Thursday, July 15, 2010

The Australian Synchrotron Winter School.

I've decided to blog about this weeks happenings on a day-to-day basis because this trip to Melbourne is kind of a big deal for me. Since I haven't had access to the internet for the duration of the trip, I've compiled all the pictures and my ramblings into one big 6-page post. Enjoy!


I am in Melbourne and writing this from the comfort of a comfortable hotel room on the outskirts of the city. I'm down here because I am attending the ANZAAS Australian Synchrotron Winter School to lean about the facility, methods, procedures, and current research. I applied to attend the school a few months ago. Among other students who applied I was fortunate to be selected on the basis of my research and academic record. I'm not entirely sure how many other students will be here tomorrow, but I am excited to meet them, and to find out what their research entails.

This morning I boarded an early flight with Jetstar. The flight was packed and there wasn't much room to move about. I avoided making conversation with my neighbouring passenger who resembled a female Mick Jagger and slept for most of the flight (trying to catch up on the hours of sleep I had missed out on). Despite being nagged by the persistent flight attendants trying to sell me something to eat, I held out on something to eat until I arrived in central Melbourne, where I had planned to meet JJ. Once we met up, we ventured the city, had coffee and lunch and chatted for a bit, tried out the trams and basically looked like a couple of gay tourists.

The vibe of this city is that the people are comfortable with their metropolitan sexuality – infatuated with their machiatos their french toast, pilchards on driftwood and soufled truffles. It's not all about food though, the city mingles with art galleries, fashion label shopping malls and exhibitions. I know it's a rather superficial interpretations but I can't really figure out why that the appeal is, or what else people have on their minds.

- Just pictures.
- No entry – see 13_7_10 for a recount.


I didn't have much time to myself yesterday, hence the reason why I didn't make an entry. I was busy socialising with a bunch of other students about their PhDs and Honours projects. I must admit that I am certainly out of my depth on a number of topics they bring up since most students are working in chemistry or physics.

Upon arrival at the the Australian Synchrotron we were given a tour of the linear accelerator, the booster ring and the storage ring. We walked around the control room and past a couple of end-stations before being quickly hurried out of the facility because the engineers had something important to do. I was in awe of the grand scale of the machine. There are cables everywhere, computers, generators, coolers and vacumme pumps humming away and engineers tweaking components and checking components with oscilloscopes and multimeters. The synchrotron was down for maintenance, which gave us the opportunity to go in and stand next to many of the magnets which guide, shape and accelerate the beamline. I took the opportunity to take more pictures. I was most impressed with the 'wobblers' and 'undulators' which are able to tune outgoing beamlines to specific frequencies. We later learned that these undulators are particularly useful for a number of applications such as medical imaging and short angle X-ray spectroscopy.

In the afternoon we were treated to a dinner and trivia night with the staff at the synchrotron. It was good fun, and I got to make friends with a few students on my table. We came last in the trivia, embarrassed ourselves completely, but still enjoyed ourselves. In the afternoon I had a few drinks and socialised a bit more, then knocked off around 12:30am for a fairly rough night's sleep... I guess the excitement still hadn't worn off. I also struggled with the bedsheets for an hour which doesn't help; I don't know what it is with hotel bed sheets, but it seems like they're stapled down so that it's near impossible to get into them!

Today we basically sat in a lecture theatre and listened to some of the beamline scientists talk about their work. My mind is blown. I've taken the liberty of typing up abstracts of each talk, because each of them were incredibly interesting facets of beamline science. A part of me almost hopes that one day I'll get to work here.

Protein Crystallography at the Australian Synchrotron:
Tom Caradoc-Davies, Australian Synchrotron.

The macromolecular crystallography (MX1) and microcrystallography (MX2) beamlines at the Australian Synchrotron comprise a dedicated facility for determining the crystal structures of proteins, viruses, and nucleic acids as well as smaller molecules such as inorganic catalysts and organic drug molecules. The technical capabilities of the MX1 and MX2 beamlines will be briefly described as the advantages of synchrotron radiation for protein crystallography will be highlighted. An introduction will be given in the application of single wavelength anomalous dispersion (SAD) and multiple wavelength anomalous dispersion (MAD) to protein structure solution.

