Project Title: Stochastic modelling of repeat-mediated phase variation in Campylobacter jejuni

Project Reference Number: SCI/1141

Associate Supervisor: Dr. Christopher D. Bayliss, Department of Genetics (Leicester)

Location: School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD.

Project Description:Multidisciplinary collaborations are a critical feature of bioscience research enabling integration of data collection with computational and/or mathematical modelling. This PhD study provides an exciting opportunity for an individual to participate in a project spanning research into a food-borne pathogen, high frequency mutation, population biology, mathematical modelling and biostatistical analysis of data sets.

Campylobacter jejuni is a commensal of chickens that is responsible for many cases of gastroenteritis in humans due to consumption of contaminated, undercooked chicken meat. Many surface structures of these bacterial pathogens are subject to stochastic, reversible ON and OFF switches in gene expression mediated by changes in the numbers of tandem DNA repeats (also termed microsatellites). Changes in repeat number cause switches in gene expression by altering the reading frame of genes encoding surface determinants. The genomes of this bacterial species contain 14-27 genes, which are subject to phase variation due to mutations in repeat tracts. This modular behaviour can be coded as a 0-to-1 or 1-to-0 switch, produces a vast range of genotypes and is amenable to mathematical treatment. We are currently performing biological experiments to analyse the frequency with which switches occur in particular environments and the selective/population factors driving these changes. We have also done some preliminary mathematical modelling.

The specific aims of this project are: (i) to participate in stochastic modelling of mutation and selection of Campylobacter jejuni; (ii) to participate in modelling of bottlenecks; (iii) to program and calibrate the models to experimental data; (iv) analyse outputs of the models; (v) to create a software (preferably Web-based) which will make the developed models accessible to the community.

The PhD programme contains a training element, which includes research work as well as traditional taught material. The exact nature of the training will be mutually agreed by the student and their supervisors and will have a minimum of 30 credits of assessed training. The graduate programs at the School of Mathematical Sciences and the Centre for Mathematical Medicine and Biology provide a variety of appropriate training courses.

Training in the development of mathematical approaches to modelling will be provided by Prof. Michael Tretyakov. Dr. Christopher Bayliss will provide training in the specifics of phase variation in bacterial species.

We require an enthusiastic graduate with a 1st class degree in Mathematics (in exceptional circumstances a 2(i) class degree can be considered), preferably of the MMath/MSc level, and with good programming skills. A candidate with a solid background in Probability and Stochastics will have an advantage. A working knowledge of biological systems, particularly microbial replication and DNA replication, is desirable but not essential.

The studentship is available for a period of three and a half years from September/October 2012 and provides an annual stipend of £13,590 and full payment of Home/EU Tuition Fees. Students must meet the EPSRC eligibility criteria.

Further Information and Application: Informal enquiries should be addressed to Prof. Michael Tretyakov  and applications should be made via the online application form. Please mention in your application the reference number for this scholarship.

Closing date: This studentship is open until filled. Early application is strongly encouraged.

Project Title: Computational modelling of plasma reactors

University of Nottingham Supervisors: Professor K A Cliffe and Professor P Houston 
(School of Mathematical Sciences)

Element Six Supervisor: J Dodson (Element Six Ltd, Unit 2, King’s Ride Park, King’s Ride, Ascot, Berkshire, SL5 8BP)

Location: School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD.

Project Description: Technological plasmas are used in industry for applications ranging from depositing coatings on glasses to growing thick films of specialised materials. This PhD will concentrate on developing a model of a diamond growing plasma reactor, using the AptoFEM finite-element software platform. The challenges of the project lie in understanding plasmas, ranging from how the energy is deposited, the chemical reactions taking place, and the transport processes for the energy and the chemical species, and in developing suitable numerical methods for solving the equations describing these processes. The benefits of a successful project will include enabling the growth of higher quality diamond products useful in applications ranging from lasers to fusion reactors. The successful student will spend approximately three months during the course of the project at Element Six transferring the model so that it can be routinely used within the company.

Eligibility and Funding: Applicants should have (or expect to receive) a first or upper-second class degree (or equivalent) in mathematics, physics or a related physical sciences discipline. Some computer programming experience is essential and familiarity with FORTRAN 95 highly desirable. The studentship is available for a period of three and a half years from October 2011 and provides an annual stipend of £13,590 per annum, together with a CASE enhancement of £2,000 per annum and full payment of Home/EU Tuition Fees. Students must meet the EPSRC eligibility criteria

Further Information and Application: Informal enquiries should be addressed to Professor K A Cliffe or Professor P Houston . Applications can be made on-line stating clearly that they wish to be considered for this studentship in the personal statement section of their application.

Closing date: This studentship is open until filled. Early application is strongly encouraged.

Applications are invited for fully funded PhD studentships in any area of Mathematics, including Statistics and Probability, at the School of Mathematical Sciences, University of Nottingham. In the 2008 Research Assessment Exercise all units of assessment performed well with applied mathematics placed 5th in the research power ranking and statistics ranked 6th for quality. Over 95% of research across the school was judged to be of international standard.

The School of Mathematical Sciences is a large and thriving research centre. Areas of research specialism include Algebra, Number Theory, Analysis, Applied Nonlinear Mathematics, Mathematical Medicine and Biology, Complex and Disordered Systems, Continuum Mechanics, Industrial Mathematics, Quantum Gravity, Quantum Information, Epidemic Modelling, Statistical Shape Analysis, Probability Theory and Financial Mathematics.

EPSRC studentships will cover all study fees for EU nationals. For UK nationals, or EU nationals who can demonstrate a relevant connection with the UK (usually established by being ordinarily resident for a period of 3 years immediately prior to the date of application for an award), it will also provide a stipend for either three or three and a half years, currently £13,290 per annum, increasing in line with the EPSRC rates. Students taking projects in statistics or probability may be eligible for an enhanced stipend. Details of eligibility can be found  from the Office of Public Sector Information .

School funded studentships and University funded studentships cover all study fees for EU nationals and also provides a stipend for either three or three and a half years at the EPSRC rate mentioned above.

Applicants should have a First or Upper Second class degree in Mathematics or Statistics, or in a subject with a high mathematical content.

Applications should be made online via the Applicants' Portal .

The School has available a number of Studentships for students from the UK and the EU, including EPSRC and BBSRC studentships funded through Doctoral Training Grants, Nottingham University Research Scholarships (URSs) and School Scholarships.

URSs and School Scholarships

The URSs and School Scholarships provide full funding (fees and living expenses) for UK and EU students.

EPSRC and BBSRC Scholarships

The EPSRC and BBSRC studentships provide full funding for UK students and for EU students who have been resident in the UK for at least 3 years prior to PhD study, and cover fees only for other EU students.

These studentships are awarded on a competitive basis. 

Vice Chancellor's Scholarship for Research Excellence

EU students are also eligible to apply for the Vice Chancellor's Scholarship for Research Excellence (European Union).To apply for this scholarship you must first apply the school and received an offer of a place and then apply for the scholarship itself. The scholarship deadline is in early March.

International Office Scholarships

The university's International Office administers a number of  scholarships and assists with external scholarships. Many of the scholarships require an offer from the School before you can apply so early application is encouraged. Once you have an offer from the School we will assist you in applying for scholarships.

The university's Vice Chancellor's Scholarship for Research Excellence (International)

The University of Nottingham Vice Chancellor's Scholarship for Research Excellence (International) is open to all nationalities. To apply for this scholarship you must first apply the school and received an offer of a place and then apply for the scholarship itself. The scholarship deadline is in early March.