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Vacancies at the University of Southampton


Project Title:
EngSci-BIO-142: A fusion of in vivo Neutron and X-ray Computed Tomography to understand water dynamics in biological systems
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Project Supervisor(s):
Dr S Keyes , Dr G Burca
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Research Group:
Bioengineering and Human Factors
Funding Availability:
Funded PhD Project (European/UK Students Only)
Application Deadline:
30 September 2016

One of the essential functions of plant roots is the uptake of water. Due to increasing water restraints on agriculture, there is increasing motivation to truly understand plant water uptake. This requires new methods to allow the measurement of water fluxes in roots and the soils that surround them. This studentship provides the opportunity to work in a world leading group which develops sophisticated methods for non-destructive 3D imaging at the single root scale in vivo. The X-ray computed tomography (XCT) approaches usually applied are not well- suited to visualising water distributions, however, the high neutron attenuation coefficient of hydrogen makes neutron radiography and tomography (NCT) very attractive techniques for measuring water dynamics in plant soil systems. We seek a student with a good technical background in engineering, physics, computer science (or similar discipline) who wants to conduct exciting interdisciplinary research across two world-leading institutions.

This fully-funded project will develop methods to fuse X-ray and neutron computed tomography, combining the strengths of both methods to synthesise greater understanding of hydrological processes in biological systems. It provides a unique opportunity to use the new IMAT neutron imaging beamline at the UK’s national spallation neutron source, as well as the I13 X-ray micro-tomography beamline at the UK’s synchrotron light source, both less than an hour from the University of Southampton. Using these facilities, you will develop tools to elucidate the 3D structure of complex soil pore networks using XCT, then quantify the corresponding 3D water distributions of the same samples using NCT. You will carry out experiments using both i) in vivo plant root assays, and ii) hydrodynamic validation assays which use microfluidic approaches to deliver precise fluxes of water at a point source in a soil matrix.

The techniques you develop will allow: i) quantification of the dynamics of water transport and uptake from soil by roots, ii) quantification of the diffusion rates of water-rich gels (exudates) from root tips into the surrounding soil, iii) the comparison of NT measurements of water fluxes with those estimated by image-based mathematical models parameterised using 3D soil-structure data from XCT.
The nature of the project will require time to be spent embedded working at the STFC campus at Harwell (year 1 and year 3), which is <1 h from Southampton University, with good road and rail links. A vibrant community of postgraduate students exists at both the University and the Harwell campus.

If you wish to discuss any details of the project informally, please contact Dr Samuel Keyes, Bioengineering research group, Email:

Project Title:
EngSci-BIO-132: Comparative chemical mapping of plant-soil interaction
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Project Supervisor(s):
Dr T. Roose , Dr S Keyes
Research Group:
Geomechanics and Environmental Geotechnics
Funding Availability:
Funded PhD Project (European/UK Students Only)
Application Deadline:
Applications accepted all year round

All the food humans eat comes directly or indirectly from plants. It is thus of great importance to understand the fundamentals of how plants grow and interact with the environment. Human life and health hinge on the physical, chemical and biological processes taking place where plant roots make contact with soil. We are seeking a PhD student to investigate the dynamics of essential nutrient uptake by plants through the development and application of novel chemical sensing and mapping technologies. In particular, we are looking to compare in vivo and ex vivo plant/soil systems using X-ray fluorescence surface mapping (XRF), energy dispersive X-ray mapping (SEM-EDX), and soil solution analysis (using microdialysis probes and mass spectroscopy). The project will develop application of the technologies, calibrate the methods, and then integrate the resulting data into a mathematical modelling framework that will be developed alongside this work.

Southampton has world-class facilities for this work. At the National Oceanography Centre Southampton (NOCS) we have facilities for the bulk micro-beam and in situ measurement of elemental concentrations and isotopic (stable, metal, radiogenic) compositions of environment samples (including soils, rocks, fluids, gases, tissue, organic materials, and atmospheric particles). These analytical instruments are coupled with excellent sample preparation facilities. Scanning electron microscopes with energy dispersive and wavelength dispersive X-ray detection (e.g., Leo 1450VP SEM with PGT EDS detector) provide major and high concentration elemental mapping coupled with textural analysis. An EDAX Eagle III micro-X-ray fluorescence spectrometer provides high resolution (~40 µm and below) mapping of major and trace element concentrations for samples up to 15 cm across. Soil solution chemical analysis facilities include ThemoFisher Xseries2 Inductively Coupled Plasma Mass Spectrometers (ICP-MS) and ThermoFisher Element II ICP-MS for higher sensitivity analysis, and ThermoElemental XSeriesAtomic Emission ICP.

If you wish to discuss any details of the project informally, please contact Tiina Roose of Bioengineering Sciences Research Group, Email: or Sam Keyes, Email:

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