I’m feeling a little more like a proper member of Riken, plus I have my badge and dosimeter, making everything feel more official.

Now the interesting stuff. So I’ve actually been following Song-san’s research for a couple of months as, although not entirely the same, it is somewhat related to my own.

His field of expertise is in X-ray diffraction microscopy, or lens-less diffractive imaging. A lot of scary words there for a non-specialist but allow me to break it down. This technique is used as a new method for imaging biological samples on the micron scale, such as cells and their internal structures, known as organelles, about an order of magnitude large than the proteins I’m interested in.

To achieve this samples are first fixated as gently as possible, usually in a dilute fixing solution the composition of which isn’t very important for the theory, onto thin film of silicon nitride. The sample holders look like 1cm, see through time capsules, I was actually shocked at the small scale of the device when I saw it in person. Anyway this set up is very unlike what you’d consider a microscope in the traditional sense.

Once samples are fixated they are mounted in a sample holder and exposed to a hard x-ray, or UV free electron laser beamline. At the other end of the set up is a powerful photon detector. This reads two things. First it will measure the absorbance of the light photons, i.e. compares the intensity of photons that pass through the sample to those of the direct uninterrupted beam. This works similar to a standard medical x-ray. From this absorption you can get an impression of the surface structure as well as the areas of relative density from a sample, the more dense the sample the more absorption will occur.

Right that's the microscopy bit out the way now onto the diffraction part. So this set up is similar to those I’ve mentioned before. Here the detector will be measuring discrete packets of photons that are diffracted by the sample.. The detector needs to be a fair distance away for this as the photons are only weakly diffracted and so need a large distance for the small angles to extend far enough away from the direct beam. The diffraction pattern, essentially a circular arrangement of spots of various sizes, can be used to determine the position of internal structures within your sample.

By combining the diffraction data with the absorption data you can simultaneously get a picture of the internal and external configuration of, for example, and individual cell. Amazing.  Normally to do this very thin slices of cells need to be taken, stained and then imaged and put back together. Wilst the resolution is higher the process is very destructive and it is not possible to know how the images you capture compare to nature. This new method is a lot less invasive.

So where do I come in? Well the Song initiative consists primarily of physicists and Material scientists. Their knowledge of biology is limited. So I’ll be looking at the best ways of preparing samples, what samples to selected, whether readouts are in fact accurate to nature and so on. Also this group plans to be using the XFEL when it comes online so it would make sense for me to be involved in their work.

That brings me on to the next point. The XFEL. It’s coming on line in just under 2 months. That means the first round of experiments will be starting in mid June. The nerd in me is very excited. I’m going to be around at the point when some truly groundbreaking experiments are carried out. Plus I can’t wait to have a look inside the experimental hall.

So this week although I’ve been suck in the lab with Josie quite a bit, some good results have been obtained. We’ve managed to successfully 2 out of the 5 samples that we want to run when we move the beta5 to the beamline next Thursday. This has of course been the product of a week of 9am-10pm working days ugh. It should be worth it in the long run though.

I have also been able to meet some new people, something I was concerned about not doing due to all the lab work. The members of the Song initiative are all really nice, Kim-san has not long joined so he’s experiencing all the problems I’m having sorting accommodation and Nam-san is a PhD student like myself and lives pretty close by. We’ve also met some other gaijins. Two French guys named Ignace and Arneaud who also seem pretty interesting. 

There is so much incredible science going on around here that I can’t help but remain fascinated by everyone I meet. I’m, as I’ve mentioned on numerous occasions, very keen on my writing. So when I found out about the welcome trust writing competition I leapt at the chance. This has been occupying my time between DIT runs. I’m still drafting my entry so if anyone fancies a read let me know.

Anyway you’ll notice there are not many pictures of food. The canteen is starting to rotate its meals haha so nothing really exciting, except baby squid for breakfast yum.

Anyway kon shumatsu holds a trip to Himeji so expect some interesting snaps of locations from the last samurai, a film I’m still yet to watch, and hopefully I’ll have some gear for my rather barren new flat hurrah.

