School of Physics & Astronomy

Find a PhD Project Here

Opportunities for fully funded PhD or EngDoc research projects are available in all fields of research within the School. You may search for current projects on this page. APPLY HERE for a PhD Place.

 PhD in Photonics
 PhD in Condensed Matter
 PhD in Astrophysics

Search current PhD opportunities in the School of Physics & Astronomy:-


organic semiconductor polariton light emitters
Samuel, Prof Ifor -
Turnbull, Prof Graham -

When light is confined on the nanoscale it is possible to observe light-matter interactions that are not normally observed in bulk materials. One example is the strong coupling of photons and excitons in wavelength-scale microcavities which leads to a number of unusual phenomena [1,2]. The modes of the cavity couple with the exciton to make a hybrid-light-matter state called a polariton. One can make polaritons lasers that emit coherent light [3] and it has been shown that polaritons can form a Bose-Einstein condenstate [4].

This project will explore the properties of polaritons in microcavities based on organic semiconductors [2,4-6]. It will involve the fabrication of microcavities that include J-aggregate dyes or semiconducting polymers to explore how the energy states of organic materials can be modified when coupled to the cavity modes, and be applied in photonic devices including lasers and LEDs.

[1] C. Weisbuch et al., Phys. Rev. Lett. 69, 3314 (1992)
[2] D.G. Lidzey et al., Nature 395, 53 (1998)
[3] S. Christopoulos et al., Phys. Rev. Lett. 98, 126405 (2007)
[4] J D Plumhof, T Stöferle, L Mai, U Scherf & R F Mahrt, Nature Materials 13, 247–252 (2014)
[5] T. Schwartz, J. A. Hutchison, C. Genet, and T. W. Ebbesen, Phys. Rev. Lett. 106, 196405 –(2011)
[6] S Kéna-Cohen*, S A. Maier and D D. C. Bradley, Advanced Optical Materials 1, 827–833, (2013)
Plastic Lasers
Samuel, Prof Ifor -
Turnbull, Prof Graham -

Conjugated polymers are a very special class of plastics that are both semiconducting and efficient light-emitters. They have been widely applied as flat and flexible light emitting displays, as well as visible lasers, optical amplifiers, solar cells and electronic circuits. As novel laser media, polymers are particularly attractive because they can be easily and inexpensively formed into flexible shapes and structures that are inaccessible to crystalline materials.

This project builds on our internationally recognised research programme in polymer lasers. We have demonstrated plastic lasers driven by a light-emitting diode and are currently developing lasers and optical amplifiers integrated with nitride LEDs and CMOS control electronics. Novel photonic nanostructures are used to control
laser emission, develop new modes of operation and applications in sensing and datacomms.
Advanced Imaging for the Biomedical Sciences (with Dr F Gunn-Moore, School of Biology)
Cizmar, Dr Tomas -
Dholakia, Prof Kishan -

the aim of this project is to explore new routes for imaging both in vitro and in vivo using concepts of light transmission through disorder. In turn this will allow us to shape light at will for example at the end of an optical fibre and use this perhaps in an endoscopic scenarios. Other forms of microscopy to consider will involve using a light sheet for imaging larger biological systems (eg embryos). The study will involve advanced photonics, numerical studies and practical work. The research will also investigate strategies to image beyond the diffraction limit. Samples under investigation will include tissue and, at later stages of the work, potentially neuronal cells/tissue to target advanced understanding of neurological disease using these methods.
Aligning molecules to improve efficiency in next generation organic LEDs
Gather, Prof Malte -

Organic light-emitting diodes (OLEDs) are novel type of LEDs in which electroluminescence is generated by plastic-like organic molecules. OLEDs are at the heart of modern smart phone displays and are likely to become the dominant technology for computer screens and large area TVs in the future. In addition, OLEDs are considered for general illumination, an area where efficiency is of key importance. While OLEDs can operate with close to 100% internal electron-to-photon conversion efficiency, typically less than 20-25% of the generated light is extracted into the surrounding air; the rest is trapped in waveguided modes and eventually lost to absorption.

