Exploring the physics of imaging
The Third Physics Symposium was held in the Laby Theatre at the University of Melbourne on Tuesday 5 July. The Symposia are not primarily held to present research results: they are intended to be a forum to explore new ideas and new directions that might be pursued within the Centre, or to discuss issues that stand in the way of progress. This Symposium was attended by almost 50 people and covered a wide range of topics and emerging research.
Professor Keith Nugent, who leads the Physics activities within the Centre, surveyed the Physics programmes in his State of the Union address. He presented the progress that we have made in both experimental and theoretical physics of X-ray free-electron laser science, including detailed simulation work and the development of sample delivery systems and crystallographic analysis. He also identified new directions that he described as “opportunistic”; the work led by Tim Gureyev in the application of X-ray phase contrast imaging to clinical mammography, the development of new tabletop light sources, and potential developments in the emerging area of micro electron diffraction.
Associate Professor Jeff Davis, Swinburne University, is a long-term collaborator of the Centre physicists. He described his exquisite high-precision measurements of quantum coherence effects in photosynthetic systems and recent progress towards a deeper understanding of energy transfer processes in biomolecular systems. An understanding of these processes at the quantum electrodynamical level is required to be able to manipulate such systems, or to devise biomimetic devices to capture and store solar energy through photosynthetic processes. Dr Timur Gureyev discussed the current state of the art X-ray phase contrast imaging and its application in the clinical diagnosis of breast cancer using reduced radiation doses. The first steps in this research were taken by Nugent, Gureyev and others almost 20 years ago in pioneering fundamental research on X-ray imaging techniques based on the transport of intensity equation. These techniques are now being assessed by clinicians as a potential diagnostic tool in cancer screening.
The Centre Director’s challenge of inviting lectures at Centre meetings with the title ‘If only I could…’ was taken up by Dr Harry Quiney, who suggested that recent progress in theoretical chemistry on the solution of the N-representability problem in density matrix theory might circumvent the adverse scaling properties of truly ab initio computational approaches to the determination of biomolecular structures. The organisational principles that determine the structures of biomolecules in solution are dictated by fundamental principles of quantum mechanics and statistical mechanics, but the complexity of conventional approaches grows exponentially with the number of atoms. These recent theoretical developments, which exhibit a polynomial growth in computational complexity, may well stimulate the rapid growth of ab initio computational structural biology. Certainly this was the goal that stimulated work on the N-representability problem for over half a century.
A major theme addressed the recent development of micro electron diffraction from protein crystals. Professor Les Allen, University of Melbourne, is a recognised international expert in the area of theoretical condensed matter physics that makes this approach potentially rather challenging as a method for routine de novo structure determination: the ‘multiple scattering problem’. Les gave a masterful account of the history of this subject and the results of detailed calculations of electron diffraction in protein crystals. While there has been some experimental progress in this field in recent years, there is every reason to believe that there are fundamental problems in physics to be overcome before structures using micro electron diffraction can be obtained routinely, or can be regarded wholly reliable.
Dr Nadia Davidson took time out from her busy life as research associate at the Murdoch Children’s Research Institute – and new mother – to give us a brief introduction to bioinformatics. Nadia has a background in computation and particle physics, but also helped the physics group implement partially-coherent imaging techniques in a software package that is now known as NADIA (Nadia’s ADvanced Imaging Algorithms, a recursive whimsy amusing mainly to computer scientists). Nadia gave fascinating insights into how training in physics, mathematics and computation can be applied to the analysis of complex problems in the life sciences.
Thanks also go to Dr Uli Felzmann for taking time out of his role as Science Faculty IT Manager to make it possible for Nadia to come and speak to us at the Symposium.
Associate Professor Andy Martin, University of Melbourne, presented work at the interface between statistical physics and biology with his talk on the collective behaviour of complex systems and, in particular, the principles that lead to collective behaviours in flocks of birds and how shoaling fish exhibit schooling behaviour and avoid predators. The mathematical description of these phenomena can be applied to many other events that exhibit apparently spontaneous self-organisation and collective responses to external events, including the correlated behaviour of revellers in a mosh pit.
The Centre is fortunate to boast two distinguished Richard Garretts. One is Facility Director of ANSTO’s Australian Synchrotron Research Program and the other is a student at La Trobe University, with a Major in Biochemistry and Physics, and an Advanced Diploma in Japanese.
The second Richard Garrett works in the experimental physics group and brought us up to date with the Centre’s development of microfluidic technologies, which play such a key role in our wider XFEL program of sample handling and delivery. Also from La Trobe was Dr Leonie Flückiger, who has done a great deal of work looking at the dynamics of rare gas clusters exposed to intense femtosecond pulses. These are prototypes for studying the expansion and explosion of molecules subjected to intense XFEL pulses, but are amenable to detailed experimental investigation, X-ray imaging and computational modelling. Leonie presented some preliminary results on the imaging of such systems, which is an important step towards the Centre’s goal of producing ‘molecular movies’.
The Centre’s in vivo imaging group asked if it might be possible to use X-rays to perform quantitative elemental analysis on tissues. X-ray fluorescence microscopy (XFM) is an area of expertise developed at the Australian Synchrotron; one of its alumni, Dr Simon James, now at the Florey Institute, presented the current state of the art in XFM and its application to living organisms and tissue samples. After some subsequent discussion and a meeting after the symposium with Centre members at the University of Melbourne, it looks likely that this presentation will catalyse an ongoing collaboration between physics and the biological sciences.
It was a stimulating and thoroughly enjoyable meeting and we intend to continue to hold them, following a similar format, in the future. We try to make the presentations accessible to everyone, with not too much mathematics, and the biological applications made as clear as possible. Centre members from the biological community are encouraged to attend Physics Symposia because they are designed to foster discussion and interaction. This inevitably leads to post-symposium interactions at the local Clyde Hotel, to which all Centre members will also be warmly welcomed.