Applied photonics in the Southern Ocean

Dr Tom Brown,
School of Physics & Astronomy

So why did I, a physicist who is most at home in the darkened, well-controlled confines of a laser laboratory, find myself dressed in high-viz clothing climbing aboard a big orange ship in Tasmania in January 2016 about to set off for a three-month trip to one of the most isolated areas of the planet?

The story starts with a technique known as Optical Coherence Tomography (OCT), an imaging technique developed in the early 1990s that has had real impact – many optometrists now rely on these systems to provide 3 dimensional images of the retina and its underlying structure and it provides a unique method of diagnosing many important visual impairments. The technique has also found application in many other fields including imaging plaques within arteries and mapping the boundaries of cancer tumours. We have used the system we developed at St Andrews in many medical areas however we have also sought to develop its application in other fields, most recently in providing high resolution structural imaging of Antarctic Krill (Euphasia Superba), one of the most important animals within the food chain of the Antarctic that stretches all the way from microscopic algae to the Blue Whale the planet’s largest animal.

Antarctic Krill (Euphasia Superba)

OCT provides imaging of structure by relying on accurate depth measurement of light which is reflected from the boundaries between different tissue types within a sample. The depth can be measured to a thousands of a mm accuracy by relying on the phenomenon of interference, the effects produced when two waves interact with one another either causing cancellation of a large growth in the signal. A typical OCT system can give resolution of a few thousandths of a mm or better in three dimensions to depths of a few mm within living tissue.

Our studies on Krill started from important biological questions on the effects of ocean acidification on the structural development of the animals. We began by examining preserved lab specimens before shipping the system the Australian Antarctic Division aquarium in Tasmania, Australia to produce the first three-dimensional imaging of living animals.

In the last year we have also taken our technology to the Antarctic itself by taking part in the Australian Government’s K-Axis marine science voyage based on the icebreaker Aurora Australis, which brought together around 50 scientists from a range of disciplines including Physics, Biology, Oceanography, Ecology and Chemistry, to study an area of unusual productivity in Eastern Antarctic between the Kerguelen Islands and the Antarctic itself. We showed that our OCT system, which is normally used within a specifically built optics lab, can be deployed and generated high quality data within the marine science environment with measurements taken even as the ship was rolling by more than 12 degrees in each direction. We have also shown that a wide range of interesting species can be imaged using these techniques and look forward to starting a host of new collaborations with partners from a very broad group of interests contributing new knowledge to globally important effects of climate change and ocean acidification.

The work described in this post has been supported from several sources with EU funding enabling the original development of the system, EPSRC providing ongoing support through a Platform Grant and the Australian Antarctic Division, providing major in kind contributions for voyage costs and hosting experiments.

Throughout the marine science programme our photonics technology performed exceptionally and provided an important compliment to the other photonics-systems on board that provided both imaging and advanced experiments on plankton development. The fact that the ship then ran aground and we had to be rescued by a major international mission – well that might be a story for another post!

Dr Tom Brown, School of Physics and Astronomy

Research: 
M.J. Cox, S. Kawaguchi, R. King, K.Dholakia and C.T.A. Brown, “Internal physiology of live krill revealed using new aquaria techniques and mixed optical microscopy and optical coherence tomography (OCT) imaging techniques”, Marine and Freshwater Behaviour and Physiology, 48, p. 455 (2015)

N. Bellini, M.J. Cox, D.J. Harper, S.R. Stott, P.C. Ashok, K. Dholakia, S. Kawaguchi, R. King, T. Horton and C.T.A. Brown, “The Application of Optical Coherence Tomography to Image Subsurface Tissue Structure of Antarctic Krill Euphausia superba”, PLOS ONE, 9, Art. No. e110367 (2014)

New research uses bioluminescent jellyfish as optical engineers

Researchers at St Andrews have produced the world’s first solid-state protein lasers, capable of record performance and some capable of self-assembly, by harnessing the optical engineering skills of bioluminescent jellyfish.

The findings, reported in the international journal Nature Communications ("Bio-optimized energy transfer in densely packed fluorescent protein enables near-maximal luminescence and solid-state lasers", doi: 10.1038/ncomms6722), have the potential to transform biomedical diagnosis of conditions such as cancer and advance the design of new materials. The work was inspired by the discovery that nature may have optimized - with sub-nanometre precision - the size of the molecules driving the bioluminescence of jellyfish to allow them to shine as brightly as possible. Professor Malte Gather from the School of Physics and Astronomy, together with Dr Seok Hyun Yun at Harvard Medical School and Massachusetts General Hospital, calculated that the green fluorescent protein molecule, which allows certain jellyfish to emit bright green light, has just the right size to strike an optimal balance between not losing energy to unproductive quenching and being able to squeeze as many molecules as possible into the light-emitting cells of the animal.

