University of St Andrews

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  • Funder: UKRI Project Code: 1795537
    Partners: University of St Andrews

    In this postgraduate project optically stable, small resonators for the investigation of biological processes in living cells will be developed. In the beginning of this project, there will be an introduction to cell biology and training on cell culture techniques, so that the student can broaden her knowledge on biology and familiarize herself with biological concepts. Apart from this, great emphasis will be given to the development of experimental physics skills. Initially the student will work on two research projects developed in the group, with the aim to use the basics of these projects to combine them into a novel optical technique, during her postgraduate studies. Optical resonators are essential for the generation of laser light and the laser spectra change significantly when small changes happen in the medium with which the laser light interacts. By implementing micro-lasers into living cells, we can study in detail the different processes that cells undergo. Small changes in the cell or different types of cells, emit a different and unique laser light, which provides information about the cell and provides an opportunity for cell tracking. Another aspect that will be studied during this PhD project is the mechanism that the cells exert force, in particular measuring cell forces and understand the mechanism behind them. Cell forces play a very important role for cell motility, proliferation, apoptosis as well as in certain types of cancer. The weak nature of these forces makes the measurement particularly challenging. In the very first months of this project, force measurement will be taken using a stress microscopy technique, based on an elastic resonator, which has already been developed in our group. In that way, the PhD student will get familiar with our novel optical technique and study photonics, biology and physics even further. During the postgraduate studies, and after the student has acquired all the necessary knowledge and skills from our research projects, she will attempt to create a deformable optical resonator for cell force measurements. The light emitted from the resonators will be analysed to take useful information about the cells investigated. In addition, except cells, measurements can be taken in a living organism such as in the Drosophila larvae, with the aim to understand the behaviour of cells during the transition of this organism from larvae into an adult fly. The challenges are many, from fabricating these optical resonators to introducing them into the cell assay and taking a light signal, making this PhD project quite demanding as well as interesting. Quantitative measurement and explanation of biological processes will be attempted and at the same time, the student will develop skills from various fields, given the multidisciplinary character of this project. Training will be provided by researchers in the group, in the beginning of the PhD studies. Also, the first 2 years, the student should take a few courses related to the project. These courses are provided by the Scottish Universities Physics Alliance (SUPA) and the ones chosen are: 1. Biophotonics (semester 1) 2. Problem solving skills for physicists (semester 1) 3. Ultrafast photonics (semester 2) Keywords: optical resonators, elastic resonator, living cells

  • Funder: UKRI Project Code: 2747953
    Partners: University of St Andrews

    The project will involve a collaboration between Professor David O'Hagan's laboratory and the pre-clinical imaging centres at the University hospitals in Aberdeen led by Dr Sergio Dall'Angelo and in Edinburgh led by Dr Adriana Tavares. The project will explore a fundamentally new concept in molecular recognition and apply it to cancer diagnosis and treatments. If successful it could be applied more widely to any targeted disease cell type. The project builds on the recent discovery that cyclohexane rings which have fluorines on one face of the ring, and hydrogens on the other face have extraordinarily polar properties [1]. These have been termed 'Janus face' rings. The polarised faces of the rings strongly self-associate and have no counterpart in Nature and thus they constitute a novel molecular motif that is 'orthogonal' to biochemistry. Chemistry that is orthogonal to biochemistry is of wide current interest for controlling molecular precision within cells in chemical biology. Organic bound fluorine forms only very weak hydrogen bonds, so it is anticipated that these rings will not hydrogen bond to proteins and other cellular components, and that self-association will be stronger than other interactions in the cellular environment [2]. We wish to explore this concept by preparing radiolabelled molecules of this class for positron emission tomography (PET) and cancer cell imaging. To facilitate this, collaborations are established with the pre-clinical imaging centres at Aberdeen and Edinburgh University hospitals, where they have ready access to the radio-isotope 18F-fluoride and to xenograft mouse models. The project will synthesise Janus ring tagged RGD peptides and tagged 5'-chlorodeoxyadenosine for [18F]-radiolabelling with a C-F bond forming enzyme (fluorinase) [3]. Cyclic RGD peptides bind to specific protein motifs (epitopes) that are abundant on the surface of breast cancer cells, and therefore they are used to target such cells. The chloro-adenosine construct will then be radiolabelled with [18F]-fluoride using the enzyme. With the chemistry and radiochemistry in place small animal studies will be investigated in PET imaging experiments using xenograft mice models in Edinburgh.

