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The Australian The Australian Synchrotron is one of the nation’s largest and most significant scientific facilities. It is a powerful machine of great utility that enables investigators to determine the structure and composition of all materials, including living specimens, with extremely high detail. By Dr David Maddison T he Australian Synchrotron, located adjacent to the Monash University campus in Clayton, Victoria, was completed in 2007 at a cost of $221 million. Funding came from the Victorian Government with a contribution of $157 million, with additional funding of $50 million from other state government, university and research organisations and a $14 million dollar contribu- tion from the Commonwealth government. About 65% of the initial funding was spent with local suppliers and contractors. As well, substantial design input was made by Australian scientists and engineers. The facility has an annual operating budget of $25 to $30 million. When not undergoing scheduled maintenance, the synchrotron runs 24 hours per day, year round, producing a Bird’s-eye view of the Australian Synchrotron (bottom right). Some idea of the size of this facility can be gleaned by comparing it with the oval in the grounds of the Monash University at left! 14  Silicon Chip siliconchip.com.au Synchrotron What is a synchrotro n? wealth of scientific results and important industrial research. It is one of about 50 similar devices around the world, although not all are as new or as advanced. Typically 3,500 scientists visit the facility each year and work on more than 600 experiments. In order to probe a material’s structure the Synchrotron produces what is essentially very high quality light, tunable over a wide variety of wavelengths from the microwave part of the spectrum through to “hard” X-rays (see diagram). Note that non-visible electromagnetic radiation such as X-rays is also considered a form of light. The beam is very intense with a brightness of around one million times greater than that of the Sun and the X-rays produced can be millions of times more intense than those produced by conventional X-ray tubes. The Synchrotron is a state-of-the-art, third generation device. It was conceived at the outset to produce bright The range of wavelengths produced that the Australian Synchrotron. Image: Australian Synchrotron. siliconchip.com.au As described on the Au stralian Synchrotron website, in simple terms, a synchro tron is a very large, cir cular, megavoltage machine about the siz e of a cricket ground. From outside, the Australian Synchrotro n, for example, looks very much like a roofed football stadiu m. But on the inside , it’s very different. Instead of grass and seating, there is a vast, circular network of interconnecting tunne ls and high tech appa ratus. Synchrotrons are a typ e of particle accelerato r and when used to accelerate electron s, can produce inten se beams of light, a million times brighter than the sun. The light is produced when high-energy electrons are forced to travel in a circular orbit inside the synchrotron tunne ls by ‘synchronised’ ap plication of strong magnetic fields with ve ry powerful electrom agnets. The electron beams tra vel at just under the speed of light – about 299,792 kilom etres per second. Th e intense light they produce is filtered and adjusted to travel into experimental workstations, where the lig ht reveals the innermos t, sub-microscopic structure of materials under investigation, fro m human tissue to plants to metals and more. With this new knowled ge that synchrotron sc about the molecular str ience provides ucture of materials, res earchers can invent ways to tackle disease s, make plants more productive and metals more resilient – am ong many other bene ficial applications of synchrotron science . More technical inform ation about how the Au stralian Synchrotron and other similar facilities work is availab le from the ‘ABOUT US/Our facilities’ secti on of the www.synchro tron.org.au website. X-rays and other wavelengths of light compared with the first generation of such devices in which synchrotron radiation was utilised essentially as a by-product of particle accelerators.. Other characteristics of the generated light are that it is highly collimated meaning that the light rays in the beam all travel parallel to each other as in a laser beam. The light beam is also polarised and different polarisation modes can be produced as required for different experiments. In addition, the light is also pulsed. Information about the structure and composition of matter is revealed by the way the light beam interacts with the object under investigation. The beam may be absorbed, transmitted, refracted or diffracted by the object and by carefully measuring the beam May 2012  15 , Australian Synchrotron control room. Image: the author. properties after it has interacted with the test specimen, it is possible to determine its structure and composition. The Synchrotron is used by Australian and New Zealand scientists and industrial researchers and by many other scientists from around the world. These scientists and associated staff are extremely dedicated and enthusiastic about their work in this facility. To accommodate the many visiting scientists there is an accommodation block currently under construction. Schematic view of the Australian Synchrotron. Image: Australian Synchrotron. 