Two PhD positions in Biophysics and rheology of bacterial biofilms

Two PhD positions in Biophysics and rheology of bacterial biofilms
100%, Zurich, fixed-term

The bioMatter Microfluidics Group of Dr Eleonora Secchi at ETH Zurich is seeking two PhD candidates. Our research focuses on uncovering the physicochemical mechanisms that control microbial surface colonisation and biofilm assembly, structure, and rheology. We use a broad spectrum of technologies in materials science, microbiology, and microfluidics, as well as advanced imaging techniques to address our questions. We are a highly interdisciplinary, international, and collaborative team of about 10 members, hosted within the chair of Prof. Roman Stocker in the Institute of Environmental Engineering.

Project background

The two PhD positions are part of a recently funded SNSF project aimed at systematically investigating nonlinear biofilm rheology, with emphasis on the role of extracellular DNA (eDNA). Biofilms are a ubiquitous form of microbial life with important implications in medicine, industry, and the environment. They are responsible for persistent infections, antibiotic resistance and biofouling, leading to economic costs of billions of dollars annually and thousands of deaths. Biofilms are microbial communities encased in a polymeric matrix that provides mechanical stability and protection from mechanical stresses through its viscoelastic properties. While the linear viscoelastic response under small deformations is well characterised and recognised as a virulence factor, the response to large deformations remains poorly understood. In particular, there is a lack of systematic investigation of the nonlinear regime, where externally applied loads can induce stress-hardening and stiffening of the biofilm matrix.

Recent findings from our group suggest that eDNA may play a central role in the stress-hardening of biofilms. We hypothesise that this behaviour arises from the entropic elasticity of the eDNA network, a mechanism well described in polymer physics but largely unexplored in living biofilms. This could enable both short- and long-term adaptation to flow fluctuations. While initial experiments are consistent with this hypothesis, further investigation is required to validate the underlying molecular mechanisms and to determine whether stress-hardening is specific to streamers or constitutes a broader feature of biofilm mechanical adaptation across different morphologies. This project will test these hypotheses through a combination of structural, biochemical, and rheological analyses of the biofilms and mathematical modelling, with the potential to reveal fundamental principles of biofilm resilience.

Job description

• Experimentally investigate nonlinear rheology and stress-hardening in bacterial biofilms with different morphologies using custom microfluidic and rheometry platforms.
• Quantify the role of eDNA and its interactions with biofilm matrix components using mutant libraries, enzymatic/antibody assays, and controlled physicochemical conditions; assess incorporation of exogenous DNA into biofilms and its impact on morphology and mechanics.
• Develop and apply advanced fluorescence/confocal imaging approaches to resolve biofilm network structure and eDNA conformation in situ.
• Contribute to the development of a numerical predictive model of biofilm mechanics.
• Collaborate within an interdisciplinary team and with external partners; communicate results through publications and presentations.

The tasks include wet-lab experimentation, project management, numerical modeling and teaching duties.

Position details:

Start date: February 1st, 2026, or by agreement

Fully funded PhD position (approximately 4 years). Final admission to the doctoral programme follows a successful Aptitude Colloquium at the end of year 1; contracts are extended annually.

Profile

The ideal candidate holds a Master's degree in:

• physics, biophysics, materials science, microbiology or a related field with a strong interest in interdisciplinary research at the interface between soft-matter physics and microbiology
• Experience in experimental work such as microfluidics, rheology, microscopy, or culturing microbes and familiarity with data analysis and quantitative modelling is highly valued
• The candidate should be motivated to work both independently and collaboratively within an international research environment and to contribute actively to teaching activities

Workplace
Workplace
We offer

• Training opportunities
• Perspectives for career development
• Support programmes (e.g. mentoring) and networks
• Your (team) culture and team composition
• Working environment and employment conditions
• Your commitment to diversity (e.g. flexible working hours, possibility for part-time work, home office)

We value diversity and sustainability

In line with our values, ETH Zurich encourages an inclusive culture. We promote equality of opportunity, value diversity and nurture a working and learning environment in which the rights and dignity of all our staff and students are respected. Visit our Equal Opportunities and Diversity website to find out how we ensure a fair and open environment that allows everyone to grow and flourish. Sustainability is a core value for us – we are consistently working towards a climate-neutral future.

Curious? So are we.

We look forward to receiving your online application by November 30th, 2025, including the following documents:

• Curriculum vitae
• Cover letter (including motivation, research interests and possible start date)
• Full transcript from undergraduate studies (both Bachelor and Masters)
• Copy of Master's or Bachelor's thesis (PDF)
• At least two reference letters

Applications will be reviewed as they are received. Please note that we only accept applications submitted through our online application portal. Applications sent by email or post will not be considered.

For questions regarding the position (but not for submitting applications), please contact Dr Eleonora Secchi ).

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