PhD Projects 2020

Background

PhD students are sought in the School of Computing at the University of Leeds, UK. These studentships form part of a larger collaborative and interdisciplinary project, that currently includes two academics (Thomas Ranner and Netta Cohen), two postdoctoral fellows and three PhD students.

We study the neuromechanical basis of behaviour in the nematode worm C. elegans. Research combines biological experiments, mathematical and computational modelling of the neural control as well as investigations of the physics of the worm and its interaction with the environment. We are seeking to appoint up to four further PhD candidates focusing on the undulatory motion of this worm: one project on the mathematical understanding of numerical methods for biomechanical models (with Thomas Ranner), one on modelling the neural control of locomotion (with Netta Cohen), one experimental project, combining behavioural experiments and machine vision (with Netta Cohen) and one exploring the dynamics of the worm’s behaviour (with Netta Cohen). All projects are envisioned within this multidisciplinary setting. You will join a multi-disciplinary, dynamic, and creative group within the School of Computing at the University of Leeds, with close ties to the Fluid Dynamics Centre for Doctoral Training and to the Hope Laboratory in the Faculty of Biological Sciences, where additional biological experimental facilities are housed.

Informal enquires are welcome from all potential candidates. For more details please contact Dr Thomas Ranner (T.Ranner@leeds.ac.uk) and/or Prof Netta Cohen (N.Cohen@leeds.ac.uk).

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Project descriptions

Project 1: Modelling, simulation, analysis of Cosserat rods with application to microswimmers

Supervisor: Dr Thomas Ranner

The theory of Cosserat rods is very classical and understood from many different view points. A Cosserat rod is a long, thin structure which can bend, twist, stretch and shear. Cosserat rods have recently been proposed as the fundamental building block for modelling long, thin microswimmers (such as sperm cells or snakes). In this project, we are interested in developing finite element methods for their dynamical simulation. We aim to produce efficient, accurate and robust computation tools. The demonstration of the good properties comes by both detailed numerical analysis as well as thorough simulation.

The specific aspects of this project to be worked on will depend on the strengths of the candidate. Different contributions to this project are welcome.

Entry Requirements: Candidates should have a strong undergraduate degree in a relevant area (including but not restricted to mathematics, physics or computer science). A good candidate for this project should have some knowledge of aspects of the design, analysis and implementation of finite element methods for partial differential equations. Programming (implementing novel finite element methods) is an essential part of this project. Prior experience in research (e.g. a Masters degree or work in industry) is a plus.

Suggested start date March or October 2020.

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Project 2: Modelling the neural control of locomotion

Supervisor: Prof. Netta Cohen

The microscopic roundworm Caenorhabditis elegans is a relatively simple animal, with a small and fully mapped anatomy and nervous system. Dubbed the “hydrogen atom” of systems neuroscience, it is also the subject of intensifying efforts to model this creature completely. We are interested in understanding the neuro-mechanical control of locomotion in this animal. Our approach combines models of neural dynamics with biomechanics: we construct and test computational models of the dynamics of neural circuits that are integrated within a biomechanical framework. We are interested in developing and implementing the models, validating them against experimental observations, performing dynamical systems analysis, e.g. to identify targets and modes of modulation, and generating experimentally testable predictions. This project will focus on modelling the dynamics of neural circuits that control locomotion. Specific topics could focus on a specific circuit or behaviour, for example:

Specific topics will be chosen from the scope and remit of the project, but tailored to individual interests and skills.

Entry Requirements: All candidates should have a strong undergraduate degree in a relevant area (including but not restricted to mathematics, physics or computer science). A good candidate for this project should have some knowledge of nonlinear differential equations and an interest in dynamical systems. Interest and knowledge in biomechanics and/or computational neuroscience are a plus, but not required. Prior experience in research (e.g. a Masters degree, or work in industry) is a plus. Programming and extensive simulations are an essential part of this project.

Suggested start date March or October 2020.

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Project 3: 3D microscopy of swimming worms

Supervisor: Prof. Netta Cohen

The microscopic roundworm Caenorhabditis elegans is long and thin, and moves by undulating its body. While its locomotion behaviours have been characterized in detail on the surface of a dish, little is known about its locomotion in more natural habitats. In the Cohen lab, we have been recording the motion of the animal in 3D volumes. We have collected about 20TB of video data (primarily from healthy wild type animals, across a range of fluid environments) and have in place a data analysis pipeline for the 3D reconstruction of body postures and coordinates over time.

