2016 CDT ISM Student Cohort

Tomas Aidukas

University of Glasgow

Hybrid Computational-Optical Techniques for Microscopy and Retinal Imaging

The student will work in the exciting and fast-moving field of computational optical imaging, combining optics and imaging science with computational techniques for recovering images. S/he will devise new opticaltechniques for recording image information in the presence of high levels of aberrations or clutter introduced by the optics or by the sample to be imaged and will develop algorithms for recovery of three-dimensional images from this information. The new techniques will then be adapted for application in microscopy (for example, fluorescence and two-photon microscopy) for life-science applications for in vitro, ex vivo and in vivo imaging. It is expected that the student will also apply computational imaging to enable enhanced imaging of the retina.
The student will work within the Imaging Concepts Group consisting of two academics, ten PhD and EngD students and six post-doctoral researchers conducting fundamental research into the development of a range of advanced imaging techniques and their application in biological, medical, consumer imaging, remote sensingand surveillance fields. The group conducts collaborative research with industry and academic researchers across, Glasgow, the UK and Internationally within newly refurbished researcher laboratories benefitting from over £1M of recent investment in equipment.
The position will suit somebody with a good first degree in a Physics, a related physical science or Engineering who enjoys combining with theory, experimental computational techniques. An enthusiasm for innovation and speculative thinking is particularly encouraged.

Lavrentis Galanopoulos

Lavrentis Galanopoulos

University of Edinburgh

Development of a Mass Spectrometry Platform for the Measurement of Protein Electrochemical Potentials in Biological System

In this multidisciplinary project the student will work with analytical chemists, biologists, and engineers to develop a new platform for the multiplexed measurement of protein thiol modifications. Oxidation/reduction of thiol residues in proteins is emerging as an important and widespread biological regulation mechanism.  The technology, which is based on isotope labelling and molecular mass measurement using state-of-the-art high resolution mass spectrometry, will be applied to the study of important biological pathways in collaboration with colleagues from the College of Medicine and the School of Biological Sciences.

Laura Boyd

University of Glasgow

Neutron Time of Flight Counters with ns Resolution

The detection of neutrons over a wide energy range with high energy and timing resolution remains a big challenge in the development of radiation sensors. Possible applications of a successful neutron detection system range from instrumentation of the target stations of neutron sources like the European Spallation Source (ESS) to instrumentation for nuclear decommissioning and waste characterisation to nuclear threat detection. The global shortage of He-3, the previous standard detection material paired with an increasingly wider range of applications only amplifies the problem.
The project will investigate a wide range of candidate materials paired with novel photon detection devices to evaluate and optimise their applicability for neutron detection over a large range of energies. Some studies will be performed in close collaboration with Lund University and ESS. The studies will include materials testing, detector simulation, construction and evaluation.

Sergio Bermudez

University of Edinburgh

Photonic Crystal Fibres for Chemical Sensing and Photochemistry

The aim of this project is to exploit the unique optofluidic properties of photonic crystal fibre for applications in chemical sensing and photochemistry. A primary objective will be the development of a PCF-based system for evaluating the performance of photo-activated drugs in response to two-photon excitation, in the context of photodynamic cancer therapy.

Photonic crystal fibre (PCF) is a novel optofluidic system in which light and chemical samples can strongly interact, over extended path-lengths, for quantitative, ultrasensitive spectroscopic analysis or photo-activation. In PCF, light is trapped in the hollow core of the optical fibre by the surrounding 2D periodic ‘photonic crystal’ cladding. This permits the infiltration of a sample of gas or liquid into the hollow core, while maintaining the high optical transmission efficiency of the fibre. This project will build on our pioneering studies on intra-fibre excitation of solution-phase samples, which have started to reveal the potential of PCF for chemical sensing and photochemical applications. A PCF-based optofluidic platform will be developed to measure the performance of newly developed, two-photon-activated anticancer agents by ultrasensitive luminescence detection of singlet oxygen production. This will exploit our recent discovery that two-photon excitation can be sustained over exceptional path-lengths in PCF.

Cameron Gilroy

University of Glasgow

Using Chiral Metamaterials for Biosensing

The project will develop a new detection methodology of the levels of the antibody IgG in blood serum samples taken from transplant patients.  The ultimate aim of the project is to determine the efficacy of our injection moulded plasmonic substrates as a diagnostic tool for flagging potential organ rejection; high IgG levels is a symptom of organ rejection.  The projects builds on work performed as part of a joint EPSRC / NSF grant (“Chiral plasmonic biosensors” Kadodwala and Cooke (end date 01/03/17)) and is a collaboration with Prof. Vince Rotello of UMASS Amherst and U.S. based M.Ds.  We have established that our sensors can detect physiologically relevant changes of IgG in spiked blood serum models, this studentship will take the project to the next stage; trials with real patients.

