PhD projects

We're recruiting PhD students to work on the following projects. We encourage you to do some research on our academics to really get to know how their work and expertise fits with your interests before you apply.

If you wish to learn more about a particular academic's research, or discuss a project you have in mind, they are happy to answer specific questions by email or telephone.

Biophysics

Combining single-molecule biophysics, DNA origami construction and low temperature plasmas to develop more efficient ways to kill harmful cells

The DNA in a human cell is folded and compacted for storage by proteins and mechanisms that are incompletely understood; without these processes the DNA in one human cell would be around two metres in length. In vitro, we can fold smaller lengths of DNA into 2D or 3D DNA origami by careful design of specific binding sites. Plasma is an overall electrically neutral state of matter created by passing an electromagnetic field through a gas; it breaks bonds and forms positive, negative, and neutral species, along with gamma rays. Low temperature plasma (LTP) is currently being developed as a novel prostate cancer treatment which acts to induce necrosis in the tumour cells via DNA damage. LTP may provide considerable advantages over existing treatments for prostate cancer as plasma can be guided down a needle to allow treatment in the patient without highly invasive surgery. Key to killing harmful cells is to the ability to controllably induce DNA damage. However, existing methods to characterize the extent of DNA damage are relatively imprecise. This project will enable you to develop methods to controllably and precisely characterize the extent of DNA damage in a range of test DNA origami structures using LTPs.

Your project will allow you to:

1. Develop DNA origami structures. You will develop a range of DNA origami structures to act as biomimetic test structures for characterizing DNA damage.

2. Optimise LTP-mediated DNA damage. You will optimise and develop methods to induce controllable DNA damage in DNA origami samples, and compare these against other more traditional methods of damaging DNA.

3. Characterise DNA damage. You will develop methods of single-molecule biophysics, including super-resolution fluorescence microscopy and atomic force microscopy, to precisely characterize the efficacy and mechanism of LTP-mediated DNA damage on DNA origami structures.

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Developing next-generation technology touching life physics tools to tackle debilitating infections and cancers

Our knowledge of many debilitating human diseases is limited by technology: conventional approaches fail to render the quantitative details needed to address key mechanistic questions. This project will develop new biophysics tools for molecular observation in live cells to aid understanding of two diseases of high biomedical importance - (i) Determining roles of a key haematopoietic cytokine receptor, MPL, which interacts with ‘oncogenes’ in rare blood cancers; (ii) Investigating the assembly/disruption of a druggable unique protein structure in protozoan parasites that causes sleeping sickness in humans:

1. Develop new microfluidics for high-throughput immobilization and optical imaging of cells, facilitating rapid exchange of cell microenvironments, screening of cell types/states and other biophysics investigations including genetics profiling.

2. Design and construct optical instrumentation to enable rapid tracking of labelled proteins in cells to nanoscale precision in 3D and improve the time scale of sampling to sub-millisecond levels to probe rapid molecular conformational dynamics.

3. Develop optical tools to determine cell physiology using novel probes for ratiometric imaging and Förster resonance energy transfer (FRET) to quantify precise pH, ionic strength, membrane voltage, viscosity, and molecular crowding.

4. Develop new computational methods of machine learning/AI, principal component analysis and Hidden Markov Modelling.

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Dissecting cell complexity using super-resolution microscopy, one molecule at a time

The stress response of sporulation in bacteria is a fantastically system for studying biophysics processes of emergent complexity. This project involves high resolution bioimaging studies in living bacteria of proteins involved in sporulation.

You will study sporulation as a model system to understand how structural and functional complexity emerges in living cells. We aim to understand the: (i) structure and function of proteins involves in regulating sporulation and forming channels between the spore and the mother cell; (ii) roles of the cell wall remodelling during spore formation engulfment. You will use, and develop, pioneering imaging approaches of in the Leake group enabling you to monitor spatiotemporal dynamics, kinetics and interactions of these processes in functional, living cells in real time, one molecule at a time.

This is particularly timely since we have acquired compelling preliminary single-molecule data from several new functional B. subtilis bacterial strains with significant progress in the required molecular biology underway: it is an ideal time to capitalize on these developments by performing extensive functional imaging and analysis combined with complementary new biochemical and genetics investigations.  

