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Advanced agent-based modelling of biofilms

PGR-P-275

Key facts

Type of research degree
PhD
Application deadline
Ongoing deadline
Country eligibility
International (open to all nationalities, including the UK)
Funding
Competition funded
Additional supervisors
Dr David Head
Schools
School of Computing
Research groups/institutes
Computational Science and Engineering
<h2 class="heading hide-accessible">Summary</h2>

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 />

<h2 class="heading">How to apply</h2>

<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 Stusy 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>&nbsp;</p>

<h2 class="heading heading--sm">Entry requirements</h2>

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.

<h2 class="heading heading--sm">English language requirements</h2>

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.

<h2 class="heading">Funding on offer</h2>

<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>Please refer to the&nbsp;<a href="https://www.ukcisa.org.uk/">UKCISA</a>&nbsp;website for&nbsp;information regarding Fee Status for Non-UK Nationals starting from September/October 2021.</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>

<h2 class="heading">Contact details</h2>

<p>For further information regarding your application, please contact Doctoral College Admissions by&nbsp;email:&nbsp;<a href="mailto:phd@engineering.leeds.ac.uk">phd@engineering.leeds.ac.uk</a>, or by telephone: +44 (0)113 343 5057.</p> <p>For further information about this project, please contact Dr David Head by&nbsp;email:&nbsp;<a href="mailto:d.head@leeds.ac.uk">d.head@leeds.ac.uk</a></p>


<h3 class="heading heading--sm">Linked research areas</h3>