Giulia Deiana

University of Edinburgh

Biosensor system for the monitoring of chronic lymphocytic thyroiditis

Point-of-care testing is defined as “testing that is performed near or at the location of a patient with the result leading to a possible change in the care of the patient”. With the aim of shifting the diagnostic and monitoring process from standard laboratory methods to the hands of patients and healthcare practioners, point-of-care testing is a fast growing field with an increasing number of applications. In the past decades, the technology necessary for the development of point-of-care sensors was not mature enough to attain miniaturisation and low production costs without significant compromises in sensitivity and accuracy. The newest advances in microelectronics and microfluidics are gradually addressing this issue, paving the way for the development of novel miniaturised medical devices with effective and clinically significant testing ranges.

A classic example of the impact of such technologies on disease management are glucose sensors, which are still heavily researched and constitute the core of the point-of-care diagnostic industry. These devices have revolutionised the life of diabetic patients, who are now able to better monitor their condition and establish a more effective treatment plan. This successful self-monitoring approach can be applied to a wide range of other chronic conditions.

Initial research activity will focus on specifying possible biological recognition elements for the key biomarkers involved and identifying the transduction method to be used to build a robust biosensor with the required limit of detection.  For some of the biomarkers this is likely to be in the nano or pico-molar concentration level in whole blood which represents a significant challenge.  The current state of the art involves some form of immunoassay and so similar transduction methods (generally optical or electrochemical) to state of the art immunosensors will be identified.  Development of biosensing molecules (antibodies, peptides etc.) are likely to require collaboration with researchers in synthetic chemistry or biology. Sample preparation and sensor costs will also be important considerations and the project will make use of resources for microfluidic fabrication and rapid prototyping available at the University of Edinburgh

Jose Cortes Guzman

University of Glasgow

The Multicorder: CMOS Sensor Technology for the Metabolome

Microelectronics technology has led to a revolution in computer and communication technology that began almost immediately that the transistor was invented. The exponential rate of technological advancement that is described in Moore’s Law has been propelled by $1Tr of investment over 50 years. However, CMOS technology, which now dominates the microelectronics industry, has proven itself to be immensely versatile. For example, the digital camera chip that uses silicon photodiodes (PD) is now ubiquitous. More recently CMOS has been exploited to make the large arrays of ion sensitive field effect transistors (ISFET) used in the Ion Torrent and Ion Proton Next Generation sequencing systems. Exciting new opportunities now lie in pursuing non-roadmap “More than Moore” technology to discover and exploit the as yet unfulfilled potential of CMOS in markets and applications that have historically lain outside the realm of microelectronics. The Multi-Corder chip must have very broad sensor modalities, from fundamental metabolite detection andquantification, through ligand-binding-based detection thence on to whole organism detection. The sensors we propose to deliver this range of functionality are not purely CMOS, but require both small and large surface features, on the scale of MEMS technology, to interact effectively with the different measurands. Achieving the objective of multi-modality on a single chip will be a major technological challenge in both engineering and biology. Using CMOS we will design and fabricate a range of detectors that must be functionalised in order to create sensors. We will do this by lithographically surface patterning the CMOS chip surface that we will have prepared with suitable immobilisation chemistries. We will select chemical moieties and use these to prepare new materials, as well as investigating commercially available products.

Markus Ronde

University of Edinburgh

Developing Release Technologies for Improved Performance of Free-Standing Sensors

Microfabricated free standing structures are used in a wide range of sensor applications. Cantilever, bridge and membrane structures are widely used in accelerometers, gyroscopes, pressure sensors, gas detection, biochemical analysis, healthcare monitoring, microphones, and many other sensing devices.  The release of these structures through the controlled etching of underlying sacrificial layers is often a critical process that can have a significant effect on the performance of the sensor.  Vapour etching has replaced wet etching as the primary release process for these layers. However, even using vapour etching, care must be taken to selectively etch only the sacrificial material without undercutting anchor regions or over-etching structural layers, the thickness of which can strongly influence sensor device performance.  In order to improve the reliability and reproducibility of sensors and ensure their performance, this project will look to gain an understanding of the mechanisms associated with vapour etching, in particular those that effect the etch selectivity of one material against another.  In collaboration with Memsstar, this project will:

Investigate etch parameters and their effect on selectivity, including the control of elements such as temperature currently not managed by the commercial toolset; Investigate etch chemistries to determine if additives to the etch gas can help in the control of selectivity;
Statistical modelling, process simulation and design of experiments to determine optimized processing, including design of the tool chamber; Design and manufacture of a range of test structure devices that will enable analysis of the selectivity as well important processing criteria including uniformity, and rate of vapour etching.