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DNA-based biosensors for detecting drugs in drinking-water

  • Supervisor Dr Agnes Noy
  • Funding Self-funded students only
  • Application deadline n/a

The presence of tiny amounts of pharmaceuticals (including antibiotics, hormones, mood stabilizers and other drugs) in our drinking water supplies has raised concerns regarding the potential risks to human health and environment. Many of these molecules pass through wastewater treatment plans designed to get rid of traditional pollutants. Although there is a strong interest to detect, measure and capture them from water, the amount and type of sensors available is unsatisfactory, not solving the challenges raised by this question. DNA is currently at the forefront of nanotechnology research, as it has become one of the best materials available for creating molecule-sized devices and materials. This interest is mostly due to its innate programmability and capacity to rationally be design in any particular sequence.

In this project, we will use DNA as the basis to construct molecular biosensors for detecting important pharmaceuticals like drugs and antibiotics. In particular, we will test the capacity of DNA to bind this type of molecules with high affinity by using computational methods as a first step to examine the potential of this approach. Modelling methods which are widely used in drug design on pharmaceutical companies will be used and they will include molecular dynamics simulations and molecular docking techniques.

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Single-molecule imaging in live cell to study gene geography and the role of DNA biophysics in regulating genes

Your project will address the key question of what is the importance of the physical location of genes in determining their state of activity. We will aim to address this question by studying the effects of bacterial chromosomal gene order on spatiotemporal expression in the context of folded, native genomes. You will use single-molecule bioimaging and computational analysis to determine the output from genes are their location is changed, and how this is affect to whether or not the cell is stressed. This will give a unique insight into how the very local state of DNA topology affects whether or not genes in live cells are switched on or off. Specifically:

1. You will characterize the spatiotemporal localization of new E. coli bacterial strains which expressing genomic fusions to a key enzyme DNA gyrase which relieves DNA torsional stress. These are constructed to use a nucleoid associated protein Fis as a marker for DNA supercoiling inside each cell.

2. You will use super-resolution millisecond Slimfield microscopy which is sensitive at a level of single-molecule detection to determinate the dynamic pattern of spatial localization and stoichiometry of these gyrase subunit proteins GyrA and GyrB to nanoscale precision in single live E. coli cells.

3. You will help to construct under expert teaching several dual-colour fluorescent protein fusion constructs integrated into the E. coli genetic code to pairs of DNA gyrase subunits, and also to Fis, and to a range of different established genome loci markers.

4. You will use nanoscale co-localization microscopy, real-time FRET, and FRAP/FLIP to determine the dynamic moelcular interactions, kinetics and molecular turnover of gyrase components in live cells under a range of bengin and stressed conditions including the appliation of gyrase targetting antibiotics.

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Super resolution imaging of the eukaryotic carbon fixing organelle

One of the greatest challenges facing civilization is the sustainable production of food to feed a rapid growing global population. To meet this ever-increasing demand novel technologies and ingenious engineering approaches are necessary to enhance crop production. One exciting approach is the improvement of crop photosynthesis by introducing a mechanism from eukaryotic algae that concentrates CO2 in the proximity of Rubisco, the principal carbon-fixing enzyme. At the centre of carbon uptake in algae, is an enigmatic organelle called the pyrenoid. Using microscopy and proteomics approaches in Chlamydomonas reinhardtii, we discovered that the pyrenoid is composed of 6 spatially distinct protein regions, identified an additional 86 pyrenoid proteins and shown that the pyrenoid is highly dynamic with liquid-like properties. This data is now guiding the engineering of a pyrenoid in plants to increase crop yields, however we still have gaps in our knowledge of pyrenoid structure and function.

The project will involve using millisecond super-resolution single-molecule ‘Slimfield’ microscopy established in the Leake Lab on representative proteins to the six different pyrenoid regions. Target proteins will be tagged with the fluorescence protein a monomeric variant of yellow fluorescent protein, mYPet, which has superior photophysical and maturation properties, compatible with the above super-resolution method. You will use, and develop, this technology to: 1) Build a biophysical model the Chlamydomonas pyrenoid based on your super-resolution experimental data. Target proteins will be tagged with the fluorescence protein a monomeric variant of yellow fluorescent protein, mYPet, which has superior photophysical and maturation properties, compatible with the above super-resolution method. 2) Explore the biophysics molecular crowding of different pyrenoid regions. We will further explore liquid-like properties of the pyrneoid2 using a FRET based molecular crowding sensor to monitor pyrenoid protein crowding during liquid-liquid phase separation 3) Characterise the biophysical protein-protein interactions of core pyrenoid components. To gain a detailed insight into pyrenoid protein function we will take protein-protein interactions discovered in Mackinder et al.and explore their dynamics using FRET pairs in response to CO2 availability.

