**Mathematical modelling of phase variation.** *Jamie Wood, with Marjan van der Woude and Jon Pitchford*

Phase variation is the mechanism by which bacteria are able to express multiple, distinct phenotypes with the same genotype. This process has significant consequences for the resistance of bacteria to various human interventions; a phenomenon often termed persistence. This project has multiple threads depending upon the skills and interests of the student. Possibilities include: 1) detailed stochastic simulation of a case study system (ag43 switch in E.coli) 2) examination of the role of gene-transfer in the phase varying system within a spatial structured population 3) extension of existing analytical work on the optimal conditions for stochastic switching.

This is strongly mathematical project, but some experience of computational would be required. The candidate should demonstrate an interest in problems in mathematical biology and immunology

For further ideas and projects please see visit my hompage.

**Modelling electron transfer chains in prokaryotes.** *Jamie Wood*, *with James W. B. Moir*

In prokaryotes, a respiratory chain is necessary which to pass electrons from their initial production from the oxidation of NADH through to their eventual usage at the terminus of the chain to reduce Oxygen (aerobic) or a differing substrate, typically Nitrogen (anaerobic). The design and complexity of this chain varies significantly between organisms adapted to living in different environments and the aim of this project is to investigate the function and working of these varied respiratory systems. The primary model of interest is the asymmetric exclusion process (ASEP) which we will use as the basis for the modelling of the chain.

The project will require strong analytical skills as well as computational modelling; it represents an opportunity for a student with a background in Mathematical Physics to investigate applications to the life-sciences interface as well as work in an interdisciplinary team. This project also supports the work of experimental projects funded through the White Rose network MICROSYS.

For further ideas and projects please see visit my hompage.

**Virus structure.** *Reidun Twarock*

For further ideas and projects please see visit my hompage.

## Stochasticity in Evolution. *Jon Pitchford*

For further ideas and projects please see visit my hompage.

## Bioconvection; Biological Fluid Dynamics; Mathematical Ecology; Pattern formation. *Martin Bees*

I have several projects available. PhD students can choose to get involved in experiemental work in my wet laboratory.

*Project 1) Hydrodynamic interactions of swimming micro-organisms: from individuals to suspensions*

*Project 2) Biodiesel from algae*

**Project 3)** Porous media, micro-organisms and gas exchange

*Project 4) Morphological characterization of spatial patterns in bioconvection using integral geometry*

*Project 5) Biological control of agricultural pests*

*Project 6) Chemically induced hydrodynamic instabilities*

*Project 7) Mathematical physiology*

*Project 8) The ecology of plankton patchiness and the impact of turbulence*

For further ideas and projects please see visit my hompage, or send an email.