Various strategies have been proposed to improve light extraction from OLEDs. Very recently controlling the average orientation of the electroluminescent molecules inside an OLED has been identified as a promising avenue. However, accurate measurement of molecular orientation is difficult and it remains unclear how molecular orientation can be controlled efficiently. Within this project, these challenges will be approached by making use of different spectroscopic and computational methods. Provided certain formal criteria are met, the student can benefit from placement with a major commercial developer of OLED materials and technology.

Further reading:
Biophysical Aspects of Photodynamic Therapy (Ninewells Hospital, Dundee)
Brown, Prof Tom -
Wood, Dr Kenny -

Photodynamic Therapy (PDT) is a treatment for cancer that involves light-activation of a photosensitiser and causes cell death by release of singlet oxygen and free radicals. The Scottish PDT Centre was established in Ninewells Hospital, Dundee in 2000 thanks to a generous donation from the Barbara Stewart Charitable Trust. Since its introduction in Dundee, over 2,000 treatments have been carried out. The photosensiters used for PDT also have the property that they fluoresce and so they can be used for photodiagnosis (PD), which is performed at the Scottish PDT Centre to direct the surgeon towards tissue that is likely to be cancerous.
The purpose of the proposed PhD program is to gain a fuller understanding of the interaction between the incident light and the tumour. Optimal treatment regimes have not been established. We would like to be able to model both PDT and PD. To assist in this, we propose to develop theoretical radiation transfer models using Monte Carlo techniques in order to simulate the incident light and the fluorescent emission. This will be done for the range of tissue types where PDT is performed in Dundee. This includes skin (the most accessible), the oral cavity, the brain and bladder.
The work will also find application in a wide range of other areas in the drive towards minimally invasive and highly targeted therapies. In addition to the PDT described above, the techniques can be applied to so-called ‘caged compounds’ that are a range of biologically active compounds that are activated with light. In order to apply such compounds within a therapeutic environment, understanding the light tissue interactions is of key importance.
Light distribution measurements will be made around a range of light delivery devices, including cylindrical diffusers and miniature balloons filled with light-scattering media. Further measurements will be carried out using optical fibres embedded in tissue samples and using ultrashort pulses to probe two-photon activation at depth within the body. Fluorescent emission spectra will also be measured using a specially constructed optical biopsy system.

This project provides many opportunities for the student to study PDT and other light activated therapies from theoretical, experimental, and clinical perspectives.
There will be joint supervision from Dr Harry Moseley, who is Technical & Scientific Director of the Scottish PDT Centre and Honorary Reader at the University of Dundee, and Drs Tom Brown and Kenny Wood, who are Lecturers in the Department of Physics and Astronomy at the University of St Andrews. Dr Wood will supervise the theoretical aspects of the PhD (Monte Carlo radiation transfer), Dr Brown the experimental light tissue studies and Dr Moseley will supervise the clinical applications at Ninewells Hospital.

EPR for Structural Biology
Lovett, Dr Janet -

Electron paramagnetic resonance (EPR) spectroscopy is a valuable tool for structural biology. It can detect the environment of radicals and can be used to measure nanometre scale distances between pairs of radicals.

This PhD program will principally use the pulsed EPR method of DEER to measure distances between spin labels - radicals that have been placed site selectively on proteins and nucleic acids.

A range of systems are available to study including the Sec transporter from E coli in collaboration with Prof Ian Collinson in Bristol.

This PhD is likely to involve both applying the technique and developing it through finding new ways to spin label proteins and nucleic acids.

St Andrews Physics has excellent EPR facilities. The necessary sample preparation will be carried out in the Biology with a fully equipped laboratory.

Harnessing Quantum Mechanics to Create Improved Solar Cells
Lovett, Dr Brendon -

The operation of a modern design of a solar cell consists of three stages: light absorption, movement of electronic excitation, and charge separation. We recently showed that the rate of the first of these, light absorption, can be markedly improved in a symmetric ring of molecules by exploiting quantum interference [1]. In this project you will consider both light absorption and exciton transport, and probe the extent to which quantum mechanical models can be used to improve the operation of solar cells. You will go beyond idealised designs to look at realistic quantum systems. You will focus on systems that are available for immediate testing in the laboratories of collaborators - for example, semiconductor quantum dots or organic molecules.

You will work to understand how these systems interact with their environments, and model the combination as open quantum systems. This will be done using a variety of simple and more sophisticated techniques, as it becomes clear which approximations can be made. The final aim of the project will be to propose an experiment in which a clear signature of enhanced light absorption could be seen.

[1] Superabsorption of light via quantum engineering, K. D. B. Higgins, S. C. Benjamin, T. M. Stace, G. J. Milburn, B. W. Lovett and E. M. Gauger, Nature Communications 5 4705 (2014)

Hawking radiation in the laboratory
Koenig, Dr Frieder -

Black holes can be understood in a simple picture: Imagine a river flowing towards a waterfall with ever increasing flow speed. Also imagine fishes in the river swimming upstream. At some position in the river the maximum speed of the fish will equal the flow speed and all fish beyond that "point of no return" will be flushed into the waterfall. Here the flow speed corresponds to the gravity of a black hole and the point of no return to the event horizon.
Arguably the most facinating aspects of astronomical black holes is the emission of Hawking radiation from the event horizon, an intriguing quantum effect combining gravity, thermodynamics and quantum mechanics.

Unfortunately, the astrophysical Hawking radiation is far too weak to ever being detected directly. Recently, however, we have invented a method to create moving artificial event horizons with short pulses in optical fibers. Moreover, the expected Hawking radiation is strong enough to be detectable with single photon coincindence counting.

The idea of the PhD programme is the calculation, detection, and characterization of this elusive Hawking radiation for the first time. The work has already gained momentum in our group and a setup is built using optical pulses of just a few cycles pulse length. In addition we will explore further quantum field theory effects in curved spacetime.
In-Cell Structural Biology using EPR spectroscopy
Lovett, Dr Janet -

Structure underlies function in biology, and determining the structure of proteins gives us a window onto the mechanisms of life, and the cause of disease. In this project you will use electron paramagnetic resonance (EPR) spectroscopy to determine how life’s building blocks -- proteins -- fit together.

EPR allows us to measure the energies of electron spins, and so determine the interactions they have with each other. The interactions change with the distance between spins, and so we can use EPR to infer spin separation. By attaching spins to proteins at particular positions we can then establish how proteins interact with one another. EPR is best suited to measuring nanometre distances, and so is a tool that is complementary to the more familiar methods of X-ray crystallography, electron microscopy and NMR. To-date most structural studies with EPR have been carried out outside the cell. There is however great scope to use EPR for measurements inside cells and thus obtain structural information in a truly native environment. The motivation for studying the structure of biomolecules such as proteins is to learn how nature performs so exquisitely and what happens when there is a problem, with the aim of improving aspects of human health through better understanding of these processes.

This PhD offers the chance to develop EPR for native environment structural studies of biomolecules, and to answer real biological problems.

You must have a good scientific degree (2:1 or above for Honours or a relevant MSci) for example in a such as chemistry, biochemistry, biology or physics. No prior knowledge of EPR or protein preparation is necessary but you must be motivated to learn and work across scientific disciplines.

The PhD will be run through the School of Physics and Astronomy at the University of St Andrews and you will also be a member of the Biological Sciences Research Complex. The teaching and research environment in the University of St Andrews is excellent.
Integrated Magnetic Resonance Doctoral Training Centre
Smith, Dr Graham -

The new EPSRC Doctoral Training Centre in Integrated Magnetic Resonance is a collaboration between 6 of the UK's leading Universities in Advanced Magnetic Resonance Instrumentation and Techniques and includes St. Andrews, Dundee, Aberdeen, Warwick, Nottingham and Southampton.

The aim is to provide a coherent training program for doctoral students whilst working on new research topics in instrumentation and methodology, associated with Magnetic Resonance Imaging, Electron Magnetic Resonance, Nuclear Magnetic Resonance and Dynamic Nuclear Polarisation (which collectively represent £multi-Billion annual markets). Training is delivered from all centres, through residential workshops and over the Access Grid, primarily in the first two years of study.

Funded 4 year PhDs include fees and maintenance of £14000 (tax free) per annum as well as an enhanced travel budget. All PhDs will have internal and external mentors from other centres.

At St Andrews, PhD projects are available on themes associated with major advances in Electron Magnetic Resonance and Dynamic Nuclear Polarisation and are likely to involve collaborations with other centres and other interdisciplinary groups.

PhD topics are likely to involve a combination of instrumental, methodological and computational techniques that would normally be associated with Basic Technology programs.

Representative PhDs from all 6 centres are listed on, but other PhD topics may be available on request.

For PhDs at St Andrews, applications can be made directly to St Andrews or via Warwick where the DTC program is administered.

Light harvesting networks
Lovett, Dr Brendon -

Recent ultrafast optical experiments on photosynthetic complexes reveal the possible presence of quantum coherence between excitations on different parts of the protein complexes involved. It has been conjectured that these quantum correlations may lead to enhanced energy transfer, and thus to more efficient solar cells.

In this project, you will explore the interplay of quantum and classical mechanisms for moving electronic energy around networks of molecules. On the one hand, quantum correlations can lead to constructive interference between different parts of the network, leading to a faster transport of energy. On the other hand, such correlations may lead to destructive interference, and cause excitations to get stuck. Classical hopping may relieve this problem. You will predict the optimal balance of classical and quantum processes that lead to the highest rate of energy extraction from the network. You may need to explore the role of length scale, network topology, and use thermodynamic concepts to address this problem.

The project will be in collaboration with theorists at the University of Oxford, and may be tested in the laboratories of collaborators both in St Andrews, and at the Universities of Oxford and Cambridge.
Linear and nonlinear properties of 3D optical Metamaterials.
Di Falco, Dr Andrea -

Metamaterials (MMs) are man made materials with engineered optical properties. They are made assembling their artificial atoms at a scales much smaller than that of light, so as to appear homogenous. They are at the basis of very thought provoking proposals, including super imaging and cloaking applications.
In the group of Synthetic Optics we have developed a large portfolio of fabrication techniques for one- and two-dimensional MMs.

The aim of this project is to develop the fabrication protocol and applications of three-dimensional MMs obtained with a bottom up approach. The student will combine the extraordinary physical and optical properties of silica based aerogels with the flexibility of the design of nanoplasmonics to realise effective materials with bespoke optical behaviour. The aerogel is an ultra light material with refractive index close to unity and thermally more insulating than air. Combining these features with the field enhancement offered by infiltrated metallic nano particles is specially suited to address nonlinear effects at ultra-low powers.

This challenging but rewarding project requires a thorough understanding of the physics involved and the experimental rigour to fabricate and test the MMs, but offers the student the chance to learn a broad range of design, fabrication and experimental techniques.

Living Lasers: Lasing from biological cells
Gather, Prof Malte -

Optical phenomena in biological structures have fascinated mankind for centuries and biological materials with optical functionality are currently a major topic of research. In the future, photonic devices may indeed be based on natural or genetically engineered optical function.

Recently, we developed a biological laser – a device based on a single living cell genetically programmed to produce the fluorescent protein GFP. The laser is biocompatible and biodegradable, and thus offers unique physical and biological properties not shared by any existing device.

However, so far our biolasers require an artificial resonator and an external pump source. This project is aimed at gaining a better understanding of lasing and stimulated emission in biological materials and at developing new avenues to biolasers. For example, this can include the study of bio-assembled resonators based on naturally occurring structures, photophysical investigations aimed explaining why fluorescent proteins are such efficient laser materials, or the development of biocompatible nanolasers.

The project is inter-disciplinary, involving photonics, laser physics, genetic engineering, proteomics, and material science and adequate training in these fields will be provided within the school and through external collaborators.

Further reading
MM-wave Radar, Components and Techniques
Smith, Dr Graham -

MM-waves represent the area of the electromagnetic spectrum that sits between microwaves and Terahertz frequencies. It is the part of the spectrum where electronics meets optics and a wide variety of physical techniques are used to design components and systems. MM-waves are used in high resolution radar, fusion diagnostics, earth resource studies, magnetic resonance and security systems.

The mm-wave group at St Andrews is one of the largest and most well established groups in this field in the UK, and has a strong track record in designing components, sub-systems and full system. Much recent work ahas concentrated on developing radar imaging systems for earth resource studies (imaging volcanos, monitoring rainfall) and for various security related systems.
There is also a very strong program in mm-wave magnetic resonance.

A variety of PhD topics are always available and any interested student should get in touch with Dr Graham Smith in the first instance.
New photonics tools unravel the mysteries and mechanics of biological cells
Gather, Prof Malte -

Biologists have compelling evidence that in addition to biochemical signals, mechanical forces have a major impact on a wide range of processes in cell biology, with examples ranging from cell migration and cell growth to the spreading of cancer and the differentiation of stem cells. However, there is at present a shortage of suitable tools to measure the force exerted by a cell which often is well below 1nN (i.e., < 10-6 N (!)).

By developing a novel optical micro-cavity-based sensor technology, the Gather Lab seeks to overcome current limitations in measuring cellular forces and – for instance – investigate the mechanics involved in the formation and the growth and repair of nerve cells.

The basic working principle of our sensors is to detect shifts in the resonance frequency of a micro-cavity due to mechanical forces applied by cells cultured on the sensor. These shifts can be detected with high spatial and temporal resolution and the forces at play are then computed from this by a finite element method.

A PhD in the field of cellular mechanics provides you with a broad, interdisciplinary skill set: You will learn and apply a range of micro- and nano-fabrication methods and work in a state-of-the-art cleanroom. You will use different types of optical spectroscopy and work with atomic force microcopy. You will receive hands-on training in cell culturing techniques and perform studies of e.g. stem cell differentiation.

The project is part of an international collaboration with leading scientists at Harvard Medical School and University of Cambridge which is funded by the Human Frontier Science Program, the leading funding institution for interdisciplinary and international collaborative research into complex biological systems.

Nonlinear Optical Micromanipulation
Dholakia, Prof Kishan -

New uses of trapped colloid as nonlinear media and uses for observations of soliton-like waves and new forms of in-situ imaging as well as nonlinear processes (eg 4 wave mixing). This is a very exciting project based on novel ordering of colloidal particles in the presence of light fields as well as the use of these colloids as new media for nonlinear effects.
OLED micro-displays as biophotonic platform
Gather, Prof Malte -

Organic Light Emitting Diodes (OLEDs) are novel optoelectronic devices with potential applications ranging from displays (e. g. in smart phones or for flexible screens) to general illumination. In contrast to conventional LEDs, OLEDs are based on plastic-like organic materials. Thus, they can be mechanically flexible and are believed to offer improved biocompatibility.

In this project, micro-displays based on >200,000 individual OLEDs, each smaller than a single biological cell, are used as a platform for advanced studies in cell biology. Potential applications include lens-free, low-cost, continuous microscopy of cells and structured illumination for optogenetic studies. Optogenetics is a technique which allows controlling the biological activity of genetically modified cells by exposure to light. Over the past decade, the technique has greatly improved the understanding of various fundamental processes in biology, in particular in neuroscience. OLED micro-displays may enable optogenetic experiments, like stimulating growth or movement of neurons, with improved temporal and spatial control, higher degree of parallelization and over longer times than currently possible.

This project is highly interdisciplinary involving photonics and materials science but also cell biology and genetics. Training will be provided in all these aspects from within my group and through collaboration with the School of Biology and external collaborators at University of Cambridge and Harvard Medical School.

Further reading:
optical antennas for visible light communications (Li-Fi)
Samuel, Prof Ifor -
Turnbull, Prof Graham -

Visible light communications is an emerging field that aims to deliver high-bandwidth wireless data through solid-state (LED) lighting. This project will be part of a multi-disciplinary research collaboration between the Universities of St Andrews, Strathclyde, Edinburgh, Oxford and Cambridge which will develop the next generation VLC technology.

The aim of this project will be to develop nanophotonic hybrid light sources and detectors based on luminescent polymer films. The student will design novel optical antennas, and fabricate these using thin film depostion and nanoimprint lithography. Working with the partner universities, these components will be combined with gallium nitride LEDs and CMOS detectors to develop next generation tranceiver technologies for visible light communications.
Optical Imaging of Biological Specimens
Brown, Prof Tom -

ptical imaging can provide detailed information about a range of biological specimens from whole animals to small tissue samples. A drawback however is that such imaging often only provides data from structures at or near the surface. By contrast Optical Coherence Tomography (OCT), a low coherence interference imaging technique, can provide detailed information on tissue structure at depths of a few mm with resolution of around 10 um in living animals.

In this project we will apply OCT to a range of biological specimens to provide information which has proved to be unobtainable using other techniques. In particular the project will use OCT to provide information on tissue regeneration in amphioxus (fish-like marine chordates with close affinity to vertebrates) which are used as a model for testing concepts in nerve cord growth and repair. We will also apply OCT to Antarctic Krill (Euphasia superba), perhaps the key species in the Antarctic food web. The information these studies provide will be used to develop advanced models for acoustic imaging Krill and may also support studies on the effects of global climate change on this key species. We may also apply the system to recently launched studies of surface vasculature in Southern Elephant Seals to support ongoing studies into the diving physiology of this species.

The projects described are interdisciplinary and will require an open mind and a willingness to work with partners within Biology and Marine Science in the UK and at the Australian Antarctic Division. Australia. In order to fully develop our systems and to enable in vivo testing some travel and extended stays may be required to partner institutions.

The main supervisor for the project will be Professor Tom Brown in the School of Physics, with co-supervision by Dr Ildiko Somorjai within the School of Biology.

Prospective students should have a good background in Physics with an interest in applying their work in other fields. We are also interested in applications from students in Biology who have a strong background in imaging techniques.

Examples of the application of OCT to Krill can be found at:

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
Optical manipulation: air/vacuum trapping for cavity optomechanics
Dholakia, Prof Kishan -

Optical trapping leads to the confinement of microscopic and nanoscopic objects using light. In the domain of optomechanics we would like to cool small "trapped" mechanical oscillators down to the quantum regime. This project aims to experimentally explore new ways to levitate and trap microparticles in air and vacuum. The ultimate aim is to slow down or 'cool' spheres to the ground state of motion. The topic is currently one of the most exciting and rapidly growing areas of physics and will involve both theory and experiment.
Organic light-emitting diodes
Samuel, Prof Ifor -

Visible light emission can be stimulated by applying a voltage to a thin layer of an organic semiconductor. The light emitted provides a window on the physics of the material, enabling us to learn about the nature of the excited states in the material. It is also useful for information display, lighting, and even for the treatment of skin cancer. We have developed a new class of light-emitting organic semiconductor, which could be used for high efficiency lighting, thereby reducing energy consumption.
Organic Solar Cells
Samuel, Prof Ifor -

The energy crisis is probably the most important problem facing the world today. Sunlight is the most abundant renewable energy source, but at present the cost of photovoltaics is too high for solar cells to be a serious alternative to fossil fuels. Organic semiconductors offer the prospect of low cost solar cells, but their efficiency needs improvement. We are working on new measurements to understand organic solar cell operation, and new materials to improve it.
Redefining optical resolution limit
Mazilu, Dr Michael -

Classically, Abbe’s relation on diffraction gives the optical resolution limit. This means that every imaging device, such as a microscope, will not be able to resolve features smaller then this limit. Physically, this limit is defined by the area of the diffraction pattern (Airy disk) of a circular aperture illuminated by a plane wave. Recently, multiple methods have been proposed to focus light and image with resolutions beyond this limit. This project will look at redefining the 140 years old optical resolution limit theorem to include recent new developments such as those based on non-linearity, structured illumination, propagation of the optical degrees of freedom and compressive sensing. The project is theoretical in nature where the beams are numerically modelled to determining their resolving powers in the different configurations. The project can also have an experimental component where the novel theoretical understanding is checked in the lab. Ultimately, the questions we want to answer are: What is the optical resolution limit of a given optical setup? How is this limit extended when including non-linear effects? What is the role of structured illumination and structured detection in defining this limit? How can compressive sensing be used to overcome this limit?
Single Molecule Spectroscopy of Semiconducting Polymers
Penedo-Esteiro, Dr Carlos -
Samuel, Prof Ifor -

This project combines two rapidly advancing fields of physics. One is the field of “plastic” semiconductors which are of interest for light-emitting diodes, solar cells and lasers. The other is single molecule spectroscopy in which light emission from a single molecule is studied. The aim of the project is to perform single-molecule measurements on semiconducting polymers in order to gain new insight into the light-emission process, and how it relates to the structure of the material. Single-molecule spectroscopy is particularly powerful for doing this because it enables the differences between individual molecules to be observed, whereas most measurements just average over many molecules. The project aims to observe and manipulate the structure and light-emission of individual polymer molecules in real time. This is in turn will lead to new understanding of how their properties relate to their structure that could lead to improved optoelectronic devices.

Single-molecule TIRF and FCS spectroscopy of protein-lipid interactions involved in Alzheimer's disease
Penedo-Esteiro, Dr Carlos -
Samuel, Prof Ifor -

The ability of proteins, nucleic acids and lipid molecules to assembly in a variety of structures underpins of life processes. However, under cellular stress, some of these biomolecules organize into structures not only unable to perform their biological function but in fact into toxic species with severe consequences in human health. In this context, the aggregation of the amyloid peptide is a hallmark of Alzheimer’s disease and has become a model system for the study of toxic aggregation pathways [1,2].
In this project, we aim to develop and apply specifically tailored wide-field total internal reflection (TIR)[3] and fluorescence correlation single-molecule fluorescence imaging methods (FCS)[4] to investigate amyloid structure and dynamics in the presence of artificial lipid vesicles and supported lipid bilayers as models of the cellular membrane. The combination of both single-molecule approaches is particularly powerful as enables to interrogate the aggregation mechanism with temporal resolutions from microseconds to seconds in freely diffusing samples (Fluorescence Correlation Spectroscopy) and from milliseconds to minutes and even hours using surface-immobilized techniques (wide-field TIR). In collaboration with Prof. Ifor Samuel, also in the School of Physics, we will investigate the interaction of fluorescently labelled amyloid aggregates and other neurologically relevant proteins with lipid membranes at single-molecule level using protocols already developed in our team.

1. Eisenberg D, Jucker M (2012) The amyloid state of proteins in human disease. Cell, 148: 1188-1203.
2. Miller Y, Ma B, Nussinov R (2010) Polymorphism in Alzheimer amyloid organization reflects conformational selection in a rugged energy landscape. Chem. Rev. 110: 4820-4838.
3. Roy, R. et al (2008) A practical guide to single molecule FRET. Nature Methods 5(6): 506
4. Haustein, E., Schwille, P. (2007) Fluorescence correlation spectroscopy: novel variations of a established technique. Ann. Rev. Biophys. Biomol. Struct. 36: 151
The Development of Ultrafast Laser Systems
Brown, Prof Tom -

Ultrafast laser systems generate short pulses of light which may last on a few femtoseconds (fs.) These lasers are used in a wide range of applications from highly sensitive metrology to the 3D imaging of biological specimens.

In this project, we will continue our develops of ultrafast laser systems based on novel-glass gain media supplied by our partners within the UK. The student will be responsible for the design and operation of new laser systems. We will also use these systems to test advanced new components including saturable absorbers based on e.g. graphene and MoS2 and testing new approaches for dispersion compensation. As the project progresses we will also investigate the development of integrated ultrafast sources combining with other staff in the School of Physics and Astronomy and further afield. The lasers developed will be used in a range of new applications including the development of new techniques in dentistry where we will replace worn out enamel using laser sintered materials.

Students undertaking this project should have an interest in lasers and photonics systems. Experience of work within an advanced photonics laboratory would be advantageous (though not necessary) and students should be prepared to work closely with collaborators around the work to develop the laser systems.

Examples of previous work within the group can be seen at:

A. Choudhary, A.A. Lagatsky, Z.Y. Yang, K.J. Zhou, Q. Wang, R.A. Hogg, K. Pradeesh, E.U. Rafailov, W. Sibbett and C.T.A. Brown, “A diode-pumped 1.5 mu m waveguide laser mode-locked at 6.8 GHz by a quantum dot SESAM”, Laser Physics Letters, 10, Art. No. 105803 (2013)

N.K. Metzger, C.R. Su, T.J. Edwards and C.T.A. Brown, “Algorithm based comparison between the integral method and harmonic analysis of the timing jitter of diode-based and solid-state pulsed laser sources”, Optics Communications, 341, p.7 (2015)

A.D. Anastasiou, S. Strafford, O. Posada-Estefan, C.L. Thomson, S.A. Hussain, T.J. Edwards, M. Malinowski, N. Hondow, N.K. Metzger, C.T.A. Brown, M.N. Routledge, A.P. Brown, M.S. Duggal and A. Jha, “β-pyrophosphate; a potential biomaterial for dental applications”, In Press, Materials Science & Engineering C (2017)

A.A. Lagatsky, Z. Sun, T.S. Kulmala, R.S. Sundaram, S. Milana, F. Torrisi, O.L. Antipov, Y. Lee, J.H. Ahn, C.T.A. Brown, W. Sibbett and A.C. Ferrari, “2 µm solid-state laser mode-locked by single-layer graphene”, Applied Physics Letters, 102, Art. No. 013113 (2013)
Unveiling the structure of long RNAs using EPR Spectroscopy
Lovett, Dr Janet -

Electron paramagnetic resonance (EPR) spectroscopy can measure nanometre distances with Angstrom precision. Applying this to the structural-elucidation of RNA has great potential for the progression of our understanding of fundamental processes and for the future of targeted drug discovery. However, in order to apply EPR, the RNA must have a paramagnetic probe – a spin label – attached. While this can be achieved with solid-phase synthesis methods this restricts the RNA length to less than c.a. 50 nucleotides.

This project will explore a bioconjugation method to enable the labelling of long RNAs. The successful applicant will prepare suitable nucleotides and spin labels and then test these both in solid-phase synthesis and for suitability in bioconjugation. The synthetic chemistry will be learned in the groups of Professors Edward Anderson and Tom Brown in Oxford, UK during extended visits. These methods will be employed in St Andrews for further preparations. The long RNA synthesis will be in collaboration with Dr Carlos Penedo in St Andrews. St Andrews has excellent EPR facilities for the measurements.

Appropriate background reading for this project is Haugland et al, Journal of the American Chemical Society (JACS), 2016, 138, pages 9069-9072 (DOI: 10.1021/jacs.6b05421).

You will be a member of the School of Physics and Astronomy and the Biological Sciences Research Complex at the University of St Andrews.

You must have a good scientific degree and be competent in organic synthesis methods.

St Andrews University is situated in the beautiful and bustling seaside town of St Andrews with stunning beaches, a great history and tradition and close to Edinburgh, Dundee and the wider attractions of Scotland. The School of Physics and Astronomy at St Andrews (joint with Edinburgh) was ranked 3rd in the UK in the latest Research Excellence Framework (REF) exercise.