Fluorescent proteins derived from bioluminescent jellyfish
allow fabrication of efficient solid-state microlasers.
Under the right conditions, the protein molecules self-assemble
into a ring-shaped laser structure. Shown above are two such
lasers in action, made from a green and a red fluorescent protein, respectively.

Bioinspired by nature’s design, the researchers were able to make tiny solid-state lasers from these fluorescent proteins. The green fluorescent protein, generally known as GFP, is found the pacific jellyfish Aequorea Victoria where it is involved as energy acceptor in the natural bioluminescence of the animal. Several years ago molecular biologists isolated the section of DNA that tells the cellular machinery of the jellyfish how to produce GFP. Using genetic engineering this DNA can be used to confer the bright green fluorescence to other species - to bacteria, fruit flies, even to mice - a method that is widely used today to visualize cells or structures within cells under the microscope. Such measurements require only relatively modest protein concentrations. In the light-emitting organ of the jellyfish, however, the protein concentration is believed to be more than thousand times higher.

The scientists developed a number of different laser configurations. A particularly efficient design began to emit laser light when the power provided to it was less than what can be achieved in lasers based on state-of-the-art synthetic dyes. Another design makes use of the concept of self-assembly and allows the structure of the laser to form by itself. Professor Gather believes that beyond using GFP and other fluorescent proteins, the study of their structure and their optical properties can bio-inspire improvements of artificial emitters. [Press release]

Innovators from Physics scoop lucrative start-up support

PhD research students Alexander Ward and Jack Barraclough, and postdoctoral researcher Dr Clifford Hicks, of the School of Physics and Astronomy, were recently awarded third place in the Converge Challenge 2014 for their company Razorbill Instruments. Converge Challenge is a national competition aimed at encouraging innovation and entrepreneurship amongst academics.

The technology behind the company, and for which they won the award, is a nanopositioner – a device which can move with minute detail, especially useful in the manufacturing of microchips, and in physics and biomedical research. As a prize for third place the partnership received a cash sum, as well as a range of business support from leading legal, financial and branding companies, to the tune of over £13,000.

Razorbill Instruments was one of 111 entrants from across Scotland to apply for the competition, undergoing a rigorous selection process including business plans, a number of pitches, and a Dragon’s Den style Q&A with a panel of judges. Alexander has also received a fellowship from the Royal Society of Edinburgh, which will allow him to work on a prototype of the product. [press release]

Two St Andrews scientists to receive Wolfson Research Merit Awards

Prof. Malcolm White

Two leading scientists from the University of St Andrews are to receive Wolfson Research Merit Awards from the Royal Society. ‌ Professor Malcolm White (School of Biology) and Professor Sven Hoefling (School of Physics and Astronomy) are named in an exclusive, recently published list of only14 outstanding UK scientists to receive the honour.

Prof. Sven Hoeling

Professor White’s award, the CRISPR-Cas system for prokaryotic antiviral defence, recognises his research into a recently discovered immune system in microbes. His work is aimed at understanding how these complex molecular machines detect and destroy invading viruses.

Professor Hoefling's award, Quantum engineered semiconducting and transition metal oxide materials, is in appreciation of his work to understand and exploit light-matter interactions.

Jointly funded by the Wolfson Foundation and the Department for Business, Innovation and Skills (BIS), the scheme aims to provide universities with additional support to enable them to attract science talent from overseas and retain respected UK scientists of outstanding achievement and potential.
[press release]

New at St Andrews: Institute for Data-Intensive Research

The St Andrews Institute for Data-Intensive Research (IDIR) is a new institute set up to provide a focus for research and teaching activities across the University driven by access to “big data”. 

IDIR will bring the University’s strengths in humanities and social sciences with those in computer, mathematical, life, and physical scientists to share insights and techniques. IDIR results from the enormous volume of activity taking place across the University that could broadly be described as data-driven – from data science, through digital humanities and digital social science, to digital medicine, which all share common characteristics. They are exploring new techniques and opportunities brought about by the availability of large volumes of data and the processing power needed to manipulate them.

