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Cambridge NERC Doctoral Training Partnerships

Graduate Research Opportunities
 
Numerical simulation of the flow field created by a swimming bacterium (D. Das and E. Lauga)
Brief summary: 
Mathematical modelling of the response of swimming bacteria to chemical cues in the ocean
Importance of the area of research concerned: 
Marine bacteria constitute the bulk of the biomass of our oceans. They outnumber any other species, with every litre of seawater containing over a billion bacteria, and as a result they play an important role in the marine cycle of many chemicals and in the life of higher organisms. Marine bacteria are known to respond to chemical cues (so-called `chemotaxis’) around a variety of organisms and sediments, which is crucial for ocean ecology: they can swim up the gradients of chemical attractants, and down the gradient for repellants. However, most of our knowledge on the biophysics of bacterial chemotaxis results from work on the model organism Escherichia coli (E. coli), which typically lives in the intestines of animals. Being located in very different physico-chemical environments, marine bacteria display therefore a very different type of chemotactic behaviour. In this project, we will investigate theoretically how the chemotactic response of marine bacteria are adapted to the patchy and unsteady ocean environment. Our results will lead to a better understanding of the distribution of marine bacteria in the oceans, with impact in ocean ecology and evolution.
Project summary : 
Compared with the situation faced by model organisms such as E. coli, the oceanic environment is spatially inhomogeneous (this is referred to as `patchy’). This leads to the creation of sharp micron-sized chemical gradients in many situations, including near the surface of sinking phytoplankton, near motile zooplankton, in the excretions of higher organisms or near a variety of sediments. Furthermore, the flow itself is often time-varying (this is referred to as `unsteady’), and is even turbulent. As a result, marine bacteria employ a different type of chemotactic behaviour compared to the classical `run-and-tumble’ of E. coli. This includes `run-and-reverse’ or `run-reverse-and-flick’. The ultimate goal of this project is to understand the biophysical origin of the evolution to this different chemotaxis strategy.
What will the student do?: 
In the first part of the project, the student will, in parallel: (i) develop mathematical models for swimming bacteria in patchy and unsteady oceanic flows; this will involve understanding the hydrodynamics of flagellated cells in external, possibly turbulent, flows; (ii) develop mathematical models to capture chemical (advection-diffusion) transport near stationary, sinking and swimming oceanic bodies (sediments, phytoplankton, zooplankton). With this methodology acquired, the student will move to the second part of the project, which will involve coupling the motility part of the model (part i) with the chemical transport (part ii) via chemotaxis: bacteria swim, they measure chemical concentrations, apply a behavioural response, which changes their swimming. The student will use computations to compare the performance of `run-and-reverse’ and `run-reverse-and-flick’ against the dimensionless numbers that characterise both the flow and the chemical transport, culminating in phase map of `ocean bacterial chemotaxis’. The student will then use mathematical modelling for biased random walks in time-varying cues to rationalise theoretically the computational results.
References - references should provide further reading about the project: 
P. Falkowski, T. Fenchel and E. F. DeLong (2008) ``The microbial engines that drive Earth’s biogeochemical cycles’’ Science, 320: 1034 –1039.
R. Stocker and J. R. Seymour (2012) "Ecology and physics of bacterial chemotaxis in the ocean." Microbiology and Molecular Biology Reviews, 76: 792-812.
E. Lauga (2016) ``Bacterial hydrodynamics’’ Annual Reviews of Fluid Mechanics, 48: 105-130
Applying
You can find out about applying for this project on the Department of Applied Mathematics and Theoretical Physics (DAMTP) page.
Prof Eric Lauga
Department of Applied Mathematics and Theoretical Physics PhD Admissions