16  Silicon Chip Applications Most experiments fall within three main categories. These are (a) X-ray diffraction and scattering to determine the crystal structure and other structural properties of samples; (b) spectroscopic analysis down to nanometre resolution (one millionth of a millimetre) to determine the chemical composition of samples and (c) high resolution imaging at any wavelength of light that can be produced at the Synchrotron of biological and non-biological materials, animals and, in the future, humans. Some research highlights from the Synchrotron are as follows: • Determination of whether a proposed coating on electrode wires used on the Monash bionic eye would damage the wires. The rapidity with which the results were obtained saved a large amount of development time and money. • Improvement of processes to extract pharmaceutical substances from poppies by determining their chemical structure from minute samples. • Development of microbeam therapy to treat cancer. • Imaging of lung function in newborn animals to better understand breathing processes in premature babies. • Discovery of new information about an immune system protein leading to a better understanding of treating diseases. • Research on the life-cycle of the malaria parasite in blood cells which will lead to the development of better drugs to control the disease. • Research on immune system T-cells to develop better drugs to boost immune system function. • Use of imaging techniques to develop new procedures to accurately place cochlear implants and improve their function. • Development of techniques to accurately identify healthy human egg cells for use in IVF procedures. siliconchip.com.au “MASSIVE” Computing Facilities Part of MASSIVE1. Image: the author. Each experiment at the Synchrotron produces large quantities of data which need to be stored and processed. The Synchrotron facility has a supercomputer cluster to perform this task. MASSIVE (Multi-modal Australian ScienceS Imaging and Visualisation Environment) provides the hardware, software and personnel needed to service this task, among others. This facility, which actually consists of two machines connected by a high-bandwidth link, is also accessible by scientists working in areas outside the Synchrotron such as in neuroimaging, geosciences and microscopy or any other area that requires advanced image processing and visualisation resources. The great computer power allows three-dimensional images to be generated and manipulated in real time, enabling researchers to adjust their experiment and/or the beam parameters without having to wait for postprocessing of image data. MASSIVE1 is located at the Synchrotron facility and MASSIVE2 is located next door at Monash University, Clayton campus. The computer utilises both CPUs (Central Processing Units) and GPUs (Graphics Processing Units) for its computing tasks. The CPUs are used for regular computing while the GPUs are used for graphic processing and can also be used for matrix and vector operations for non-graphic tasks. siliconchip.com.au MASSIVE1 has a capacity five teraflops for traditional CPU computing and 50 teraflops when using its GPU coprocessors and MASSIVE2 has a capacity of 10 and 100 teraflops respectively. (One teraflop is 1012 floating point operations per second.) The specifications are as follows: MASSIVE1 at the Australian Synchrotron • 42 nodes with 12 cores per node running at 2.66GHz (504 CPU-cores total) • 48GB RAM per node (2,016GB RAM total) • 2 nVidia M2070 GPUs with 6GB GDDR5 per node (84 GPUs total) • 58TB of fast access parallel file system (IBM GPFS) • 4x QDR Infiniband Interconnect MASSIVE2 at Monash University • 42 nodes with 12 cores per node running at 2.66GHz (504 CPU-cores total) in two configurations, 32 nodes identical configuration to MASSIVE1 • 48GB RAM per node (1,536GB RAM total) • 2 x nVidia M2070 GPUs with 6GB GDDR5 per node (64GPUs total) • 10 nodes (visualisation/high memory configuration) • 192GB RAM per node (1,920GB RAM total) • 2 x nVidia M2070Q GPUs with 6GB GDDR5 per node (20 GPUs total) • 250TB of fast access parallel file system • 4x QDR Infiniband Interconnect May 2012  17 Distribution map of titanium (blue), niobium (green) and thorium (red) in ilmenite, an iron titanate mineral and an important source of titanium dioxide for pigment. It was produced using the innovative Maia detector. The field of view is 10 x 6 mm. Image: La Trobe University, CSIRO, Australian Synchrotron. • Development of techniques to track stem cells as they repair the