Some of the Schools included are Computer Science, Mathematics & Statistics, Physics & Astronomy, Medicine, Chemistry, Biology, International Relations, Earth and Environmental Sciences and History.

Novel microscope for biological imaging

A new form of ‘light sheet imaging’, has been developed by an interdisciplinary team led by Professor Kishan Dholakia and Dr Tom Vettenburg of the School of Physics. A light sheet microscope creates 3D images of cells by seeing how a sample lights up slice-by-slice when moved through a sheet of light. This sheet would ideally be as thin as a razor’s edge to be able to probe the inner workings of all cells, yet gentle as light to avoid cell damage. The St Andrews group achieved this by exploiting a beam of light that moves on a peculiarly curved trajectory. The beam is known as the Airy beam after the British astronomer Sir George Airy consists of multiple parallel sheets of light, achieving high resolution without being thin. Using this method, the light is used more efficiently to see the inner details of hundreds of cells with clarity.

It is hoped that the development will lead to improved understanding of biological development, cancer, and diseases such as Alzheimer, Parkinson, and Huntington that affect the human brain.
Partners are sought for the commercialization of the technology.

The work was funded by a UK EPSRC Programme Grant and carried out with St Andrews colleagues Dr Heather Dalgarno and Jonathan Nylk (School of Physics & Astronomy), Dr David Ferrier and Clara Coll-Lladó (Scottish Oceans Institute), Dr Tomáš Cižmár (School of Medicine), and Professor Frank Gunn-Moore (School of Biology).
Nature Methods, "Light-sheet microscopy using an Airy beam", doi:10.1038/nmeth.2922

Prof Samuel awarde esteemed Wolfson Research Merit Award

Professor Ifor Samuel of the School of Physics and Astronomy is one of 22 newly appointed Royal Society Wolfson Research Merit Award holders. Jointly funded by the Wolfson Foundation and the Department for Business, Innovation and Skills (BIS), the scheme aims to provide universities with additional support to enable them to attract science talent from overseas and retain respected UK scientists of outstanding achievement and potential. Prof. Samuel is working on "Organic semiconductor optoelectronics: challenges and opportunities". Congratulations to Prof. Samuel for this prestigious award!

New laser technique for detection of illicit and adulterated spirits

Writing in the “Journal of Raman Spectroscopy”, Dr Praveen Ashok, Bavishna Balagopal and Professor Kishan Dholakia of the School of Physics and Astronomy, reveal how they can carry out detailed analysis of a droplet of an alcoholic beverage to confirm whether it is toxic or not using a laser light scattering. It’s hoped the testing breakthrough will help develop a device to cut the number of deaths and serious injury arising from consumption of illicit and adulterated spirits. [full article] [press release]

Royal Society of Edinburgh Fellows 2013

The Royal Society of Edinburgh (RSE) has today announced the new intake of Fellows for 2013, which includes three academics from the University of St Andrews:

• Professor Peter Cawood - Department of Earth Sciences
• Professor Moira Jardine - School of Physics and Astronomy
• Professor Alan Sutherland - School of Economics and Finance

This year, there are 47 new UK and International Fellows to add to our 1500-strong Fellowship. Fellows are elected following a rigorous five-stage election process, and will now play an important role in ensuring that the RSE can continue its work for the advancement of learning and useful knowledge.

Best of Scottish Science from St Andrews

University of St Andrews will be exhibiting three of the exciting seven exhibits presented at the Best of Scottish Science at Dynamic Earth 1-4 April 2012 as part of the Edinburgh International Science Festival. Try out the interactive exhibits and question the scientists themselves about your discoveries.

Culture Evolves
Does culture really separate humans from the rest of nature? No! Discover the roots of culture in apes, meerkats and other animals, and how human cultures themselves evolve. Try your hand at learning a chimp tradition, contributing to the evolution of 'spaghetti towers' or shaping a new language! [more...]

Arctica Islandica: The Longest Lived Animal on Earth
Living to over 400 years old, the marine clam Arctica islandica is helping scientists investigate climate change and ageing processes. Like tree rings, the annual layers forming the clam's shell can be used to measure its age as well as acting as a natural archive of changes in its environment. [more...]