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The Calcium-mediated condensation of biomaterials: where molecular modelling meets nano-scale microscopy

Calcium is an essential ion for the condensation of biomolecules and for the formation of materials in living organisms. It is a major component of the mineral phase formed in bones and teeth as well as sea shells and hard corals, in bacterial biofilm and it even has been shown to control chromosomal DNA condensation during cell division. The capacity of Ca2+ to coordinate a large variety of atoms and molecules in biological systems is the key advantage for this function and a well-known property. Despite this enormous impact, the initial steps of calcium-molecule interaction and their impact on the nucleation of biominerals are not well understood. These processes are central to the understanding of calcium interaction with organic molecules and how this interaction affects the composition, microstructure, shape and size of the resulting biomaterials.

On this project we will describe the first stages of the interaction between Ca2+ and the protein osteopontin (OPN), which has been identified as a key protein regulating the growth of bone mineral. Further, the role of Ca2+ in the organisation of DNA will be investigated. To this end, we will use modelling techniques for obtaining a description of the interactions at atomic level. These calculations will be compared with high-resolution electron microscopy data on the condensation of Ca2+ in the presence of OPN and DNA and the nucleation and growth of the calcium phosphate mineral in the presence of collagen obtained by the group of Roland Kröger partially using instrumentation at the York JEOL Nanocentre.

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The long and winding roads of the cell

Intracellular membrane trafficking is essential for many cellular processes and its impairment leads to over 80 major human diseases. Elaborating our understanding of the molecular mechanisms regulating membrane trafficking will be invaluable for developing future strategies to tackle trafficking related pathophysiologies, resulting in improving the quality of life for those afflicted. We seek to address fundamental, open questions in membrane trafficking by assembling a highly interdisciplinary research team to integrate biochemical, genetic and cutting-edge biophysics tools.

Your project will allow you to:

1. Determine spatial localization patterns for recycling. To test the hypothesis that cargo trafficking occurs via two distinct surface recycling routes we will map the patterns of dynamic spatial localization of the endolysosomal system and recycling cargoes in live yeast.

2. Characterize transcriptional/metabolic control of recycling. We will use glucose depletion as a stress factor to study the interplay between transcriptional and metabolic control of recycling, testing hypotheses that transcriptional upregulation of endocytosis is mediated through the Mig1 repressor, and inhibition of surface recycling is initiated by novel factors we have identified.

3. Determine factors driving endosomal protein sorting. We predict surface recycling depends on the physical separation of endosomal proteins from maturing endosomes, and will test how the local intracellular

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Condensed Matter Physics

Atom by atom designer devices for future technologies

  • Supervisor Dr Richard Evans
  • Funding (TBC) External funding
  • Application deadline 1 July 2018

Magnetic materials and devices are essential to a huge range of modern technologies such as wind turbines, hybrid electric cars, MRI contrast enhancement, and digital data storage in hard disk drives and magnetic random access memory. Common to all these applications is the necessity of engineering the materials devices for optimal performance at the nanoscale, either using complex alloys such as Nd2Fe14B or artificial structures of different materials. However, the ability to control the materials and improve device performance is now fundamentally limited by the ability to understand the material and device operation at the atomic level. The properties of devices no longer scale predictably with the device dimensions at the nanoscale leading to erratic performance.

The aim of this PhD project is to use our state-of-the-art atomistic spin dynamics code VAMPIRE to engineer new devices for future technologies in data storage and permanent magnets with atom by atom design. This will require new software capabilities such as GPGPU programming, device models, and world leading materials simulations to address these challenges.

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Atomic scale modelling of magnetic random access memory

  • Supervisor Dr Richard Evans
  • Funding Self-funded students only
  • Application deadline n/a

MRAM is a data storage device which utilises a magnetic material to store information, and is a potential replacement for current charge-based devices such as DRAM due to its non-volatility and low power consumption. MRAM technologies are particularly challenging due to the small dimensions of around 1nm thickness and the use of spin electronics for retrieving the stored information.