Introduction to small Angle Scattering
Nigel Kirby, Australian Synchrotron

Small angle scattering is a popular and rapidly growing technique for analysis of structure at the molecular and nanometre to sub-micrometre scale. The SAXS/WAXS beamline at the Australian Synchrotron is one of the most advanced x-ray scattering instruments in the World, and there are two additional neutron instruments are under development at ANSTO. This lecture will present some basics of small angle scattering theory, practice and instrumentation, and gives a few examples of what it can be used for an information can be readily extracted from data.

Synchrotron Powder Diffraction Research
Kia Wallwork, Australian Synchrotron

The ability to relate the properties of a material with its crystal structure is arguably the most valuable capability of powder diffraction research. Routinely in the synthetic materials chemistry arena, and in the natural world, poly-crystalline materials are readily produced that have interesting and/or important properties. To further understand the manner in which materials or minerals are formed, processed, and/or used it is often critical to accurately the constituent phases and subsequently the crystal structure(s) of those phases. By its very nature powder diffraction allows the study of bulk materials and provides a robust alternative for structural characterisation when single crystals cannot be found. Such studies may include the in situ study of reaction mechanisms, the examination of crystal chemistry, phase identification, and the trend of physical properties with crystal structure. Synchrotron powder X-ray diffractometry affords greatly improved angular and energy resolution, over laboratory studies in addition to benefiting from the greater flux (X-ray) density delivered by the synchrotron source.
This presentation highlights the value of synchrotron X-ray diffractometry through the examination of a variety of practical and applied uses of powder diffraction, including the development of waste forms and the examination of archeological problems.

Biomedical Imaging with Synchrotron Light
Daniel Hausermann, Australian Synchrotron

X-ray imaging is familiar to a lot of people. It is used extensively in industrial non-destructive testing and in medicine. Many people will have encountered x-ray pictures from radiographic examinations in hospitals or from security scans at airports. So it may seem an obvious thing to use synchrotron generated x-rays for synchrotron radiography, and even microscopy. However there are some obstacles which need to be surpassed. The huge difference in power between the synchrotron and other x-ray generators, the ease with which broad spectrum x-rays can be generated from relatively inexpensive x-ray tubes, along with the difficulty of producing optics for x-ray light means that the adoption of synchrotron sources for radiography has been relatively slow. However the pace is set to change as the technology to control the beams, and the science that can be gained from using those beams is being investigated and developed. In this talk we will explore the peculiarities of the x-rays produced from the synchrotron. Understand why the synchrotron is a very good source for x-ray imaging, and see more examples of the science that scientists from around the world are producing.

Soft X-ray Spectroscopy
Anton Tadich, Australian Synchrotron

Soft x-ray spectroscopy, incorporating Soft X-ray Photoelectron Spectroscopy (SXPS) and Near Edge X-ray Absorption Spectroscopy (NEXAFS), are important, extremely surface sensitive, tools for the chemical and electronic-structure characterisation of materials, particularly those containing the low Z elements (CNOF, …). An introduction to these techniques is given, highlighting the importance of synchrotron radiation in each case. This will be complemented with examples taken from recent users. The latter half of the presentation will outline the soft x-ray beamline itself, briefly covering the undulator light source and the beamline operating principles. The features of the current endstation are detailed, including the detector suite and sample preparation facilities. Importantly, some practical aspects about samples and experiments will be given, in order for students to gain understanding of what can, and cannot, be done on the beamline.

Basically, today was a full day of trying to understand the principles behind each technique and their applications. We had short 5 minute breaks in between lectures a morning tea and lunch which was well catered for. Once the lectures were done with, we had were returned to the hotel by bus. I had spent most of the last few days with a group; Matt D & Ben (from University of Sydney), Pat (from University of Adelaide), and 3 students from the University of Canterbury in Auckland; Sarah, Nikki and Demetri. We decided to go out and grab something to eat and go watch Toy Story 3.

I'm looking forward to tomorrow because we will be able to participate in two 4 hour session practicals. I've been assigned to participate in the 'MX' (molecular x-ray crystallography) and 'SXR' (soft x-ray beam-line) practicals. After todays lectures, I think that the flourescence microscopy (XRF) practical seemed more relevant to my research than SXR. I think the soft-x-ray beamline is more practical for inorganic chemists and solid-state physicists rather than structural biologists.


It was an awesome day at the synchrotron today. I got my first hands on with the synchrotron MX beamline, and managed to get onto the XRF beamlines rather than the SXR.