Right off to my First Sprng8 no Nihongo no ressun. Dewa matta mina-san

I’m a legal alien: Flowers, Frisbee and failure.

Well its been all go here since my last entry, totemo isogashi desu ne. Fortunately the beta 5 has been behaving itself a bit more but its still not working as well as I’d like it to be. Sadly I’ve not been able to tinker with it too much, life has been getting in the way.

Thursday was the day I officially became a foreign resident in Japan. The day started with a trip to Apato heights, the apartment block that was too be my new home. I set out with Takahuchi-san, one of the many secretaries here and a totemo kawaii onna no hito (a very lovely lady), in a car as we had a lot of travelling to do. The apartment is pretty barren and on the expensive time, I’ve been assured this is the norm in Japan and the company are fronting all the money for my apartment, I’m not fully reassured but I don't have much choice sadly, and everyone here is so nice that I’m sure they’re doing the best they can.

Anyway next it was time to sort out that residency registration. As I mentioned I’d tried to do it earlier but failed due to the distance. This time we had a car so all was good. It was only about a 15-minute drive to the Sayo prefectural office. It was, like every other administrative office I’ve seen so far, packed and abuzz with activity. Still we were seen very quickly and Tahakuchi-san helped me to fill out the myriad of forms, all in Japanese of course. I swear all this bureaucracy will be the end of me.

So one hour later and an official resident it was time to get me a bank account. This was a lot more straightforward though I did manage to muck things up by putting my name the wrong way round on the form (surnames come first in Japan doh).

Friday was then fairly uneventful, barring a bit of a stress when I was presented with the costs of internet installation at my new flat eep, not so grand. Anyway I don’t want to dwell on that so here is the obligatory montage of cool things Ive eaten/drunk.

So now the fun bit. The weekend, and what a weekend it was. About three days previously I'd managed to get in touch with some guys who play Frisbee out in Osaka and found out what times they were playing. This in itself was cool Id’d been itching for some Frisbee since I’d got here. Not only that but it turned out a they were having a big get together in Osaka castle park for a Japanese festival called Hanami. How could I resist?

 

A bit of background here. Hanami (from the word “hana” which is flower and “miru” which is to look) is about the viewing of the sakura (cherry blossoms) in the brief one-week period that they blood. Sakura are very important in Japanese culture. They only last about a week and their fleeting nature is seen as a metaphor for the brief time we spend upon this earth. For that reason there tend to be many Sakura planted at Japanese gravesites.

Anyway Hanami itself is one big party and it's a big deal over here. People will literally camp out days in adance to get a good spot under a tree. Also when hanami time actually hits all the parks are rammed with people from all walks of life.

So anyway Saturday morning I set of bright and early to Aioi to catch a train to Himeji and then on to Osaka. The weather was a bit muggy but I was still optimistic of a good time. Not too many pictures of the train journey sadly as it moved so friggin fast I couldn’t keep up.

Anyway 2 hours later and I was in Osaka. Wow. This place was busy, crowded and cool as hell. I would of liked to have a better look around but I was already running late. I couldn’t find Graham, the guy from Osaka Frisbee, so In typical Marcus fashion I blundered my way to Osaka-Jo park.

This trip was exciting for another reason. I finally got to practice some of the Japanese I'd been learning for the past month or two. Admittedly I din;t use too much but I now am a bit more confident that I can get by with what I know, and have a new drive to learn more. So after a few Doko desu ka? (where is ) and Dochira desu ka (Which dirction to?) I made it to Osaka-jo.

The main castle is actually quite something. The wall on which it I built, according to a sign I read, reach down nearly one kilomeer, and the surrounding moat is over 75 metres at its wides point. The main courtyard was pretty cool as well, many nice arches and the castle itself was very pretty, I didn’t get to go in unfortunately, maybe another time, but I did scramble about the walls a bit haha.