Invisibility Science: Geometry & Light

Invisibility has been a subject of fiction for millennia, from the myths of the ancient Greeks and Germans to modern novels and films. Now fascinating new developments in optics have resulted in a new science of invisibility - although it will still be a long time before you can get a real invisibility cloak from your nearest shop. Meet some of the scientists doing the research and see things disappear right in front of your eyes. [more...]

Meet the minds behind seven of Scotland’s most exciting scientific advances, selected for the Royal Society’s prestigious annual summer science exhibitions in London.

APS Fellowship for Prof. Mackenzie

Prof. Andy Mackenzie, Director of the Scottish Doctoral Training Centre at the School of Physics and Astronomy, has been honoured with a fellowship of the American Physical Society for his "outstanding contributions to physics". No more than one half of one percent of APS members are able to be fellows of the society. Andy was nominated by the Division of Condensed Matter Physics of the APS for his research over a number of years on the collective behaviour of electrons in ruthenium oxides, notably Sr2RuO4 and Sr3RuO7. [more]

Riboswitch development could impact new antibacterial drug development

A team of researchers led by Dr Carlos Penedo of the School of Physics and Astronomy and Professor Daniel Lafontaine, a biologist at the University of Sherbrooke (Canada), has deciphered the folding pathway of a genetic control element essential to the functioning of bacterial cells, a riboswitch. A riboswitch is part of a messenger RNA molecule. It can sense the concentration of chemicals in a cell, and turn gene expressions on or off in response. Because riboswitch structures are mostly found in bacterial organisms, understanding these molecular machines is fundamental to developing new and more resistant antibacterial drugs. The team managed to develop a unifying theory that explains various outcomes of the scientific literature on the mechanisms of genetic regulation by messenger RNA structures. Article in Nature

Exciting times for astronomy

The School of Physics and Astronomy have been in the news several times lately:

·        

·         18^th April – WASP-12b: A Magnetic Bow Shock. Aline Vidotto and colleagues, working with data from the Hubble Space Telescope, have been studying the exoplanet WASP-12b, a ‘hot Jupiter’, to investigate how planetary ‘bow shock’ can protect an exoplanet’s atmosphere from emissions for its host star.

·         19^th April – Pluto has carbon monoxide in it atmosphere. A team of scientists led by Dr Jane Greaves have discovered carbon monoxide gas in the atmosphere of Pluto, after a worldwide search of nearly two decades. Pluto’s atmosphere, previously, was considered to be over a 100 km thick, but is now thought to be over 3,000 km. Unlike the greenhouse gas carbon dioxide, carbon monoxide acts as a coolant, while methane absorbs sunlight and so produces heating. The research could provide clues to help scientists better understand the Earth’s atmosphere. Video link.

·         20^th April – Could black trees blossom in a world with two suns? Jack O'Malley-James, supervised by Dr Jane Greaves and others, has studied the potential for photosynthetic life in multi-star systems with different combinations of sun-like stars and red dwarfs. The simulations suggested that plants with dim red dwarf suns may appear black to our eyes, as they would absorb across the entire visible wavelength range.

·         21^st April – Astronomers peer into the dark. Astronomers from SUPA, including Dr Aaron Robotham, have produced a completely new catalogue of approximately 15,000 groups of galaxies which gives new insight into dark matter, the material of unknown composition that makes up 20% of the mass of the Universe.

Prof. Mackenzie receives Royal Society Wolfson Research Merit Award

Professor Andrew Mackenzie of the School of Physics & Astronomy is one of seven individuals in the UK to be selected to receive a Royal Society Wolfson Research Merit Award. The award helps to fund research of outstanding achievement and potential and will support Professor Mackenzie’s work in creating, understanding and exploiting novel quantum order in oxides.

Silver Award from International EPR Society

Graham Smith, of the School of Physics and Astronomy, has been awarded the Silver Medal for Instrumentation by the International Electron Paramagnetic Resonance (EPR) Society along with Keith Earle of University at Albany, NY. The award was in recognition of their outstanding contributions to the design and implementation of quasi-optical techniques for High Field EPR instrumentation.

Outstanding physics PhD thesis wins prize

The Springer Outstanding Thesis Prize for research at PhD level has been awarded to Andreas Rost from the School of Physics and Astronomy. In addition, Andreas' thesis, "Magnetothermal Properties near Quantum Criticality in the Itinerant Metamagnet Sr3Ru2O7", will be published as a book (a rare occurrence in the Physical Sciences) as part of the 'Springer Theses' series. Congratulations Andreas!