I found the MX particularly fun on the grounds that we got to burn holes in lysozyme crystals with full intensity X-ray light at the end of the session! The lightsource is incredibly powerful, so powerful the entire end-station is encapsulated in steel and or lead walls and a lock-down procedure is undertaken before the beamline is operational. I mounted a few crystals directly onto the machine using a 0.05-0.1mm Hampton cryoloop in 15% PG cryoprotectant. We also had a go at using the cassettes which are accessible by the robot. Centering crystals is a snap with the automated goniometer interface. In about 5 minutes we had an entire data-set of 90 degrees with highly redundant data. I was also shown how to use mosfilm and another program for determining the unit-cell of the lysozyme crystal. Unfortunately there was not enough time to undertake a MAD data collection. It seems like the staff were preparing the beamline for a research group to collect data in the afternoon. I can't wait to come back and use this facility, and check out what the micro-crystal MX2 beamline can do in due course.

The XRF beamline had some amazing capabilities. We were shown the optical procedures for adapting a beamline for adequate focus, and a few examples of what the team had achieved in past scans. The flourescence microscopy is able to detect the properties of many elements beyond potassium, with the exception of lanthanide. The fast scanning capabilities enable the analysis of large cross sections of organisms up to the size of a grain of barley. One particular project mapping and quantifying the deposition of minerals among grains through supplementing (or fortifying) crops with additional minerals. The data is very rich, and could be applicable to projects looking at ion transport within cells. I would love to do something like this, perhaps as a side project with Ros working on diabetic muscle samples.
While working at the HFRC, I worked on a project studying potassium homeostasis in type II diabetic rats. Some insulin receptors (e.g. GLUT4) are coupled to potassium inward rectifier channels (e.g. Kir6.2/6.1) which govern potassium transport across the cell membrane. It was grossly hypothesised that should insulin receptors become down regulated (as is the case in type II diabetes), the potassium balance may also be severely implicated. So, we took muscle biopsies and had them analysed by flame photometry to compare between diabetic and non-diabetic rats. It so happens, the data indicated a distinctly lower level of potassium among diabetic skeletal muscle cells. However, I think it would be interesting to try and see where the potassium is depleted most in the muscle cell, and attempt to track its transport into and out of the cell, and even probe the influence of diet to see if increasing potassium intake can rectify the loss of potassium.

In the evening we headed out for dinner at Outback Jacks and then headed onwards to play two rounds of bowling. I'm pretty sure I dislocated my index finger, but it was a good time had by all.

Throughout the day I took a few pictures of the equipment – enjoy those!

I have quickly typed up brief descriptions of each practical session available;

Beamline Practical Sessions
Synchrotron Molecular Crystallography Practical

Tom Caradoc-Davies, Australian Synchrotron

Together, the macromolecular crystallography (MX1) and microcrystallography (MX2) beamlines comprise a dedicated facility for determining the crystal structures of proteins, viruses, and nucleic acids as well as smaller molecules such as inorganic catalysts and organic drug molecules. Both beamlines are equipped with sample mounting robots for rapid throughput of crystal samples.
Winter school students will use the microcrystallography (MX2) beamline to collect diffraction data on crystals of hen egg-white lysozyme (HEWL). The crystal structure of lysozyme was published in 1965 and was the first enzyme structure published. Students will learn to prepare and mount lysozyme crystals for diffraction, collect diffraction data and use their datasets to obtain an electron density map of lysozyme. Sudents will also have the opportunity to mount samples using the robot mounting system.

Synchrotron SAXS WAXS practical
Nigel Kirby, Australian Synchrtoron

No Abstract available

Synchrotron Powder Diffraction Practical
Kia Wallwork, Australian Synchrotron

During the powder diffraction (PD) practical students will be introduced to the beamline and the technique. Students will be given a guided tour of the complete beamline, including the photon delivery system (optics), the experiment end station, and the beamline controls. The practical will give students the opportunity to conduct a variable temperature experiment, familiarising them with some of the equipment available at the beamline. The experiment will allow participants to observe the rhomdohedral to cubic and cubic to trigonal phase transitions of RbNO3. The data can then be fit using the information and tools provided.