This project aims to develop a complete understanding of the material and device properties at the atomic scale in close collaboration with experimental research groups and industrial researchers and will combine molecular and spin dynamics with a model of spin transport dynamics.

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Atomistic simulations of advanced permanent magnet materials

  • Supervisor Dr Richard Evans
  • Funding Tuition fees for UK/EU students. Stipend for UK students (£14,777 for 2018/19).
  • Application deadline n/a

Neodymium permanent magnets are ubiquitous in technologies from cars to wind generators due to their inherent efficiency in converting electrical power to mechanical motion or vice versa. Next generation rare-earth-transition metal permanent magnet materials based on the TmMn12 (RETM12) structure present an exciting opportunity to double the energy efficiency of the materials. Coupled with new motor designs this presents the possibility of doubling the power output of a wind turbine or range of hybrid car with the same battery size.

The aim of this funded PhD project is to develop new atomistic models of RETM12-based permanent magnet materials to predict their performance and understand the fundamental magnetic properties. These models will be used to guide industrial magnet production in collaboration with Toyota Motor Corporation and the MagHEM project to accelerate the development of next generation magnets with ultrahigh energy efficiency. 

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Building Better Nanomaterials: Controlling Reactivity in Metal/Metal Oxide Nanoparticles

  • Supervisor Dr Andrew Pratt & Dr Roland Kroger
  • Funding Tuition fees for UK/EU students. Stipend for UK students (£14,777 for 2018/19).
  • Application deadline 1 September 2018

Nanoparticles (NPs)—clusters of atoms no larger than 100 nm in any dimension—are critical materials for a variety of high-stake applications that will address global challenges in healthcare (regenerative medicine and cancer therapy), information technologies (data storage), catalysis, and environmental remediation (contaminant/bacteria removal). Whilst significant progress in these areas has been made, key challenges remain. In medical applications such as hyperthermia and drug delivery, high-magnetic-moment NP cores are prone to oxidative degradation, which reduces their effectiveness. Similarly, catalytic NPs used in motor vehicle exhaust systems undergo rapid on-stream deactivation which is estimated to consume more than 50 times more platinum than necessary. Reactivity is clearly at the heart of these issues and a better atomic-scale understanding of how NPs react in different gaseous and aqueous environments, particularly with regard to nanoscale oxidation, is required (see, for example, Pratt, Kröger et al., Nature Materials, 2014). This project aims to provide this understanding by combining a new, unique nanoparticle growth facility with state-of-the-art characterisation techniques. Specifically, the balance between grain-boundary and interstitial diffusion during oxidation and how this can be tailored by engineering NP size, shape, coating material and strain will be investigated. More insight on these mechanisms will benefit the above NP applications with potential for significant scientific and commercial impact.

Initially, NPs will be synthesised using a new gas-aggregation cluster source which affords very careful control of NP properties such as size, size distribution, core and shell composition, and geometry. The student will then use a variety of cutting-edge characterisation techniques to monitor reactivity: aberration-corrected and in situ fluid cell electron microscopy will provide high resolution images of isolated and in-solution particles so that we can monitor changes in NP structure; a unique ultrahigh vacuum (UHV) surface analysis facility will be used to probe the electronic and magnetic properties of native, core-shell and functionalized NPs; theoretical input on magnetic properties and the role of grain boundaries/defects will also be considered. During the PhD, you will become expert in UHV nanoparticle growth and electron spectroscopy/microscopy, work on unique instruments not available anywhere else in the world, spend 3-6 months at collaborators in Japan and/or the USA, attend leading international conferences on magnetism (ICM/MMM) and materials (MRS), liaise with peers on theoretical understanding, and be involved in developing interdisciplinary projects and grants.

For further enquiries, please contact Andrew Pratt: andrew.pratt@york.ac.uk


Eligibility: UK and EU students. 3 years tuition fees plus stipend (£14,777 for 2018/19) for UK students. Students from EU countries other than the UK are generally eligible for a fees-only award. Academic entry requirements: at least a class 2:1 MSc or MPhys degree in Physics.

