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.

Measuring strain of laser-excited gold plasmonic nanoparticles with 4D-STEM

Work Activities
Recent studies have shown that defects in metallic plasmonic nanoparticles (NPs) could increase the reaction rate of catalytic reactions. These atomic defects can result in lattice strain and can for example be caused by excitation with ultrafast laser pulses. The study of lattice strain can be done with 4D-STEM, which we can perform in our recently acquired transmission electron microscope (TEM). Our TEM is unique as we can perform these strain measurements in situ under picosecond pulsed laser excitation. In this project, the goal will be to acquire 4D-STEM data under laser excitation and develop a suitable pipeline to analyze such large datasets.

Qualifications
You are currently enrolled in a Master’s program in physics, chemistry, materials science, nano-science, sustainable energy, or a related field. You have a nationality of an EU-member state and/or you are a student at a Netherlands University. The internship has to be a mandatory part of your curriculum. We expect you to be available for at least 6 months, although longer is preferable.

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

In the Hybrid-nanosystems group group, we investigate the interaction between different components in complex hybrid nanostructures and develop new architectures for such systems. The Hybrid Nanosystems group focuses on unravelling the interplay of morphology and underlying charge and energy transfer processes in metal-semiconductor hybrid nanosystems by combining advanced electron microscopy and single particle optical and time-resolved spectroscopy.

https://amolf.nl/research-groups/hybrid-nanosystems

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 Tom Veeken: t.veeken@amolf.nl and Wiebke Albrecht: w.albrecht@amolf.nl.

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

Online screening may be part of the selection.

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.

Quantum-controlled electron wavepackets in the scanning electron microscope

Work Activities
In this project, you will explore the interaction between high-energy electrons and intense nanostructured light fields in a scanning electron microscope. During this interaction, electrons can absorb or emit one or more photon energy quanta, placing them into a quantum mechanical superposition state. As a result, the electron—initially a point charge— transforms into a complex wavepacket in space and time. The goal of this project is to investigate the use of optical metasurfaces to control nanoscale light fields, with the aim of shaping the electron energy spectrum and wavepacket profile at will. These shaped wavepackets could enable novel forms of ultrafast quantum-coherent materials spectroscopy. The project involves nanofabrication of metasurfaces, setting up a system to modulate light fields, and measuring the electron energy and light emission spectra and their correlations.

Qualifications
You are currently enrolled in a Master’s program in physics, nanophotonics, photonics, materials science, or a related field. You have a nationality of an EU-member state and/or you are a student at a Netherlands University. The internship has to be a mandatory part of your curriculum. We expect you to be available for at least 6 months, although longer is preferable.

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 Photonic Materis group focuses on three main research themes:

• Quantum cathodoluminescence microscopy
• Light management in photovoltaics
• Optical metamaterials

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 Tom Veeken: t.veeken@amolf.nl or Albert Polman: a.polman@amolf.nl.

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

Online screening may be part of the selection.

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.

PhD-student: Active Hysterons and Spiking Neurons for Physical Computing

Work Activities

Qualifications
We seek candidates with a strong background in physics, electrical\mechanical engineering, materials science, or computer science with an interest in complex materials for computing and learning. Excellent candidates with training in any area of science or engineering will be considered. PhD candidates must meet the requirements for an MSc degree. Good verbal and written communication skills in English are required. Other advantageous qualities include experience with coding (Python\Matlab) and numerical methods, as well as familiarity with concepts in complex systems, physical memories or machine learning. We strongly believe in the benefits of an inclusive and diverse research environment, and welcome applicants with any background.

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

Working conditions

• The working atmosphere at the institute is largely determined by young, enthusiastic, mostly foreign employees. Communication is informal and runs through short lines of communication.
• The position is intended as full-time (40 hours / week, 12 months / year) appointment in the service of the Netherlands Foundation of Scientific Research Institutes (NWO-I) for the duration of four years
• The starting salary is 2.968 Euro’s gross per month and a range of employment benefits.
• The successful candidate is expected to spend 50% of their time in Amsterdam and 50% of their time in Eindhoven.
• After successful completion of the PhD research a PhD degree will be granted at a Dutch University.
• Several courses are offered, specially developed for PhD-students.
• AMOLF assists any new foreign PhD-student with housing and visa applications and compensates their transport costs and furnishing expenses.

More information?
For further information about the position, please contact :

Prof. Dr. Martin van Hecke
E-mail: M.v.Hecke@amolf.nl

Prof. Dr. Yoeri van de Burgt
E-mail: Y.B.v.d.Burgt@tue.nl

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

Please annex your:

• Resume;
• Motivation on why you want to join the group (max. 1 page).

It is important to us to know why you want to join our team. This means that we will only consider your application if it entails your motivation letter.

Applications will be evaluated on a rolling basis and as soon as an excellent match is made, the position will be filled.

Online screening may be part of the selection.

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.

PhD-student: Active Hysterons and Spiking Neurons for Physical Computing

Work Activities

Qualifications
We seek candidates with a strong background in physics, electrical\mechanical engineering, materials science, or computer science with an interest in complex materials for computing and learning. Excellent candidates with training in any area of science or engineering will be considered. PhD candidates must meet the requirements for an MSc degree. Good verbal and written communication skills in English are required. Other advantageous qualities include experience with coding (Python\Matlab) and numerical methods, as well as familiarity with concepts in complex systems, physical memories or machine learning. We strongly believe in the benefits of an inclusive and diverse research environment, and welcome applicants with any background.

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

Working conditions

• The working atmosphere at the institute is largely determined by young, enthusiastic, mostly foreign employees. Communication is informal and runs through short lines of communication.
• The position is intended as full-time (40 hours / week, 12 months / year) appointment in the service of the Netherlands Foundation of Scientific Research Institutes (NWO-I) for the duration of four years
• The starting salary is 2.968 Euro’s gross per month and a range of employment benefits.
• The successful candidate is expected to spend 50% of their time in Amsterdam and 50% of their time in Eindhoven.
• After successful completion of the PhD research a PhD degree will be granted at a Dutch University.
• Several courses are offered, specially developed for PhD-students.
• AMOLF assists any new foreign PhD-student with housing and visa applications and compensates their transport costs and furnishing expenses.

More information?
For further information about the position, please contact :

Prof. Dr. Martin van Hecke
E-mail: M.v.Hecke@amolf.nl

Prof. Dr. Yoeri van de Burgt
E-mail: Y.B.v.d.Burgt@tue.nl

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

Please annex your:

• Resume;
• Motivation on why you want to join the group (max. 1 page).

It is important to us to know why you want to join our team. This means that we will only consider your application if it entails your motivation letter.

Applications will be evaluated on a rolling basis and as soon as an excellent match is made, the position will be filled.

Online screening may be part of the selection.

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.