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