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EBIC environmental STEM microscopy for energy materials and gas sensors

Electron Beam induced current (EBIC) is an electron probe technique widely used in the semiconductor industry for the analysis of p-n junctions, minority carrier distributions, and material defects. It has been developed for the SEM environment with the spatial resolution limited to tens of nanometres. Aberration corrected STEM (scanning transmission electron microscopy) is able to provide atomic scale resolution but cannot benefit from commercially available EBIC packages.

This project goal is to develop EBIC analyses techniques for STEM microscopy allowing to studying material defects and electric properties of thin films down to the atomic scale. This development combined with the unique capabilities of the double aberration corrected gas environmental STEM in York, will open the path for the fundamental study of the electric properties in nanomaterials during gas environment exposure as well as the effect of electric bias on phase transformation as such as oxidation and reduction.

This technique once developed will be applied to materials for solar cell structures and gas sensing devices.

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First principles modelling of defects in solar absorber materials

  • Supervisor Dr Keith McKenna
  • Funding Tuition fees for UK/EU students. Stipend for UK students (£14,777 for 2018/19).
  • Application deadline n/a

A number of materials are emerging as promising candidates to replace silicon in the next generation of solar cells. They offer the prospect of high efficiency, low cost and flexibility allowing for their incorporation into building materials for example. It is critical to understand the properties of atomic scale defects in these materials (such as vacancies, dislocations and grain boundaries) which can negatively impact both performance and stability.

The project will involve the application of density functional theory (DFT) to investigate the properties of a range of defects in solar absorbers such as CdTe, CH3NH3PbI3 and Cu2ZnSn(S,Se)4 in order to understand how to optimise materials for applications. You will work closely with experimental collaborators to test and verify your predictions.

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Heat Assisted Magnetic Recording Using Exchange Bias

  • Supervisor Dr Gonzalo Vallejo-Fernandez
  • Funding Tuition fees for UK/EU students. Stipend for UK students (£14,777 for 2018/19).
  • Application deadline 30 June 2018

Heat Assisted Magnetic Recording (HAMR) is considered to be the next technology to improve current magnetic recording densities. The principle of HAMR is that a laser delivers heat pulses via near field optics to the surface of a conventional disc with grains oriented in the perpendicular direction. Although the concept of heating the recording layer close to its Curie temperature during the writing process to reduce the energy barrier to reversal is over 50 years old, it is only recently that such an approach has become viable thanks to the introduction of near field optical transducers. By heating to elevated temperatures, ~750K, the anisotropy of the material is thereby reduced enabling a conventional write-head to switch the grains. Once the grains have cooled, the anisotropy rises allowing higher data density. For the last 15 years the material of choice for the recording layer has been the ferromagnetic alloy FePt mainly because of its high magnetocrystalline anisotropy with a strong temperature dependence. It also has a magnetic moment comparable to CoCrPt-based alloys currently used in perpendicular magnetic recording. 

In this project, a novel approach to replace FePt is proposed based on our previous work in collaboration with Seagate Media Research (Fremont) [1,2]. It makes use of a phenomenon known as exchange bias. This is where a ferromagnetic (F) layer is grown in contact with an antiferromagnetic (AF) one. Usually exchange bias is used in the read-head sensor that reads the information stored in the media. The idea of using exchange bias in the recording layer is totally new. Due to the interaction at the F/AF interface, the hysteresis loop of the F layer is shifted along the field axis. There are several advantages to this approach compared to FePt: 

  • No phase transformation is required. 
  • Significantly lower writing temperature (~500K). 
  • Lower power consumption. 
  • Easy implementation. 

In previous work we have provided proof of principle for this technology, enabling a 2015 patent in collaboration with Seagate Media Research in Fremont. Although the original work shows promising results complete grain segregation in the CoCrPt alloy was not achieved which results in partially exchange coupled CoCrPt grains. Complete grain segregation is needed to minimise bit transition widths and, hence, further work is required to optimise this structure. 

The student will acquire experimental skills on thin film deposition and structural/magnetic characterisation via transmission electron microscopy, X-ray diffraction and a wide range of magnetometry techniques. The project will be done in collaboration with Seagate Technology in Northern Ireland and the student will be encouraged to spend time in Seagate Technology as part of their personal development. 

[1] K. Elphick, G. Vallejo-Fernandez, T. J. Klemmer, J.-U. Thiele, and K. O’Grady, Appl. Phys. Lett. 109 052402 (2016). 
[2] K. O’Grady and G. Vallejo-Fernandez, “Magnetic storage disc based on exchange bias,” U.S. patent 14/938,139 (2015).