These investigations will be applied to the two primary vapour etches of interest to Memsstar, i.e. XeF2 and HF vapours, and will consider a number of material layers of interest in the development of sensor systems.  A demonstrator in the form of a membrane based microphone structure would be used in parallel with moving beam stress sensors to determine the extent to which the research is able to optimise etching.  It is possible this could in turn lead to the development of etch stop or etch extent sensors that could be fitted to vapour etch tools.

Ryan Hawley

University of Glasgow

STED Inspired Sensors for Tomographic Imaging of Darkness

This project will develop a 3D sensor for structures of darkness. You will build a prototype tomography system based on scattering of near-resonant light from an atomic rubidium vapour and 3D fluorescence detection. The mechanism relies on the competition between a strong structured light beam which comprises braided or knotted vortex lines, and a weak probe laser with a flat amplitude and phase profile. In analogy with STED microscopy, we expect to achieve high resolution 3D imaging of the complete vortex topology. The project aims to demonstrate 3D spatial filtering for super-resolution sensing of biological samples.

Yuchen Shang

University of Edinburgh

Developing an Integrated Sensing Capability for Use in Astrobiology

Astrobiology is an interdisciplinary science that seeks to understand the limits of life and the potential for life elsewhere. At the University of Edinburgh there is a particular interest in life in extreme environments, how life adapts to single and multiple extremes, how life adapts to conditions in the planetary crust and the habitability of other planetary bodies.

This project is intended to initiate a highly interdisciplinary collaboration between the School of Engineering (Institute for Micro and Nano Systems) and the School of Physics & Astronomy (Institute for Condensed Matter and Complex Systems) that may additionally involve aspects of chemistry and biochemistry. The purpose of the project is to develop and characterize a sensing capability to detect the elements capable of supporting life in extreme environments both on earth and beyond.  There is possible scope for the initial project as described here to encompass two linked strands or possibly even become two separate PhD projects – one emphasizing the front end sensing modality and the other emphasizing the application-specific sensor technology and integration.

We expect this topic area to grow leading to follow-on research with the long-term aim of deploying sensors in extreme environments on earth and eventually in space.

Julia McFarlane

University of Glasgow

Quantitative Optical Imaging in the Eye

The Imaging Concepts Group pioneers new techniques for quantitative imaging within the eye including multispectral imaging of retinal and scleral blood oxygenation, computational scanning laser ophthalmoscopy, optical coherence tomography and imaging of retinopathy of prematurity. In this project the student will develop and apply new techniques for quantitative retinal imaging including using structured light and snapshot spectral imaging to quantify retinal chromophors, metabolism and to characterise systemic vasculature. That is, imaging of the retina will be used as a window on systemic health. The student will use and apply the principles of optics, imaging and mathematics at a deep level and will develop a working understanding of the relevant biology through specialist courses and through collaboration with clinicians and biologists. The student will work within the Imaging Concepts Group consisting of two academics, ten PhD and EngD students and six post-doctoral researchers conducting fundamental research into the development of a range of advanced imaging techniques and their application in biological, medical, consumer imaging, remote sensing and surveillance fields. The group conducts collaborative research with industry and academic researchers across, Glasgow, the UK and Internationally within newly refurbished researcher laboratories benefitting from over £1M of recent investment in equipment.

Anastasios Vilouras

University of Glasgow

Ultra-thin Bendable Sensing Systems for Biomedical Applications

Less than twenty years ago photolithography and medicine were total strangers to one another. Nowadays, these two strangers are indispensable partners in biomedicine. Examples range from ultrathin, conformable health-monitoring tapes that seamlessly mount on the skin, ‘‘electronic skin’’, to advanced imaging devices that use hemispherical detector layouts, ‘‘electronic eyeball cameras’’, to electronic microsystems that can be ingested, “lab-on-pill”. Electronics of the future will be soft and rubbery to enable new modes of use. Devices based on this new technology will be stretchable, twistable, and deformable into curvilinear shapes, thereby enabling applications that would be impossible to achieve by using the hard, rigid electronics of today. In these and other systems, mechanical design will be as important as circuit design. I would like to be an active member in the development of these devices with the goal of helping develop several applications in medicine, and in other scientific fields, despite the complexity and all difficulties of transferring a new technology into new products. As important as the goals is the evaluation of their fulfilment. The adequacy of these sensing microsystems can be evaluated from the throughput, from the sensitivity, and from the multi-functional versatility of sensors and actuators, having as norm a low cost and easily mass-produced design, which leaves room for optimization using new materials and innovative fabrication processes. Having multidisciplinary collaborations with partners on this project, both in academia and in industry, might prove beneficial, as there might be a chance of recruiting academics, as well as professional engineers as subjects which will lead to results that better predict real-world impact.