The Virtual Oviduct – Computational Simulation of interactions in the Reproductive Tract (Code: COM-05-Walker)

Details

The oviduct, (known as the “fallopian tube” in humans), connects the ovary to the womb (uterus) and is the site of fertilisation in mammals, leading to growth of an embryo. However, the oviduct is not a simple tube, but has a complex three-dimensional structure, with internal tissue folding which changes along the length of the organ. This tissue surface consists of a layer of cells which vary considerably in terms of their properties. The interaction of sperm and oocyte (egg) with this complex structure is thought to be critical in determining whether fertilisation takes place.

We have previously developed a three-dimensional virtual representation of the oviduct, and have used this virtual environment to simulate the movement of sperm as simplistic virtual “agents” or particles that follow simple rules as they progress through the oviduct. Since then, research in the laboratory of co-supervisor Professor Fazeli, and the wider reproductive biology community, has generated significant additional data, and we have learnt much more about how sperm interact with the female oviduct in a variety of ways. Some of these processes operate in two directions (so the sperm influence the properties of the cells in the oviduct, which can then influence sperm at a later time point). Additionally, some messages are mediated by “packages” of biochemical messages, known as “exosomes”.

In this project, we will extend our existing simplistic model to incorporate this additional biological data. Our sperm agents would become more sophisticated, in terms of the information they contain, and how they can change their behaviour in response to the oviduct cells they interact with. We will need to change our model so that we can represent communication processes that happen very quickly compared to sperm movement. This will be carried out in a cutting-edge simulation environment known as FLAMEGPU2, that runs on very fast graphics cards and can run large simulations very quickly. Once tested, we will be able to use this model to improve our understanding of how sperm interact with the female reproductive environment, and even suggest ways in which doctors could influence this in order to e.g. improve the likelihood of fertilisation from taking place.

The ideal candidate would have a degree in Computer Science or a related area, and previous coding experience, ideally in C/C++ or CUDA, but other languages will be considered. An interest in biology is sufficient – no prior expertise in biological science is required.

Candidates must have achieved a minimum 2:1 undergraduate and/or postgraduate masters’ qualification (MSc) in Computer Science, or a relevant subject, by the start of the PhD. The English language requirements must also be met by the start of the PhD.

Interested candidates are strongly encouraged to contact the project supervisor (Dr Dawn Walker [email protected]) to discuss your interest in and suitability for the project prior to submitting your application.

Please refer to the EPSRC DTP webpage for detailed information about the EPSRC DTP and how to apply.

Application link: https://www.sheffield.ac.uk/arpform/login.app?code=EPSRC