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Impact of grain boundary shape on magnetic properties of electrical steels

  • Supervisor Dr Keith McKenna
  • Funding (TBC) Tuition fees for UK/EU students. Stipend for UK students (£14,777 for 2018/19).
  • Application deadline n/a

Electrical steels are iron-silicon alloys (typically 3.2% silicon) that are used in electrical generators, transformers and end use devices such as motors which are important for the global economy to function. They are polycrystalline and careful refinement of the grain structure is essential for optimisation of properties for applications. However, little is currently known about the impact of grain boundary properties such as orientation difference, grain boundary shape, grain boundary chemistry and the presence of precipitates on magnetic properties.

In this project you will use theoretical models (both classical potentials and density functional theory) to model the structure and properties of grain boundaries in magnetic steels. Cogent Power, a partner in this project, will provide industrial input as well as a pathway to test predictions and deliver improvements in materials.

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Iron Oxidation at the atomic scale: an In-situ environmental TEM/STEM study

Fe and Fe-oxide (FeOx) based nanoparticles (NPs) have shown promising applications in physical and medical sciences. These include magnetic storage devices, catalysis, contrast enhancement in magnetic resonance imaging and magnetic hyperthermia. These applications rely on the magnetic and catalytic properties of the NPs. In particular, the NP magnetic properties are strongly influenced by their stoichiometry and their crystalline structure. Understanding the Fe oxidation processes down to atomic scale is paramount for the control of NPs production. It has been previously shown that crystalline defects in magnetite (Fe3O4) thin films are detrimental for their overall magnetization. In our previous work on such films, we have shown that ex-situ annealing under a CO/CO2 gas mixture can successfully produce Fe3O4 thin film virtually defect free with bulk like magnetic properties. In the first phase of this project we will expand the gas capability of the York Environmental Scanning Transmission Electron Microscope (ESTEM) by implementing a CO/CO2 gas line that will add up to the existing O2, N2 and H2 ones. In the second phase the Fe-O phase diagram will be investigated in-situ for nanoparticles and thin films from room temperature to 1100C. The phase transformations between Fe-oxides phases and their stability will be explored at the atomic scale. In particular to understand the optimal conditions to produce single crystal, defect free and chemically ordered magnetite nanocrystal with improved magnetic properties. This research will provide a deeper insight in the oxidation mechanism, crystalline defect formation, and their relation to the magnetic properties to great advantage to the field of magnetism and catalysis with potential industrial applications.

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Modelling the properties of electron and hole polarons in materials

  • Supervisor Dr Keith McKenna
  • Funding Tuition fees for UK/EU students. Stipend for UK students (£14,777 for 2018/19).
  • Application deadline n/a

The strong coupling between electrons and phonons in some materials leads to the formation of small polarons (quasiparticles comprised of a localised electron and an associated polarisation field). Predicting the properties of polarons is an important fundamental problem as well as being relevant for technologically important phenomena such as magnetism, photoconductivity, dielectric response and reactivity.

In this project you will employ first principles methods recently developed in our group to predict the formation and properties in a range of previously unexplored materials including oxides, nitrides and perovskites. These predictions will be tested in close collaboration with experimental collaborators.

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Nanophononic metamaterials: engineering phonons to convert between heat and electricity

  • Supervisor Phil Hasnip
  • Funding Self-funded students only
  • Application deadline n/a

Thermoelectrics are materials which convert temperature gradients into electricity, or vice versa. These materials can harvest waste heat from industrial processes, turning it into electricity, or use current to provide efficient cooling. These require a material with high electrical conductivity and low thermal conductivity. For metals these are contradictory, since both current and heat are carried by electrons; however, in semiconductors the heat is carried by phonons. Previous semiconductor research has focused on introducing defects to scatter heat-carrying phonons, but electrons often scatter from these too, lowering the electrical conductivity.

We propose a novel approach, using nanoscale engineering to tailor a material’s phonons. By patterning the material’s surface, specific phonon modes may be created which hybridise with heat-carrying phonons in the bulk material, reducing the thermal conductivity 100-fold. The bulk material is completely unchanged, so electrical properties are unaffected. This new class of nanostructures is known as nanophononic metamaterials (NPMs), and have the potential to have higher thermoelectric figures of merit than any previously known material.