In this project, we are interested in comparing behaviours, postures and muscle activation patterns in different media, and across different genetic strains. Specific topics will be chosen from the scope and remit of the project, but tailored to individual interests and skills.

Experimentally focused projects are likely to combine:

Entry Requirements: All candidates should have a strong undergraduate degree in a relevant area (including but not restricted to physics, biology, computer science or engineering). A good candidate for this project should be willing to learn experimental techniques and to combine experiments with data analysis and computer vision. Prior experience in research (e.g., a Masters degree, or work in industry) is a plus. Strong quantitative skills, data handling and computer literacy are essential. Fluency in at least one programming language is a plus.

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Project 4: Modelling dynamics of swimming in 3D

Supervisor: Prof. Netta Cohen

In this project, we are interested in combining data-driven and theory-driven analysis of the dynamics of locomotion in the worm. The locomotion of the worm can be quantified both in terms of the sequence of its postures and it terms of its movement through space. A better understanding of the range of possible postures, and their dynamics over time can shed light into the muscle activation patterns required to generate these behaviours. A better understanding of the trajectories of the worm and the link between postural dynamics and trajectories in space can, in turn, shed light on the movement strategies of the worm, and its biomechanics. Specific topics will be chosen from the scope and remit of the project, but tailored to individual interests and skills.

This project is likely to include any combination of:

Entry Requirements: A good candidate for this project should have some knowledge of nonlinear differential equations and an interest in dynamical systems. Interest and knowledge in physics, biomechanics and/or numerical methods are a plus, but not required. Prior experience in research (e.g. a Masters degree, or work in industry) is a plus. Programming, data handling and simulations are an essential part of this project. Experience in machine learning is a plus.

Suggested start date March or October 2020.

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Funding

UK students: Three EPSRC Doctoral Training Partnership (DTP) Scholarships (fees and maintenance for 3.5 years) are available within the School of Computing for Home/UK rated students. One award is only available for a start date of no later than April 2020. The other two are intended for a start date of October 2020. Applications will be considered on a rolling basis until the available awards are filled. For an October 2020 start date, the deadline for receiving applications is 8th January 2020.

UK/EU students: The School of Computing will be nominating up to two candidates for a further University wide competition (15 awards available).

UK/EU/International students: This year our faculty also has a number of additional awards that are funded by individual schools, and School of Computing has at least one such award.

Chinese students: We welcome applications from China for students who apply for the China Scholarship Council - University of Leeds Scholarships 2020. These awards cover fees and maintenance for three years. The application deadline is 8th January 2020. Details can be found at: https://phd.leeds.ac.uk/funding/48-china-scholarship-council—university-of-leeds-scholarships-2020

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Additional information for all projects

About us: The School of Computing has a strong track record in both research and teaching (top 10 in the UK in the 2019 Guardian league table). We have an excellent track record of high quality research in the foundations of computer science including algorithms and complexity, numerical algorithms and analysis, high performance and distributed computing, as well as in a variety of applied and multidisciplinary settings. Of particular relevance here is our expertise in the areas of artificial intelligence, computer vision, biorobotics and computational biomedicine (including computational neuroscience, biomechanics and biophysics as well as computational medicine).

How to apply: We are committed to equality and diversity and welcome applications from women and under-represented groups. The Faculty of Engineering (including the School of Computing) has received a prestigious Athena SWAN Silver Award from the Equality Challenge Unit, the national body that promotes gender equality in the higher education sector. The Silver Award demonstrates that the Faculty has taken positive actions to ensure that policies, processes and ethos all promote an equal and inclusive environment for work and study.

For details about how to apply, see http://www.leeds.ac.uk/info/130206/applying/91/applying_for_research_degrees.

Formal applications for research degree study should be made on-line through the university website. Please state clearly which PhD project you wish to be considered for. In the research information section please state the name Prof Netta Cohen or Dr Thomas Ranner, as appropriate. If you have published research papers, please list these in the 'Additional Information' section. Please include a CV and as well as a research proposal in your application.

Informal enquires are welcome from all potential candidates. For more details please contact Dr Thomas Ranner (T.Ranner@leeds.ac.uk) and/or Prof Netta Cohen (N.Cohen@leeds.ac.uk).

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© Netta Cohen, Thomas Ranner, Felix Salfelder 2019