Advanced agent-based modelling of biofilms

Biofilms are surface-associated microbial communities that can be detrimental or beneficial to human habitation. Wastewater treatment plants crucially require biofilms to function, and we would be exposed to a wide range of pathogens if not for the protection provided by our resident microbiome, which is largely biofilms. On the other hand, biofilms are also the root cause of many chronic infections, and biofouling in industry causes substantial economic losses. There is a growing need to control (rather than simply kill) biofilms, and here computational modelling can help by predicting the effects of external changes and interventions on the composition, and therefore pathogenicity, of naturally occurring biofilms much more rapidly than (costly, lengthy) experiments.<br /> <br /> The goal of this project is to develop an advanced biofilm model that includes multiple species, reflecting the community nature of almost all naturally-occurring biofilms, and also fluid flow which can apply shear stress - shedding microbes near the surface - and transport materials and metabolites to and from the biofilm. Combining agent-based models with flow is not trivial, however, and would be an example of a fluid-structure interaction problem for which Leeds houses the computational fluids CDT, for which fluid-structure interaction is a cornerstone. Once developed, it would then be possible to see how transport of nutrients affects biofilm morphology, how shear stress limits biofilm thickness, and possibly how microbubbles can disrupt pathogenic biofilms, this latter being an area of current experimental research within Leeds. As well as contact with other research groups within Leeds, it is also envisaged that the model will be used to generate hypotheses for future experimental verification in the UK and globally. There is also scope to develop parallelised code to run on one of Leeds' high-performance computing clusters.<br /> <br />

<p>Formal applications for research degree study should be made online through the&nbsp;<a href="https://www.leeds.ac.uk/research-applying/doc/applying-research-degrees">University&#39;s website</a>. Please state clearly in the Planned Course of Study section that you are applying for <em><strong>PHD Computing FT</strong></em> and in the research information section&nbsp;that the research degree you wish to be considered for is <em><strong>Advanced agent-based modelling of biofilms</strong></em>&nbsp;as well as&nbsp;<a href="engineering.leeds.ac.uk/staff/542/Dr_David_Head">Dr David Head</a> as your proposed supervisor.</p> <p>If English is not your first language, you must provide evidence that you meet the University&#39;s minimum English language requirements (below).</p> <p style="margin-bottom:11px"><em>As an international research-intensive university, we welcome students from all walks of life and from across the world. We foster an inclusive environment where all can flourish and prosper, and we are proud of our strong commitment to student education. Across all Faculties we are dedicated to diversifying our community and we welcome the unique contributions that individuals can bring, and particularly encourage applications from, but not limited to Black, Asian, people who belong to a minority ethnic community, people who identify as LGBT+ and people with disabilities. Applicants will always be selected based on merit and ability.</em></p> <p class="MsoNoSpacing">Applications will be considered on an ongoing basis. &nbsp;Potential applicants are strongly encouraged to contact the supervisors for an informal discussion before making a formal application. &nbsp;We also advise that you apply at the earliest opportunity as the application and selection process may close early, should we receive a sufficient number of applications or that a suitable candidate is appointed.</p> <p>Please note that you must provide the following documents at the point you submit your application:</p> <ul> <li>Full Transcripts of all degree study or if in final year of study, full transcripts to date</li> <li>Personal Statement outlining your interest in the project</li> <li>CV</li> <li>Funding information including any alternative sources of funding that you are applying for or if you are able to pay your own fees and maintenance</li> </ul> <p>&nbsp;</p>

Applicants to research degree programmes should normally have at least a first class or an upper second class British Bachelors Honours degree (or equivalent) in an appropriate discipline. The criteria for entry for some research degrees may be higher, for example, several faculties, also require a Masters degree. Applicants are advised to check with the relevant School prior to making an application. Applicants who are uncertain about the requirements for a particular research degree are advised to contact the School or Graduate School prior to making an application.

The minimum English language entry requirement for research postgraduate research study is an IELTS of 6.5 overall with at least 6.5 in writing and at 6.0 in reading, listening and speaking) or equivalent. The test must be dated within two years of the start date of the course in order to be valid. Some schools and faculties have a higher requirement.

<p style="margin-bottom:12px"><strong>Self-Funded or externally sponsored students are welcome to apply.</strong></p> <p><strong>UK</strong>&nbsp;&ndash;&nbsp;The&nbsp;<a href="https://phd.leeds.ac.uk/funding/209-leeds-doctoral-scholarships-2022">Leeds Doctoral Scholarships</a> and <a href="https://phd.leeds.ac.uk/funding/234-leeds-opportunity-research-scholarship-2022">Leeds Opportunity Research Scholarship</a> are available to UK applicants. <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds.</p> <p><strong>Non-UK</strong> &ndash;The&nbsp;<a href="https://phd.leeds.ac.uk/funding/48-china-scholarship-council-university-of-leeds-scholarships-2021">China Scholarship Council - University of Leeds Scholarship</a>&nbsp;is available to nationals of China. The&nbsp;<a href="https://phd.leeds.ac.uk/funding/73-leeds-marshall-scholarship">Leeds Marshall Scholarship</a>&nbsp;is available to support US citizens. <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds.</p> <p><strong>Important:</strong>&nbsp; Any costs associated with your arrival at the University of Leeds to start your PhD including flights, immigration health surcharge/medical insurance and Visa costs are <strong>not</strong> covered under these studentships.</p> <p>Please refer to the <a href="https://www.ukcisa.org.uk/">UKCISA</a> website for information regarding Fee Status for Non-UK Nationals.</p> <p>&nbsp;</p> <p><strong>Self-Funded or externally sponsored students are welcome to apply.</strong></p> <p><strong>UK</strong>&nbsp;&ndash;&nbsp;The&nbsp;<a href="https://phd.leeds.ac.uk/funding/209-leeds-doctoral-scholarships-2022">Leeds Doctoral Scholarships</a>, <a href="https://phd.leeds.ac.uk/funding/53-school-of-computing-scholarship">School of Computing Scholarship&nbsp;</a>, <a href="https://phd.leeds.ac.uk/funding/198-akroyd-and-brown-scholarship-2022">Akroyd &amp; Brown</a>, <a href="https://phd.leeds.ac.uk/funding/199-frank-parkinson-scholarship-2022">Frank Parkinson</a> and <a href="https://phd.leeds.ac.uk/funding/204-boothman-reynolds-and-smithells-scholarship-2022">Boothman, Reynolds &amp; Smithells</a> Scholarships are available to UK applicants. &nbsp;<a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds.&nbsp;</p> <p><strong>Non-UK</strong>&nbsp;&ndash; The&nbsp;<a href="https://phd.leeds.ac.uk/funding/53-school-of-computing-scholarship">School of Computing Scholarship&nbsp;</a>&nbsp;is available to support the additional academic fees of Non-UK applicants. The&nbsp;<a href="https://phd.leeds.ac.uk/funding/48-china-scholarship-council-university-of-leeds-scholarships-2021">China Scholarship Council - University of Leeds Scholarship</a>&nbsp;is available to nationals of China. The&nbsp;<a href="https://phd.leeds.ac.uk/funding/73-leeds-marshall-scholarship">Leeds Marshall Scholarship</a>&nbsp;is available to support US citizens. <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds.</p>

<p>For further information about your application, please contact Doctoral College Admissions: e:&nbsp;<a href="mailto:phd@engineering.leeds.ac.uk">phd@engineering.leeds.ac.uk</a></p> <p>For further information about this project, please contact Dr David Head: e:&nbsp;<a href="mailto:d.head@leeds.ac.uk">d.head@leeds.ac.uk</a></p>