body. This information can be used to develop methods of stem cell therapy. • Search for gold in ore samples in which the gold cannot be detected by normal techniques. This may lead to the discovery of new gold deposits. • Analysis of the structure of sheep leather, which has led to methods to strengthen it so it can be used for shoes, something which is not otherwise possible. • Understanding how the runoff from acidic soils affects Australia’s east coast fisheries and the development of methods to control soil acidity. • Understanding the reason for the buildup of scale in pipes used in the bauxite industry and the development of methods to alter processing conditions in order to minimise scale formation. • Exploration of materials for use in the electronics industry such as synthetic diamond films. • Studying the distribution of nutrients in foods after processing in order to assist in the development of plant varieties which better retain their nutrients. • Studying old paintings to look for underlying images, determine paint composition or to establish authenticity. Analysing the composition of glazes on ancient Egyptian artifacts. • Examining the internal structure of ancient fossils which are too fragile to completely remove from their rocky encasement and also imaging soft tissue impressions therein. • Analysing the structure of “green” cement and enabling VicRoads to update their standards to allow for its use. • Studying molecular structures which are suitable for hydrogen storage for its use as an alternative fuel. • Researching the interaction of carbon dioxide with various materials that may be used for sequestration of the gas. • Development of a forensic method to identify soil from crime scenes using extremely small samples. • Studies of the chemistry of fingerprints to enable improved detection. • Discovering why Phar Lap died by looking for toxins in hair follicles from his preserved hide. This indicated ingestion of arsenic in the last 30 hours of life. • Studying the distribution of elements in mineral samples (see picture above). 18  Silicon Chip Image of animal lungs clearly showing detailed structure. Such detail cannot be achieved with conventional imaging techniques. Image: Australian Synchrotron Apart from other areas of world-leading expertise indicated above, scientists at the Synchrotron are leaders in determining the structure of proteins, an essential component of all life forms. The structural determination of many proteins is extremely difficult or impossible by conventional techniques but is assisted at the Synchrotron using the technique of small angle X-ray scattering. Normally, high quality crystals are required for this work but unfortunately, some proteins do not crystallise well. In these cases, the Synchrotron can be used to determine the shape of the protein’s outer “envelope”. With this partial information it is possible to infer the rest of the structure with the aid of advanced computing methods. A particularly difficult medical imaging problem is to visualise lung tissue and the motion of the lungs during breathing. Due to the high resolution of the beam and the tunability of the X-rays, successful imaging has been achieved by Australian research groups and the findings have already found application such as in studies of cystic fibrosis and asthma. “Tricks” of light are used to image the soft tissue and air spaces of the lungs whereby X-rays are refracted differently from the tissue and the air. Tuned with the right parameters a “phase contrast” image, which can be viewed in real time if desired, can be produced to show the working lungs. How the light beam is produced In essence the function of a synchrotron is to generate a beam of charged particles travelling close to the speed of light. These can then subject them to an acceleration which causes them to emit light radiation. This beam of particles is maintained in a storage ring. Electrons are typically used as the charged particles for light generation and different magnet configurations are siliconchip.com.au Medical applications A recently built facility at the Synchrotron site is the flagship Imaging and Medical Beamline. This was built with a grant of $13.2 million from the National Health and Medical Research Council and grant of $1.5 million from the Victorian Government. It will be used for medical (and other) imaging research as well as treatment research, for example on high precision irradiation of tumours. An interesting area of research is to irradiate tumours in a “checkerboard” pattern which is possible due to the fine control possible with the X-ray beam. This has been shown to destroy tumours just as effectively as normal radiation treatment but with much less damage to healthy tissue. Other clinical research will include observing how tumours respond to treatment and the The new Imaging and Medical satellite building. The synchrotron beam is conveyed possibility of watching specially to this building via a 150m