  • Funder: UKRI Project Code: 1947940
    Partners: University of St Andrews

    Zeolites are microporous aluminosilicates with applications in gas adsorption and catalysis, prepared hydrothermally using inorganic or organic cations to direct or template the framework crystallisation. This project aims to develop co-templating routes in which inorganic and organic cations are used together to prepare zeolites with new structures or compositions. The work will include the characterisation of a series of flexible (RHO-type) zeolites, prepared using different metal and tetraethylammonium cations that show highly selective gas adsorption. Using the principles derived from this, other zeolite syntheses will then be devised using combinations of cations and other small organics to give small pore low Si/Al zeolites valuable in gas separations, including merlinoite and phillipsite. The structures will be measured in situ during gas separations. Elliott Bruce, as the best MChem student graduating this year, is uniquely placed to perform these complex analyses. Existing in situ synchrotron X-ray powder diffraction data is available on the complex RHO family structures ZSM-25 and PST-20 with and without adsorbed carbon dioxide and initial structural studies will involve their refinement using the TOPAS program, required for such complex structures. This will enable the determination of cation locations and so help understand, in combination with computational studies, their selective adsorption behaviour for a range of industrially relevant separations. Additionally, further X-ray and neutron diffraction data will be collected on zeolite Rho itself, for mixed cation systems that have been found to be of interest for industrial separations with a collaborating industrial company. Further, co-templating routes to zeolites with high Si/Al required for stable auto-exhaust catalysts will be devised. Several promising materials have been prepared using highly expensive organic templates. Here, the aim is to use combinations of inorganic and less-expensive organic templates to make such catalysts more accessible, making use of computational modelling for template design. This is of great interest to Johnson Matthey, so the project will be conducted in collaboration with them, giving Elliott insight into industrial catalytic chemistry and access to their extensive facilities at Billingham.

  • Funder: UKRI Project Code: 2274388
    Partners: University of St Andrews

    The Greenland Ice Sheet (GrIS) will be one of the largest contributors to 21st Century sea level rise, but quantifying the expected mass loss has proven difficult due to the challenge of predicting the retreat of tidewater outlet glaciers (i.e. those glaciers that drain directly into the sea). The rate of retreat of these glaciers can vary dramatically on short timescales (e.g. Howat et al, 2008), but it remains unclear whether these changes are driven by warming of the atmosphere, ocean or both (Carr et al, 2013). Improving understanding of the controls on tidewater glacier retreat is, therefore, vital if its contribution to the mass budget of the GrIS is to be predicted by models (e.g. Nick et al., 2013). However, the remote and dynamic nature of these environments makes the collection of field data extremely challenging, limiting progress in this area. Recent research by Cowton et al. (2018) has used remote sensing as a method for studying a sample of tidewater glaciers in east Greenland. In an attempt to simplify predictions of tidewater glacier retreat, this research investigated the extent to which retreat can be explained by four basic variables: meltwater runoff, ocean temperature, and two simple parameterisations of 'ocean/atmosphere' forcing based on the combined influence of these two variables. The results demonstrate that the retreat of east Greenland's tidewater glaciers is best explained as a combined function of both oceanic and atmospheric warming. Furthermore, this research found that despite the complexity of tidewater glacier behaviour, over multi-year time scales a significant proportion of terminus position change can be explained as a simple function of this forcing (Cowton et al., 2018). While this research provides an excellent starting point for the parameterisation of complex ice-ocean-atmosphere interactions, this research is limited in its scope, due to its small sample size (ten tidewater glaciers), located in a geographically constrained region of east Greenland. Additionally, the research used datasets which were temporally limited to a period of 20 years. Therefore, the research proposed here aims to take the principles established by Cowton et al. (2018) and apply them more broadly, both in geographical and temporal extent, in order to investigate the wider applicability of the findings. For an expanded sample of glaciers (covering all regions of Greenland), time series of terminus retreat will be created by digitising glacier terminus position in a range of freely-available satellite imagery (e.g. Landsat, Sentinel-1 and 2). These time series will be analysed in conjunction with temporally longer datasets of atmospheric and oceanic conditions (e.g. Noel et al, 2016). If simple relationships between ocean-atmosphere forcing and the retreat of many different glaciers can be established, this research would contribute significantly to the field of study, allowing simple parameterisations for tidewater glacier retreat that could play an important role in predicting the response of the GrIS to future climate warming.

  • Funder: UKRI Project Code: EP/I034327/1
    Funder Contribution: 72,282 GBP
    Partners: University of St Andrews

    This proposal is focused on enabling researchers to simply and rapidly deploy, execute and monitor scientific software on elastic cloud computing infrastructures. Current interfaces to cloud resources are relatively low level and do not allow researchers to easily benefit from the elasticity that cloud infrastructures offer. Researchers have to deal with time-consuming and often error-prone tasks such as managing access credentials, selecting instance types, managing elastic IP addresses, as well as monitoring resource usage and starting, stopping and terminating instances in response; this keeps researchers from focusing directly on their scientific research.In order to address this problem and to further the uptake of cloud computing services in research we will develop an elastic wrapper for scientific applications. The elastic wrapper will provide an abstracted gateway to cloud resources and will provide a one-stop-shop interface for researchers wanting to take advantage of cloud resources for their scientific research. It will abstract the complexities of setting up, configuring and managing cloud resources for scientific research applications and provide facilities for execution and collaboration between multiple research sites working on the same problem. The system will take care of issues such as managing resource usage using the elasticity of cloud resources as well as fault tolerance to insure against resource failure. This project will provide a pilot implementation of the elastic wrapper that will be a generic solution but specifically support two exemplar scientific applications and their usage models: Groups, Algorithms, and Programming (GAP), a free, open source system for discrete computational algebra with an emphasis on computational group theory and IDL is a commercial package for statistical and numerical analysis and visualization of scientific datasets.