So anyway Hanami. The sakura where in full bloom and it really is breathtaking, an absolute snowstorm of pink petals everywhere you go. The park itself was full to the brim of family groups, friends, school groups, businessmen and women. In fact pretty much every walk of life was represented. It was very cool and everyone was just having a great time. I knew the group of people I was looking for weren’t Japanese so that was a place to start right?

What I hadn't counted on was just how big Osaka-jo koen is and how important having a mobile phone is. I thankfully managed to stumble across a group of people who were part of the JET programme (Japenese exchange teacher I think) and one of them offered to phone Graham my contact for me. After a quick conversation we managed to figure out where we both where in respect to each other and agreed to meet next to a large sandstone fountain.

So onto meet the rest of the people. Knowing no one, and very little Japanese, this was a bit of a test but I had fun anyway. Everyone has their own story and I love meeting new people. I had a great chat with some of the Osaka Frisbee guys, Graham, a guy from Texas called Dennis and a big hippy called trip who had an awesome fro. They seemed like a fun bunch. Also with it being Hanami I even had a cheeky drink of some plum sake, not normal for me but when in rome and all that.

It was also interesting to interact with some people closer to my own age, to be honest I was happy to be away from Harima for a bit, I’m a city boy at heart and its just a bit too quite out here. Anyway I also had a great chat with a lady named Tomoko about climbing and I met a few other Japanese girls whose names escape me, Fuko and Akiko I think. I’m rubbish with names at the best of times but when I can barely pronounce some of the names, well that's just unfair.

By about 6:30 the temperature began to cool and so di the party, lots of people were leaving or were too drunk to put a proper sentence together, in any language. I took my leave and skiddadled to find the capsule hotel I’d found online.

Now Osaka has an extensive underground service, pretty much like London only cleaner and more pleasant. This makes it very easy to get about the city as its huge. I got off at a stop called Namba which is apparently a major shopping area (I’ve put a picture up of my swag at the end). Anyway even at around 7pm everything was stll bright and open, neon lights agogo. I Dropped into a place called book up or something like that and found to my joy a couple of copies of the Mushishi mange. I love this series and I’d been meaning t get them in English, I got a few volumes as they were only 100 yen each, I’m a bargain hunter in any country.

The next thing I came across was Game Taito station. This was a 6 storey video arcade, increders. It had all kinds, those weird claw machines, panchinko, slots, a floor dedicated entirely to trading card games that you play against opponents on line (Tom you would’ve been in heaven) and a floor of online beat-em-ups. I gave it a quick go but was thoroughly rinsed. It was time to move on anyway as I needed to get checked in and get some food.

I was a bit bewildered by all the bright lights in Namba, amazingly some of the comic/dvd/cd shops were open 24hours in a place called den den town which si the major electronics district. After a good hour of wandering I found the place I was looking for. And right next to it another hotel that was 400 yen cheaper, score.

I checked in. It was a Japanese style room, just enough space for a futon but it’d do and for 1800yen I wasn’t complaining. After that I went up to the counter and asked Doke de ii tabemasu ka? (Where is good to eat). I was pointed just 2 minutes down the road where here were loads of food places, onsen, udon, ramen, izakaya and so on. Unfortunately I was tired and all I really wanted was some takoyaki (I’ll explain this later) and ended up in a rather rubbish tempura place.  Rather unsatisfied I picked up a red bean mochi from a nearby convenience store, its like a rice flour cake stuffed with sweet essentially kidney bean paste, surprisingly oishii (delicious). After that I called it a night I was shattered.

The next morning I was up bright and early. I don’t think the Japanese believe in insulation as every little movement of the other guest was transmitted through the walls. Breakfast consisted, rather unconventionally, of vermicelli noodles with soymilk and a banana. I  also had my first hot vend, the vending machines really are mental, you can even get oxygen tanks from some.  Anyway I exited the hotel in search of an internet café. It was quite tricky actually, although in the town centre nowhere sleeps, on the outskirts it was like a Sunday anywhere else in the world. I did mnage to stop by a 100yen shop (think poundland times a thousnd) and got a few bits for my new home.