Fabricating these nanostructures is challenging, and it is vital to focus on specific NPMs which can deliver the phononic and electronic properties required for high-efficiency thermoelectrics. We propose to use state-of-the-art quantum mechanical simulations (DFT) to predict and model the electronic and phononic properties of NPMs and, coupled with larger semi-empirical models, to design realistic nanoscale device NPMs with high thermoelectric efficiency. These designs will form the basis for new collaborations with world-leading experimental groups, in order to fabricate the NPMs and verify their performance.

This work will be carried out in collaboration with Dr Mahmoud Hussein (University of Colorado Boulder, USA).

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Screened-exchange-based orbital functionals for generalised Kohn-Sham density-functional theory

The PhD student will explore and develop a new approach to ground-state and time-dependent quantum mechanics of systems containing interacting electrons such as nanostructures and solids. The approach is based on concepts from many-body perturbation theory such as the GW approximation, together with the powerful framework of generalised Kohn-Sham density-functional theory, which combines the strengths of many-body perturbation theory with the efficiency of density-functional theory.

The key computational tool will be the group's iDEA code (interacting dynamical electrons approach), a Python code suite (with some Cython extensions). The iDEA code is uniquely placed to allow us to calculate the exact time-dependent quantum mechanics for a wide variety of model nanosystems, which will allow exploration of reliable approximate generalised Kohn-Sham functionals for these systems. An example would be a voltage pulse applied to a molecular junction, taking account of exact relationships satisfied by those functionals.

The approach developed will also be coded into one of the main ab-initio DFT code packages (such as ABINIT or CASTEP) and applied to realistic nanostructures.

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The role of geometric nonlinearity in quantum nano-optomechanical systems

  • Supervisor Dr Ignacio Wilson-Rae
  • Funding (TBC) Tuition fees for UK/EU students. Stipend for UK students (£14,777 for 2018/19).
  • Application deadline n/a

Quantum mechanics, the theory that best explains physical reality, predicts counter-intuitive states where an object seems to be in two locations at once, or two separate objects seem to influence each other without interacting. To further fundamental studies of these paradoxical phenomena, a major goal in the emerging field of nano-optomechanics is to generate such quantum states with a nanomechanical resonator affording a massive macroscopic degree of freedom. This theoretical 3-year project will analyse the role of geometric nonlinearity in this context, both as a resource and a potential hurdle. Nanomechanical resonators are well described by elasticity theory, and basic differential geometry determines that in an elastic medium undergoing a deformation the local strain has contributions that are nonlinear in the displacement field (an example is the stretching of a doubly-clamped nanotube under flexure [1]). In particular, for high-quality resonators made from 1D and 2D materials (e.g. carbon nanotubes and graphene [2]) thermal and quantum fluctuations of the nonlinear strain can become dominant at low frequencies. Specific aims of this project include the analysis of:

(i) Electrostatic-buckling as a resource for studies of the quantum-to-classical transition [1,3,4].

(ii) Electrostatic-softening realisation of coupled quartic oscillators in the quantum regime [1].

(iii) Interplay between geometric nonlinearity and phonon radiation in the nonlinear dissipation of carbon-nanotube resonators [2,4].

This project will involve both analytical and numerical work bringing together techniques from quantum optics and condensed matter physics, and building upon the proposal put forth in Refs. [1,3] and the formalism developed in Ref. 4.

Applicants should have a first class Master-level degree in Physics or Mathematics and excellent proficiency in quantum mechanics.

[1] S. Rips, I. Wilson-Rae, and M. J. Hartmann, Nonlinear nanomechanical resonators for quantum optoelectromechanics, Phys. Rev. A 89, 013854 (2014)

[2] A. Eichler, J. Moser, J. Chaste, M. Zdrojek, I. Wilson-Rae, and A. Bachtold, Nonlinear damping in mechanical resonators made from carbon nanotubes and graphene, Nature Nanotech. 6, 339 (2011).

[3] S. Rips, M. Kiffner, I. Wilson-Rae, and M. Hartmann, Steady-state negative Wigner functions of nonlinear nanomechanical oscillators, New J. Phys. 14, 023042 (2012).

[4] I. Wilson-Rae, Intrinsic dissipation in nanomechanical resonators due to phonon tunnelling, Phys. Rev. B 77, 245418 (2008).

