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.