long tunnel. Image: the author. marked individual cells migrate through the body in real time. to the new building. The long tunnel is needed to allow the For patient comfort, the facility will provide patients with a X-ray beam from the Synchrotron to expand in size from clinic-like rather than a “laboratory” experience. Note that the the original dimensions of 1mm wide by 50 microns high to present intention is for selected patients to visit for clinical produce the largest X-ray beam of any synchrotron in the research and trials only – this will not be a general facility world, having a cross section of 50cm by 4cm. for patient treatment. This beam will enable images to be produced with a resoluThe facility also contains sections to house and conduct tion of one micron over large areas of a human or animal body. research on animals. Of interest is a miniature combined Typical human and animal cells are 10-100 microns in size CT and PET scanner for small animals such as mice (see so images of individual cells should theoretically be possible. picture). Images that are about one hundred times more detailed The central feature of this facility is the beamline that ar- than a hospital CT scanner will be able to be produced and rives via a 150m long tunnel leading from the Synchrotron monitored in real time. Imaging and Medical beam tunnel, 150m long (under construction). Note the black support structures which will hold stainless steel tubing under vacuum that will contain the X-ray beam. One small section of tube is installed in this picture. Imaging will occur in a room at the end of the tunnel. Image: the author. siliconchip.com.au Miniature CT/PET scanner for small laboratory animals such as mice. For scale, compare with the size of the small computer screen on the left. Image: the author. May 2012  19 Right: prototype sextupole magnet. Image: the author. Prototype magnet assembly on display in the Synchrotron building showing the bending or dipole magnet (yellow) which causes the generation of the synchrotron radiation when electrons pass through its centre (in the direction from one side of the picture to the other) at close to the speed of light. The red and green magnets at each end are quadrupole and sextupole magnets respectively and these are used to focus and steer the beam. Image: the author. used to make the electron beam either bend, “undulate” or “wiggle”, causing the electrons to accelerate and emit light. Note that in physics terminology “acceleration” can mean a change in either speed or direction. In this case it is the change in direction as the electron travels through the bending magnet that constitutes acceleration. The Synchrotron consists of the following main components: electron gun, linear accelerator, booster ring, storage ring and beam-lines where the radiation is emitted into the experimental “end stations” as shown in the diagram of the Australian Synchrotron. Generating the electrons and then boosting their speed is a multi-stage process. Electrons are first generated with an electron gun similar to one in a cathode ray tube, only larger. The electron gun produces electrons with an energy of 90keV. After leaving the electron gun, electrons are injected into the linear accelerator (LINAC) where the 90keV beam is boosted to an energy of 100MeV. Electrons are energised using a series of radio frequency (RF) resonant cavities which operate on a similar principle to the magnetron in microwave ovens. When a radio wave of the appropriate frequency is generated and enters a resonant cavity, a standing wave is created, the intensity of which increases as more RF energy is injected. Electrons in the beam absorb that energy and their speed is increased. The electrons are travelling at 99.9985% of the speed of light as they leave the LINAC. After leaving the LINAC, the electron beam enters the booster ring where the beam is further energised from 100MeV to 3GeV with the use of a 5-cell RF resonant cavity. The booster ring also contains 60 combined focusing and steering magnets. The electrons are resident in the booster ring for half a second during which time they complete one million circuits of the 130m-long ring. A new cycle for the next batch of electrons can be initiated every second. In the final stage, electrons from the booster ring enter the storage ring. This has a circumference of 216m and actually consists of 14 main sections each with a 4.4m straight 20  Silicon Chip Below: end-view of prototype quadrupole magnet. Image: the author. section and an 11m arc-shaped section. Each arc section contains two bending magnets (also known as dipole magnets) as well as six quadrupole (four pole) and seven sextupole (six pole) electromagnets. Each bending magnet generates synchrotron radiation as the electrons pass through it at close to light speed. As shown in the following diagram, the radiation (green) is Radiation pattern (green) as electron traverses the bending magnet (path shown in red). Image: Australian Synchrotron. emitted at a tangent to the direction of the electron path through the magnet. It is this radiation that is used in experiments. At each experimental station at the active beam-lines there are beam-line optics that contain filters, monochromators, mirrors, attenuators and other optical devices that help condition the beam to the required characteristics for each experiment. Following these optics is the rest of the experimental equipment such as a spectrometer or X-ray diffraction apparatus. All of the “end station” equipment sits in a radiationshielded “hutch” to protect staff from X-ray radiation. siliconchip.com.au Part of the storage ring of the Australian Synchrotron. Image: Australian Synchrotron. The quadrupole and sextupole magnets are used to keep the electron beam focused and to correct for any aberrations in the beam. In all, there are 84 quadrupole magnets and 98 sextupole magnets in the storage ring. The sextupole magnets also have extra windings to provide vertical or horizontal corrections to the beam path. Typically the electron beam is 50 microns wide with a deviation from the desired path of no more than 5 microns (one micron is one thousandth of a millimetre). The magnets are water cooled and the temperature in the main building and the beam tunnel is highly controlled to minimise errors due to thermal effects in equipment and the structure. Two of the straight ring sections contain a total of four RF cavity resonators in order to replace beam energy that is lost due to synchrotron radiation. The remaining twelve straight sections are able to accommodate “insertion devices”. These devices are used to further increase the intensity of the light and impart it with certain characteristics. There are two types of insertion devices. One is the “multipole wiggler” and the other is the “undulator”. In the wiggler, light cones are emitted at each bend in the electron trajectory and these cones reinforce each other to Multipole wiggler: the green shading represents the emitted radiation and the red line represents the electron path. Image: Australian Synchrotron. create an extremely bright, broad spectrum beam. In the undulator, weaker magnets are used, resulting in a more gentle bending of the electron’s path. In this configuration some cones of light interfere with each other cancelling out their energy, while others reinforce each other. By adjusting the spacing between the magnet poles it is possible to enhance some frequencies of light to thousands of times the intensity of other frequencies, allowing for an extremely intense beam at one particular wavelength of choice. Undulator: the radiation pattern is shown in green and the electron path in red. Image: Australian Synchrotron. siliconchip.com.au The electron beam needs to be maintained in an enclosure that is kept under an extremely high vacuum, in this case 10-13 bar (10nPa) where 1 bar is equivalent to about one atmosphere of pressure. The reason for this ultra high vacuum is so that the electrons will not lose energy or be scattered by residual gas particles. As the electrons in the beam are travelling at very close to light speed Einstein’s Theory of Relatively applies. Due to relativistic effects, including time and length contraction, from the electrons’ point of view, the time and distance through which they travel appears much shorter than a stationary observer would experience. This means that the frequency of light emitted as the electrons are accelerated through the bending, wiggler or undulating magnets is many orders of magnitude greater than would otherwise be the case if Relativity did not apply. Beam-lines and future development Currently there are nine beam-lines in use. These are used for powder diffraction, X-ray absorption spectroscopy, small and wide angle X-ray scattering, soft X-ray spectroscopy, infrared spectroscopy, macromolecular spectroscopy and micro crystallography, X-ray fluorescence microscopy and medical imaging. All these beam-lines are in constant heavy use and even so, there is not enough beam-line time available to service the demand for them. Fortunately, the Synchrotron was constructed with future expansion in mind and a total of 29 additional beam-line positions are available. The Synchrotron is subject to continual improvement and there is a dedicated accelerator physics group who are constantly working to better the device by improving control systems, beam parameters and researching theoretical aspects of synchrotron devices. Conclusion The Synchrotron provides Australian researchers with a powerful, world-leading set of tools for analysing and imaging living or non-living matter in ways that are unSC achievable by conventional techniques. OPEN DAYS The Australian Synchrotron has periodic Open Days. The last one, in November 2011, attracted over 3,000 people. The next Open Day is expected to be later this year. Keep an eye on the Synchrotron website (www.synchrotron.org.au) for details. May 2012  21