This project will be supervised by Dr Ignacio Wilson-Rae. All enquiries to ignacio.wilson-rae ’at’ york.ac.uk

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Theory-led optimisation of materials for tunnelling magnetoresistive devices

  • Supervisor Dr Keith McKenna
  • Funding (TBC) Tuition fees for UK/EU students. Stipend for UK students (£14,777 for 2018/19).
  • Application deadline n/a

Tunnelling magnetoresistive devices find applications as a magnetic sensors in hard disk read heads and in emerging non-volatile magnetic random access memory (MRAM) technologies. The active part of the device consists of an insulating MgO film sandwiched between two ferromagnetic electrodes. While great progress has been made in the performance of these devices there is a need to make further improvements in the materials to allow widespread adoption of MRAM technology for memory applications. This includes finding new barrier materials which present a lower resistance-area product and understanding and mitigating the negative impact of defects such as vacancies and grain boundaries on performance.

In this project you will employ first principles methods (density functional theory) to model materials for tunnelling magnetoresistive devices in order to guide the optimisation of this technology. You will work closely with experimental collaborators to test and verify your predictions.

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Toward next generation of solar cells: the correlation between efficiency and interface atomic structures in perovskite solar cells

  • Supervisor Dr Vlado Lazarov and Leonardo Lari
  • Funding Tuition fees for UK/EU students. Stipend for UK students (£14,777 for 2018/19).
  • Application deadline 15 June 2018

Perovskite solar cells (PSCs) have the potential to revolutionise the field of solar cells. Their efficiency in the last decades has increased by an order of magnitude, which is unprecedented in this field. In addition, they are cheap to be made and easy to manufacture. Hence the tremendous interest in perovskite solar cells as the next generation of efficient and cost effective solar cells. Further efficiency enhancement, improving their stability as well as making them environmentally friendly requires: i) the fundamental understanding of the interfaces between the TiO2 and the perovskite layer and ii) the developing of a Pb-free perovskite absorber layer. This project aims to address these two outstanding challenges by atomic level characterisation and quantum mechanical modelling using density functional theory (DFT).

Very recently, GreatCell Solar has shown that halide treatments of TiO2 nanopowders, used as electrode material in perovskite cells, further boost the perovskite solar cells efficiency. However, this important empirical finding is limited due to the lack of the understanding of the mechanism of improved efficiency. The first goal of the project is to understand how the structure and chemistry of the TiO2 electrode and its interface with the perovskite layer affects the efficiency of the solar cells. This will be done by employing state of the art atomic resolution imaging and spectroscopy coupled with quantum mechanical calculations. Achieving of this goal will enable developing a new doping strategy for more efficient cells. The second goal of the project is to develop a new absorber perovskite layer that is Pb-free, which will lead to environmentally friendly perovskite solar cells. This project will be conducted jointly with GreatCell Solar, the UK leader in perovskite solar cells research.

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Understanding bacterial communities

  • Supervisor Professor Thomas Krauss
  • Funding Tuition fees for UK/EU students. Stipend for UK students (£14,777 for 2018/19).
  • Application deadline n/a

Bacterial communities are essential for sustaining life, but they also present one of the biggest threats to human health in the 21st century. Our goal is to develop innovative technologies that help to understand and control how bacteria interact and how they cooperate to form multi-bacterial communities. We will achieve this goal by building on our leadership in bionanotechnology, photonics and nanoelectronics to extend our studies from individual bacteria to communities of bacteria, using urinary tract infections (UTI) as the model system.

The project will initially study the interaction between pairs of bacteria, specifically uropathogenic E. coli, the most common causative species of UTI and probiotics associated with treatment of UTI, particularly Lactobacilli, L. acidophilus, L. johnsonii, L. rhamnosus. The student will construct microfluidic devices which enable co-culture of pairs of bacteria. The microfluidic device will be equipped with a range of sensors to monitor the local environment and bacterial growth in situ. This includes sensors to monitor local pH, optical density and resonant imaging sensors, which can detect minute changes in local refractive index as eg caused by the change in thickness of cell walls, or localised impedance, which can see changes in metabolic rate. Having demonstrated and optimised the basic technology on pairwise interactions, the project will then extend to include multiple probiotics to compare the efficacy of single strain probiotics and probiotic mixtures.

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