Theory of near-critical fluctuations and oscillations in a bacterial “brain”

Work Activities

There is immense diversity and complexity in all biological systems. Searching for universal principles is therefore a major goal in the physics of life, one candidate being collective systems tuned close to their critical points. Phenomena arising from such near-critical tunings are present over a broad range of living systems [1]. Statistical physics teaches us that such systems exhibit a rich set of dynamical properties, including strong sensitivity to external perturbations, extended correlations in space and time, and spontaneous excitations such as oscillations.

In this project you will apply both analytical and numerical modelling techniques to the well-understood sensory systems of Escherichia coli bacteria. Like all living organisms, E. coli possess machinery to sense the world around them. Their chemotactic sensory systems allow these bacteria to swim towards favourable environments — they climb up nutrient concentration gradients, and down gradients of toxic substances. This behaviour is achieved through a network of signalling molecules that begins with input chemoeffector molecules in the environment binding to receptors in a protein array at the cell surface. The chemosensory system (the bacterial “brain”) processes sensory information before producing an output chemical signal that controls its movement.

Prior work has established that interactions among protein molecules in these chemosensory arrays can be effectively modelled by the two-state (Ising) spin models of statistical physics [2]. Recent experiments at AMOLF have established that the strengths of nearest-neighbor couplings in these arrays are poised close to the Ising critical point [3].

Goal of the project

Your task will be to study how the dynamics of these near-critical arrays are affected by the biochemical signaling network within which they are embedded. These effects drive both order (by implementing stabilizing feedbacks) and disorder (by injecting additional stochasticity), profoundly impacting information transmission [4] and bacterial navigation behaviour.

This project will be a collaboration between the groups of:

Pieter Rein ten Wolde (Biochemical Networks, Theory)

Tom Shimizu (Physics of Behaviour, Experiment)

You will be guided by a PhD student (Evan Usher) and work in the group of Pieter Rein ten Wolde, in close collaboration with Tom Shimizu.

[1]         Mora, T., Bialek, W. Are Biological Systems Poised at Criticality? J Stat Phys (2011)

[2]         Tu, Y. Quantitative Modeling of Bacterial Chemotaxis: Signal Amplification and Accurate Adaptation, AnnuRev BioPhys (2013)

[3]         Keegstra, J.M., Avgidis, F., Mulla, Y., Parkinson, J.S., Shimizu, T.S. Near-critical tuning of cooperativity revealed by spontaneous switching in a protein signalling array bioRxiv (2022)

[4]         Tjalma, A.J, et al., Trade-offs between cost and accuracy in cellular prediction, PNAS (2025)

Qualifications

​​​​We are looking for an enthusiastic student with a strong background in statistical physics and experience in modelling. You hold a Bachelor’s degree in Physics, Chemistry, Biology, or Mathematics and are currently enrolled in a Master’s program in one of these fields. You have the nationality of an EU member state and/or are enrolled at a university in the Netherlands. You are available for a minimum of 6 months.

Work environment

AMOLF is a part of NWO-I and initiate and performs leading fundamental research on the physics of complex forms of matter, and to create new functional materials, in partnership with academia and industry. The institute is located at Amsterdam Science Park and currently employs about 140 researchers and 80 support employees. www.amolf.nl

The Biochemical Networks Group combines analytical theory with innovative computational techniques to elucidate general design principles of cell signaling. To this end, it uses ideas from statistical physics and measures from information theory.

The Physics of Behaviour Group studies the overarching themes of behaviour in a diverse set of living systems, from bacteria to fungi. To achieve this, we combine experimental techniques, including fluorescence microscopy, microfluidics and genetic engineering with the theoretical tools of statistical physics.

For more information on both groups, visit www.amolf.nl.

Working conditions

At the start of the traineeship your trainee plan will be set out, in consultation with your AMOLF supervisor.

More information?

For further information about the position, please contact :

Evan Usher
PhD Student in Physics of Behaviour Group
E-mail: usher@amolf.nl
Phone: +31 (0)20-754 7336

Application

You can respond to this vacancy online via the button below.

Please annex your:
–  Resume;
–  List of followed courses plus grades.

Online screening may be part of the selection.

Commercial activities in response to this ad are not appreciated.

Diversity code

AMOLF is highly committed to an inclusive and diverse work environment: we want to develop talent and creativity by bringing together people from different backgrounds and cultures. We recruit and select on the basis of competencies and talents. We strongly encourage anyone with the right qualifications to apply for the vacancy, regardless of age, gender, origin, sexual orientation or physical ability.

AMOLF has won the NNV Diversity Award 2022, which is awarded every two years by the Netherlands Physical Society for demonstrating the most successful implementation of equality, diversity and inclusion (EDI).

Commercial activities in response to this ad are not appreciated.