Eventually as I reached the centre of the Minami district called namba I found somewhere. It was what is known as a manga or media café and they are open 24 hours. It wasn’t too expensive for an hour and it came with free drinks. I just about managed to figure out what I was doing since everything was in Japanese and chucked out a few emails. Sadly I couldn’t get hold of the Frisbee people so I decided to give it a miss and explore the rest of Osaka.

I wandered around den den town a bit more and drooled over some of the expensive electronics. This place was far more impressive in the day time pretty much anything and everything electronic could be purchased from here. After plenty of window-shopping I moved on to Doguyasuji, a shopping street dedicated to utensils and kitchenware, after all I needed some gear for my new home. I settled on a good pan and a Japanese knife, it took a while though lots of shops and very competitive prices.

All that shopping had made me peckish and I was still desperate to try some proper takyaki. I’d read in the guide that the place to go for food was Dotonbori by the river so I haded up that way. So Takoyaki, from “Tako” octopus and “yaki” fried, is a delicacy Osaka is famous for. They are these really cool octopus dumplings. Basically chunks of octopus, usually tentacle are placed onto this kind of large griddle with circular wells. Then a kind of batter is poured over them and they are periodically turned with chopsticks to form balls. They’re just the right mixture of crispy crunchy and chewy. Oishii.

I found a rather packed stand about half way along Dotonbori and waited in line, it was fun t watch them being made. Stands aren’t too hard to spot thanks to the chibi octopi chefs they are usually adorned with.

Well fed my next port of call was to try and find Osaka city rock gym, I was desperate for some climbing. I hopped back on the subway to Osaka Umeda the main station in Osaka and changed to an overground rail line. I’d looked up the gyms location on the internet, it seemed pretty simple just one stop away and a 15 minute walk.

Alas it was not to be I got very lost. So no Frisbee, apart from a few rounds of cups. and no climbing the two things I’d set out to do for the weekend. I guess in some ways I could, and the old me would, have considered this a major failure, not achieving my ‘purpose’. Looking back though I’d achieved a lot. I’d met new people, bought some gear for my house, done plenty of exploring and practiced a lot of Japanese. One thing I’ve learned is that purpose is never predefined, your end goal may not necessarily reflect your starting one, flexibility is the key to enjoying life to the fullest.

Anyway this things run to long here are some piccies of my swag. Ja ne mina-san.

Ohaiyo-Josie-san- into the heart of the synchrotron

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Just a quick foreword, this post contains explicitly geeky content that may not be suitable for all readers. I’ll compensate by putting some pretty pictures of the food I’ve eaten the past few days here.

So Monday was finally upon us and the holiday period was over, well not quite.  After breakfast, we went over to the ‘High-throughput building’ to talk to Nakamura-san, the secretary put in charge of us to ask about getting our health checks. We couldn’t enter any controlled areas till it was sorted and sadly the doctors weren’t open until 14:00, so another day of mooching around then.

I decided to take the opportunity to go and sort out my alien residency status, filling in forms seems to be japans favorite pastime. I hoped on my faithful steed once more and cruised on down to the central office in Harima. I was a bit bewildered at first but eventually managed to figure out where the central office. Not many English speakers here but we seemed to come to an eventual understanding about what I wanted. Sadly the registration office appeared to be way out of town, about 15km. When asked about how I’d gotten there I replied with ‘Jitensha de’ and got some looks as though I was completely mad, something I’m used to anyway.

Still ever the optimist I decided I could make the round trip before my doctors appointment. I glugged down some soy milk, nipped into the co-op for lunch and off I popped. Lots of hills in the Harima area and it was all down on the way out.  I literally whizzed the first 7km or so. I stopped by a few benches next to a nearby river for some lunch.

Now although I could have made it the rest of the way I figured I wouldn’t make it back in time for my medical if I carried on. How right I was. Hills seem so much smaller when your rolling down them. It was an absolute slog heading back up and took at least 3 times as long. Still I got back just in time and met up with Cheung and Liam.