Synchrotron Soft X-ray Spectroscopy Practicals
Anton Tadich, Australian Synchrotron

A hands-on session at the Soft X-ray beamline will be held to introduce students to the basics of soft x-ray spectroscopy, and to the practical aspects of what can be done at the beamline. To gain an understanding of the beamline, students will begin by interacting with some of the hardware, particularly the plane grating monochromator and adjustment of the APPLEII undulator. An overview of the endstation will also be given. The essentials of x-ray photoemmission spectroscopy (SXPS) will be outlined using our reference samples in the endstation, with emphasis placed on the advantages of using a synchrotron light source for this important surface science technique. Through the course of the session, it is hoped students will gain an understanding as to the advantages, and limitations, of soft x-ray spectroscopy, such that potential applications of the technique to their own research may be identified.

X-ray Flourescence Microscopy: How to focus, test resolution and run scans on the nanoprobe
David Patterson, Australian Synchrotron

In this beamline session we will introduce one of the microprobes used at XFM; the Fresnel zone plate nanoprobe. The nanoprobe has a sophisticated laser interferometer encoding of sample position and in capable of 60nm resolution.
We will demonstrate the procedure for establishing correct focus at 10keV with the zone plate capable of 120nm resolution. The relationship between coherent illumination and resolution or focussed beam size will be discussed and demonstrated.
We will then conduct scans of a test pattern to determine the resolution of the scanning nanoprobe. This will give students hands-on experience in defining and launching scans of regions of interest and choosing the optimum resoltion for scans of a particular sample and research question. Finally, time permitting, we will scan a biological sample to create a detailed elemental map.

Synchrtron X-ray Absorption Specroscopy practicals
Chris Glover, Australian Synchrotron

No Abstract available

Synchrotron Infrared Spectroscopy Practicals
Mark Tobin, Australian Synchrotron

The infrared practical class will take the users through an overview of the IR microscope beamline, followed by routine testing of the beamline performance through a series of “signal-to-noise” tests of the beam at high spatial resolution. The users will then be provided with a prepared sample comprising two or three thin sections (5 micron) of polymeric multilayers mounted in a diamond compression cell. The users will be instructed in the collection of infrared absorbance spectra from several layers within these polymers, followed by spectral treatment such as baseline correction. Using a spectral library it should be possible for the users to then identify each of the polymers making up the multilayers. If time allows, a 2D infrared mapping experiment may be set up allowing the users to visualise the distribution of functional groups within the samples.


The last day; not much to report.
Packed & said goodbyes
Spent most of the afternoon at the airport waiting for my flight back to the gold coast.

END of Post.

Saturday, July 3, 2010

July 3rd-4th

Well we've finally gone and got outselves an engine crane. I have uploaded a few pics of its construction. It's red, it's big and I can't stop looking at it - probably my new favourite tool in the workshop, surpassing the mighty breaker bar we purchased last week.

We've been shopping around a bit, only to be dissapointed with the outstandingly high prices of most retail stores. We ended up going out to Archerfield to Hare & Forbes Machinery House. That place has some of the most awesome drills, turning equipment and band-saws I've ever seen. One turner big enough to mount the barina onto it, crush and turn it into a bowling ball. We settled on the 1 ton engine hoist ($247.50) and threw in an 750kg engine tiller ($38.50). Went to bunnings to purchase a couple of D-shackles and 4m of galvanised chain (totalling to $46.36 (with 20% discount)).

Anyway, today is the day - it's a milestone as this symbolises a mutany against the internal combustion engine.

We've wrapped the 4m chain twice around the engine, loaded the tensioner to about 1:2 ratio to account for the additional weight in the transmission box. Took some measurements to ensure we've got enough space between the engine, the chassis and the roof when we hoist - made some adjustments, hacksawed out chunks of the battery holder (even though completely unescessary).

The result is epic;

Afterwards we started cleaning the engine

From EV 4_7_10

Everything looked pretty good until we realised the mess we left in the driveway. After a good hour of cleaning that other mess, re-shuffling the garage, we decided to call it a day. Beers all round!

This weekend has been reasonably productive. We've started preparing the house for Jessies 21st B'day party coming up this Friday. Everything is nearly in place;
- Balloons
- Guests
- Fancy Dress (Disney Theme - Jessies choice...)
- Lighting
- Tables and Chairs
- Music
- Food

I've started uploading a couple of progressive pics of the preparation. Hilarity ensues as I attempt to transform a HAZMAT suit into a dalmation costume.

P.s. A shoutout; Happy 22nd B'day to Pipi Cat & Rick!! You Guys rock :)

I look forward to next weekend!