Capabilities

Imaging Centre physicists are actively engaged in the use of new large international X-ray Free Electron Laser facilities (XFEL) at Standford (LCLS), Japan (SACLA) and Germany (European XFEL). These combine large scale accelerator technology with sophisticated detector systems and huge computer farms for data collection and handling.

Light sources: XFEL sources are able to produce incredibly bright pulses of X-rays with wavelengths ranging from 1keV-10keV and with pulse durations ranging from a few femtoseconds to 100 femtoseconds. These light sources are tunable, can be operated in two colour mode and have a repetition rate ranging from a few Hz to a few kHz. These light sources are unique because that offer the possibility of capturing chemical and biological processes in a snapshot revealing critical information about dynamical processes.

In particular these facilities have been developed to realise the long held ambition of imaging the structures of biomolecules in close to their native state without the need to form crystalline samples.

Detectors: Enormous investment has gone into the development of detection systems which are able to capture and read out the scattered signal generated by diffraction experiments using XFEL sources. The detectors are constructed from panels that are configured in such a way to maximise their ability to record scattered photons while allowing unscattered photons to pass through a central hole. The unscattered photons can be recycled in further experiments directly downstream.

Data collection and handling: Each femtosecond pulse scatters photons into a large detector array and at atomic resolution over a large angle. Each pulse therefore consists of an array of data involving several mega-words of information. Experiments typically run for more than a day and generate many terabytes of data. In order to maintain the flow of information from the detectors large processing farms are attached to these facilities to collect, store and process the data. Then use of an XFEL more closely resembles experiments in particle or astro physics than conventional laboratory based imaging techniques.

The Centre’s researchers have access to X-ray Free Electron Laser beamlines at the European XFEL through our Centre partners, the Deutsches Elektronen Synchrotron (DESY), and the Linac Coherent Light Source facility at Stanford University. The ultrahigh energy, femtosecond pulses of X-rays generated at these facilities could potentially be a revolutionary technique for protein crystallography by enabling structure determination of very small crystals.

• European XFEL
• LCLS

• The Centre’s researchers are heavy users of the Australian Synchrotron, particularly the Macromolecular Crystallography (MX) beamlines, which are a crucial and routine instrument used to determine structures of microcrystals. The Centre’s formal partnership with the Australian Synchrotron allows us to embed researchers at the Synchrotron itself. This enables us deeper insight into the design and operations of these instruments as well as provide the Synchrotron with closer access to key users and their research outputs and needs.
• Australian Synchrotron

• The Centre’s researchers are heavy users of the Australian Synchrotron, particularly theCryo-Electron Microscopy is becoming a revolutionary technology for structural biologists as unprecedented advances in detector technology, electron sources and automation have been made in the last 3-5 years. The power and utility of this technique lies in being able to image proteins that are difficult to crystallise and produce in large quantities.The Centre is positioned to play a world-leading role in developing this technique for structural biology through its strategic involvement in the recently established Clive and Vera Ramaciotti Centre for Structural Cryo-Electron Microscopy at Monash University. This facility features a Titan Krios Cryo-Transmission Electron Microscope, one of the most powerful microscopes in the world and the only one of its kind in Australia.
• Cryo-EM facility at Monash University (link under construction)
• SIMPLE 2.0

Single Molecule Science—the ability to observe and track individual molecules and monitor molecular interactions in living cells—heralds a revolution in biology. It’s a collaboration between biologists, physicists and engineers that feeds off the capacity of new microscopes and other technology to identify single molecules and analyse their behaviour in intact samples.It has emerged from developing, using and combining technologies such as single-molecule fluorescence and super resolution microscopy, atomic force microscopy, optical and magnetic tweezers, new sensors and more sophisticated computing and mathematical techniques.Single Molecule Science presents us with a new way of understanding life processes from the bottom up, following the paths and changes of many different molecules as they move through the cell, form complexes with other molecules, and influence cell function.

Data collection and handling: Researchers are developing novel algorithms that will extend the Centre’s capabilities in quantitative super-resolution imaging. Some of the tools under development are: molecular counting, stoichiometric analysis, cluster analysis, filament tracking, mapping dynamic molecular interactions, 3D membrane topography analysis, 3D organelle and cell morphology analysis. For example , the questions with respect to the 3D membrane topography analysis relate to how extra optics can be used to establish 3D maps of the cell membrane at nanometre resolution. The aim is to create a membrane landscape in order to view whether or not this will correlate to protein function and and to see if the distribution of TCRs is correlated with the surface topology of the membrane. The research will also solve fundamental questions in signal transduction such as signal integration and signal amplification.

Through working on both hardware and software solutions we hope to optimise and develop novel single molecule and super-resolution fluorescence microscopy approaches.

Advanced hardware : Imaging CoE single molecule scientists focus on transforming medicine by providing a molecular perspective on complex biological systems and processes, encompassing biophysics, biochemistry and cell biology as well as nanotechnology and nanofabrication. They are building cutting-edge instruments by gaining access to pre-commercial equipment and designing and building new microscopes. There are currently over ten different microscopes in operation at the UNSW node with five planned for 2016.

Each microscope contributes to the goals of the Centre by being optimised for different applications: speed, resolution, imaging depth, multi-colour imaging.

• Single Molecule Science Lab Microscopes
• Single Molecule Science Lab at UNSW

• The Monash Antibody Technology Facility (MATF) uses high-speed robotic platforms to produce custom-made, high quality, high affinity monoclonal antibodies for scientific and medical research.

• The Monash Protein Production Unit (PPU) offers expertise in protein expression, purification and optimisation using the latest high-throughput platforms.

• The Monash Macromolecular Crystallisation Facility provides high-throughput protein crystallisation of proteins that can provide a basis for understanding protein function and the rational design of therapeutics.

• The Monash Immersive Visualisation Platform (MIVP) operates Monash University’s advanced, immersive and large scale visualisation facilities, ranging from the ultrascale CAVE2TM down to personal head-mounted virtual reality (VR) devices like Oculus Rift.

• The Multi-modal Australian Sciences Imaging and Visualisation Environment (MASSIVE) and the Victorian Life Sciences Computation Initiative (VLSCI) are the Centre’s primary partners for high-performance computing for computational imaging, data processing and visualisation. Access to these high-performance supercomputing clusters is crucial as our imaging datasets continue to grow rapidly and can generate up to terabytes of data per day.
• MASSIVE
• VLSCI