Medical was uneventful and so we went back to Spring 8 o meet up with our supervisor Yamamoto-san. He’d been in touch with the safety office and had gotten us temporary access to the radiation controlled inner ring of the synchrotron. The geek in me jumped for joy

This place is one hell of a piece of kit. Initially an electron beam is generated from a high power electron source (8GeV to be precise) an then accelerated to relativistic (99.9%) light speed. It is then passed into the synchrotron ring itself where a series of periodically spaced magnets bend the beam to maintain the circular motion. This means electrons can be maintained without spontaneously annihilating.

Now at each point that the electrons are ‘bent’ they slow down periodically. When you slow an electron some of its kinetic energy is lost in the form of electromagnetic radiation (light). In this case it’s X-rays. Various stations are set up around these magnets to harness the X-rays for various kinds of experiments.

Anyway the inside of this place is huge, so much so that the technicians are provided with bicycles to get around. The beam had been sut down and is currently coming back online so everyone is an ‘isogashi bachi’ (busy-bee) right now.

After a short tour of beamline 45XU, the station we’ll be working at, Hakima-san brought us t one of the user rooms where the Beta-5 DIT was stored. This beast has been nicknamed Josie by James and Guenter when they first started using it in 2009, and I’d been warned she was a temperamental soul.

Needless to say she was currently in bits and looked absolutely nothing like the beta4 we had worked on in Manchester. The beta5 is essentially the same system but rotated through 90⁰. It also has an entrance and exit window through the central ring electrode of the 3D ion trap, where the ions are actually held, to allow access of an x-ray beam, so that the ions can be imaged.

Somehow we got everything together after much head scratching, particularly over the connections to various gas inlets. It was important that these were right, one inlet was for Helium and is used to keep the DIT cool, by keeping the temperature of the trapped ions low they are less likely to move apart. The second inlet was for nitrogen which was under high pressure. Clearly it was not a good idea to mix them up.

The nitrogen gas is part of a component called an ESI probe. The liquid protein sample is forced through the probe by the nitrogen gas where it eventually passes out of a fine nozzle at the end. This nozzle is highly positively charged and so causes the samples to ionize, themselves becoming positive. This process cause any solvent the samples are dissolved in to evaporate, generally it contains a lot of alcohol,  The fine mist of ionized sample will then travel past the sample cone of the DIT which is negatively charged, thus drawing them into the trap where the magic can happen.

 

Either way we weren’t getting anywhere so we decided to call it a day and go get some dinner. I noticed that pork tempura was on the menu and I was giddy with excitement. Tempura batter is like the tastiest thing ever, really light and crispy and I’d been looking forward to having some since I got here. Dinner done we had a skype call with the boss man, Professor Hasnain, back in Liverpool and then turned in. I was knackered and got a good 10 hours sleep.

 

Up bright and early it was time to get cracking with Josie once more. First things first, breakfast. I was finally fed up of not having ceral and so decided to improvise by mixing one of the tofu blocks in with my cereal and fruit, it kinda worked. After consulting a huge folder of images from previous trips to spring-8 we managed to sort out where everything went. Sadly that was the only thing that went well today. For some reason ions just don’t want to be caught in the trap. They are temperamental buggers at the best of times but so far all the mass spectrums are coming up blanks.

Since no alterations to the DIT protocols had any effect on the trapping it seemed to be a hardware problem. Thus commenced the stripping of Josie. So many little screws that could potentially get lost. We removed the sample cone (the entrance to the trap) and the Q-array (responsible for controlling which ions will be isolated in the trap itself) for a good clean in an ultrasonic bath. Hopefully this will sort out the problem as the tarnishing of these various parts can effect how well they conduct electricity. As the trap is reliant on changes in charge to work this isn’t much good.

We gave up for the night as it was getting dark and they stopped serving dinner soon. Hopefully we can sort it tomorrow after our X-ray safety training.

Oyasa minasai.