Open positions in the Endres group
3.5-year PhD position in “Physical principles underlying the assembly and adaptation of complex microbial communities”
Supervised by Profs. Robert Endres and Samraat Pawar
Centre for Integrative Systems Biology and Bioinformatics & Department of Life Sciences, Imperial College, London
Project Description
Applications are invited for a research studentship leading to the award of a PhD degree, under the supervision of Profs. Robert Endres and Samraat Pawar, to investigate the relationship between nonequilibrium thermodynamics and microbial ecosystem assembly. The post is supported by a bursary and fees (at the UK home student rate) funded by NERC. The studentship is for 3.5 years starting October 2024.
The interface between fundamental physics and complex biological systems has been an active research area in recent years. In particular, there has been immense interest in understanding the diversity, stability and resilience of microbial communities. However, despite significant progress in specific areas of microbial research, fundamental thermodynamic principles determining the assembly and adaptation of complex microbial communities are still very little understood.
In this project, we will describe microbial communities as random reaction networks of interacting species, and explore different naturally occurring network topologies, from small to large network sizes. We will study their entropy production (heat dissipation) as a measure of energy turnover and vitality. In particular, a key novelty will be studying the evolution toward minimal and maximal entropy production networks using genetic algorithms and graph theory to capture mature near and young far-from-equilibrium microbial communities, and understanding what distinguishes these. Besides their heat dissipation, resulting networks will be characterised by metrics including connectivity, mean shortest path length, degree distribution, under/overrepresented network motifs, multistability, and cycle fluxes, as well as robustness to external perturbation, relating directly to the resilience of naturally occurring microbial communities. While we will focus on fundamental theory development, at later stages real world data from collaborators and an ecosystem restauration company will be factored in.
The work will be a natural extension of previous and ongoing work in the biological-physics Endres group at South Kensington campus, done in close collaboration with the Pawar group at Silwood Park campus with expertise in individual and community-level metabolism. These works include the emergence of cooperativity in biofilms, the assembly and diversity of microbial ecosystems, and spatial pattern formation in bacterial colonies. Often a link is made between mechanistic modelling and machine learning. We anticipate that identified thermodynamic principles will be widely applicable to systems ranging from chemical reaction networks and microbial communities to economics.
The PhD student will receive training in theoretical and computational techniques required for investigating evolving microbial communities at the network level. In addition, the PhD student will learn a range of biophysical and systems biology methods, covering nonequilibrium thermodynamics, reaction dynamics, and microbial biophysics.
Informal enquiries are welcomed and should be sent to Dr. Endres (r.endres@imperial.ac.uk)
How to apply:
Please email Dr. Endres (r.endres@imperial.ac.uk) and include in your application:
A cover letter
Your CV
At least two references sent directly to Dr. Endres from the referees
and fill out the pre-application form to obtain an Unique Identifier (project number: 2024_46_DoLS_RE in the Department of Life Sciences):
Full applications made before 8 January 2024 will be considered at any time. Note funding is not confirmed yet as the Science and Solutions for a Changing Planet DTP (SSCP DTP) will choose top 16 candidates for its PhD projects.
Funding and eligibility:
A fully funded 3.5-year NERC DTP Studentship, including tuition fees and a standard research council stipend (approx. 18.6K p.a.). The fees and stipend cover UK home applicants and standard research council eligibility criteria apply:
https://www.ukri.org/what-we-offer/developing-people-and-skills/find-studentships-and-doctoral-training/get-a-studentship-to-fund-your-doctorate/ There is only limited funding available for international candidates.
The successful applicant must hold, or expected to complete, a BSc at 2:1 level or better in a relevant subject area such as physics, mathematics or bioengineering by start of the project. The successful applicant will be part of the SSCP DTP cohort, commencing in October 2024.
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​Imperial PhD scholarships for high-performance students
​There are two types of prestigious scholarships provided by Imperial College. The President's scholarships require a BSc and Masters degrees at 1st class and Distinction levels respectively and are open to all irrespective of nationality. The Schroedinger scholarship only funds UK or EU students but without the 3-year residency requirement (overseas/non-European students are not eligible). Please see following links for application details: