PhD position: biophysics of cellular time-keeping during animal development

Work Activities
In this project, you will use advanced microscopy and quantitative analysis to solve an important fundamental question: how cells in embryos keep track of time, to execute their functions at exactly the right stage of development. You will address this question in the nematode worm C. elegans. Using a quantitative, physics-inspired approach, you will measure the dynamics of molecules that function as timing regulators in growing and developing animals, to reveal how these molecules encode time with high accuracy. You will work in an enthusiastic and diverse group of PhD student and postdocs with backgrounds in physics and quantitative biology at the AMOLF institute in Amsterdam, and in close collaboration with research groups at the Hubrecht Institute, TU Delft and ENS Paris.

Background. During development from embryo to adult, a mindboggling multitude of processes unfolds with highly intricate timing, with failure to start and stop these processes at the correct time giving rise to lethality, malformations and disease. Yet, how cells measure time, to execute each process at exactly the right stage and for the correct duration, remains one of the biggest unsolved mysteries in biology. Information on time is likely encoded in the dynamics of specific timing proteins, whose concentrations rise, fall or oscillate within individual cells during development. In this picture, a cell deduces time simply by measuring the current concentration of timing proteins within the cells. However, this mechanism gives rise to many important unresolved questions. How can cells measure timing protein level accurately, despite the strong random variability in molecular dynamics that is inherent to cells? Can cells make more accurate measurements of time by combining concentration measurements of multiple timing proteins, each with their own dynamics? What molecular mechanisms do cells use to measure timing protein levels and can these be optimized to extract as much time information as possible? The comparative simplicity of C. elegans development combined with our group’s unique quantitative expertise will enable you to answer these questions for the first time.

Approach. You will use a unique time-lapse microscopy approach developed in our group to visualize and quantify timing protein dynamics in single C. elegans cells, while these cells undergo the precisely-timed division and differentiation events that are required for normal development. Here, you will make use of new fluorescent reporters developed by our collaborators at the Hubrecht institute, to quantify protein concentration dynamics with unparalleled sensitivity. You will develop quantitative analysis approaches to measure the time information encoded in timing protein dynamics, in collaboration with theoretical physicists at TU Delft. You will use mutants that perturb timing protein dynamics and, hence, time information, and study how this changes the cell’s division and differentiation timing, and how these changes give rise to developmental defects. You will connect your dynamics measurements to parallel experiments, performed at the Hubrecht institute, that study the action of timing protein using novel whole-genome techniques (ChIC-seq, EU-seq). In collaboration with ENS Paris, you will examine how dynamics is changed in different C. elegans isolated from the wild that show changed timing of their development.

Our group. We are a social and diverse research group, with a supportive and collaborative atmosphere. We use a quantitative, physics-inspired approach to understand how living organisms reliably build their bodies during development, focusing both on the free-living nematode C. elegans and in-vitro models such as intestinal organoids. We use advanced time-lapse microscopy (Nature Comm 2016, Elife 2022), AI-driven image analysis (PLOS ONE 2020, BioRxiv 2024), and quantitative analysis combined with mathematical models (Elife 2021, PNAS 2022, Science Advances 2023) to ultimately identify underlying molecular mechanisms.

Qualifications
We are looking for outstanding physicists and biologists with strong interest in quantitative biophysics questions, and ideally with experience in programming and handling of complex data. You should like the idea of working in a collaborative, ambitious and international environment. Excellent verbal and written English skills are essential.

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 2.781 Euro’s gross per month and a range of employment benefits.
• 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 Jeroen van Zon: j.v.zon@amolf.nl and .

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.

Postdoc: The single-molecule biophysics of ribosome cooperation

Work Activities
Summary - In this project, you will perform innovative (bio)physics experiments to elucidate the dynamic action of individual ribosomes. The key methodologies are optical tweezers and single-molecule fluorescence, as well as selective ribosome profiling – an exciting new RNA sequencing method. Working in the Tans biophysics lab @ AMOLF Amsterdam, you will visualize the real-time translation activity of ribosomes, how multiple ribosomes work together, detect the folding of individual polypeptide chains, and show how chaperones guide this process. You will work in an international team, with other groups specialized in ribosome profiling and cryo-EM techniques. The aim is to elucidate the fundamental mechanisms that underlie the correct and erroneous production of new proteins.

Questions - According to textbooks, ribosomes work individually to produce proteins. However, recent insights from our lab and others show multiple ribosomes cooperate as they translate mRNA. This cooperation may well be essential to produce multi-protein complexes faithfully. In our group, we aim to elucidate the highly diverse and broad implications. Questions include: Do ribosomes synchronize their translation activity in real-time, like a sequence of cars in traffic? Are mRNA secondary structures and/or direct interactions between ribosomes involved? How do the two (or more) protein chains synthesized by these multiple ribosomes fold together to form protein complexes? How many ribosomes cooperate together? Can we see cooperation between ribosomes that translate different RNA messages? Given the novelty of these fundamental questions in this rapidly expanding field, you will have a unique chance to address them first.

Approach - You will directly follow the unknown dynamics of ribosome translation, protein folding and assembly, and chaperone guidance. This is enabled using optical tweezers combined with single-molecule fluorescence, which detect changes in individual molecules at nanometer and millisecond resolution. In collaboration with our partners, you will also use selective ribosome profiling – an RNA sequencing method that provides high-level data across the genome an in-vivo. This first look may reveal a host of unexpected phenomena. You will develop new experimental schemes, Use cutting-edge single-molecule fluorescence and manipulation methods, Adapt existing biochemical protocols, Analyze the complex temporal data, formulation of new models, And explain your findings in high-level scientific papers.

International team - You will be part of a collaboration with leading groups at Heidelberg University and the ETH in Zurich, which use novel sequencing and cryo-EM methods. By working within this motivated group of young scientists, you will obtain a unique training, understanding and skill set in this expanding field. By integrating these approaches, you will provide insights of unprecedented detail, spanning from the cellular to the atomic level, from in vivo to in vitro, from genome-wide patterns to molecular mechanisms, and from bacteria to human cells.

Image left show ribosome (blue, orange) that synthesized protein chain (yellow) by translating the RNA message (red). Image right shows dynamic ribosome interactions.

Qualifications
We have a number of positions available (PhD and PD). We are looking for outstanding experimental physicists or chemists with an interest in single-molecule techniques, ambition to make breakthrough findings, programming skills to handle complex data, and who thrive in a diverse, collaborative, and supportive environment. Excellent verbal and written English skills are essential.

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

Our group - We form a lively and close-knit research group of about 10 PhD students and postdocs, which work together in small teams on various projects in a highly supportive and social atmosphere that extends to the other research groups at the AMOLF institute, which is housed in a modern building in the east of Amsterdam. The Tans group at the AMOLF institute Amsterdam has been at the forefront of studying chaperone-guided protein folding using optical tweezers. This technique allows one to mechanically manipulate individual proteins, and hence follow the movements and folding steps as they fold. We have shown striking sequences of molecular events that underlie chaperone functions, which are invisible with other methods.

https://www.sandertanslab.nl

https://amolf.nl/research-groups/biophysics

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
• Funding is available to attend regularly international conferences.
• AMOLF assists any new foreign researcher with housing and visa applications and compensates their transport costs and furnishing expenses.

More information?
https://www.sandertanslab.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. Hence, we will only consider your application if it contains 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: The single-molecule biophysics of ribosome cooperation

Work Activities
Summary - In this project, you will perform innovative (bio)physics experiments to elucidate the dynamic action of individual ribosomes. The key methodologies are optical tweezers and single-molecule fluorescence, as well as selective ribosome profiling – an exciting new RNA sequencing method. Working in the Tans biophysics lab @ AMOLF Amsterdam, you will visualize the real-time translation activity of ribosomes, how multiple ribosomes work together, detect the folding of individual polypeptide chains, and show how chaperones guide this process. You will work in an international team, with other groups specialized in ribosome profiling and cryo-EM techniques. The aim is to elucidate the fundamental mechanisms that underlie the correct and erroneous production of new proteins.

Questions - According to textbooks, ribosomes work individually to produce proteins. However, recent insights from our lab and others show multiple ribosomes cooperate as they translate mRNA. This cooperation may well be essential to produce multi-protein complexes faithfully. In our group, we aim to elucidate the highly diverse and broad implications. Questions include: Do ribosomes synchronize their translation activity in real-time, like a sequence of cars in traffic? Are mRNA secondary structures and/or direct interactions between ribosomes involved? How do the two (or more) protein chains synthesized by these multiple ribosomes fold together to form protein complexes? How many ribosomes cooperate together? Can we see cooperation between ribosomes that translate different RNA messages? Given the novelty of these fundamental questions in this rapidly expanding field, you will have a unique chance to address them first.

Approach - You will directly follow the unknown dynamics of ribosome translation, protein folding and assembly, and chaperone guidance. This is enabled using optical tweezers combined with single-molecule fluorescence, which detect changes in individual molecules at nanometer and millisecond resolution. In collaboration with our partners, you will also use selective ribosome profiling – an RNA sequencing method that provides high-level data across the genome an in-vivo. This first look may reveal a host of unexpected phenomena. You will develop new experimental schemes, Use cutting-edge single-molecule fluorescence and manipulation methods, Adapt existing biochemical protocols, Analyze the complex temporal data, formulation of new models, And explain your findings in high-level scientific papers.

International team - You will be part of a collaboration with leading groups at Heidelberg University and the ETH in Zurich, which use novel sequencing and cryo-EM methods. By working within this motivated group of young scientists, you will obtain a unique training, understanding and skill set in this expanding field. By integrating these approaches, you will provide insights of unprecedented detail, spanning from the cellular to the atomic level, from in vivo to in vitro, from genome-wide patterns to molecular mechanisms, and from bacteria to human cells.

Image left show ribosome (blue, orange) that synthesized protein chain (yellow) by translating the RNA message (red). Image right shows dynamic ribosome interactions.

Qualifications
We have a number of positions available (PhD and PD). We are looking for outstanding experimental physicists or chemists with an interest in single-molecule techniques, ambition to make breakthrough findings, programming skills to handle complex data, and who thrive in a diverse, collaborative, and supportive environment. Excellent verbal and written English skills are essential. You meet the requirements for an MSc-degree to ensure eligibility for a Dutch PhD examination.

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

Our group - We form a lively and close-knit research group of about 10 PhD students and postdocs, which work together in small teams on various projects in a highly supportive and social atmosphere that extends to the other research groups at the AMOLF institute, which is housed in a modern building in the east of Amsterdam. The Tans group at the AMOLF institute Amsterdam has been at the forefront of studying chaperone-guided protein folding using optical tweezers. This technique allows one to mechanically manipulate individual proteins, and hence follow the movements and folding steps as they fold. We have shown striking sequences of molecular events that underlie chaperone functions, which are invisible with other methods.

https://www.sandertanslab.nl

https://amolf.nl/research-groups/biophysics

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 2.781 Euro’s gross per month and a range of employment benefits.
• After successful completion of the PhD research a PhD degree will be granted at Delft University of Technology.
• Several courses are offered, specially developed for PhD-students.
• Funding is available to attend regularly international conferences.
• AMOLF assists any new foreign PhD-student with housing and visa applications and compensates their transport costs and furnishing expenses.

More information?
https://www.sandertanslab.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. Hence, we will only consider your application if it contains 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.

Postdoc: Light-induced damage at the atomic scale using in situ TEM

Work Activities
What are the atomic-scale processes behind light-induced damage?

Light-induced damage presents a challenge in applications of high-power lasers, including semiconductor device manufacturing. For the prevention of damage, it is particularly interesting to identify the changes to materials before any degradation of performance is discernible. The emergence of damage is often attributed to the creation of defects or the enhanced interaction of defect sites with external stimuli. Which defects are crucial in damage processes and how different defect types respond to laser pulses, however, remains unresolved at the atomic scale. In this project, you will address these questions using high-resolution transmission electron microscopy (TEM) with in-situ laser exposure. You will shed light on the atomic-scale mechanisms of defect generation and damage below the threshold for macroscopic changes, and connect material properties to the light-induced damage patterns of nanometer thick layers.

Your role as postdoc

You will perform your research in a collaboration between the Light-Matter Interaction group and the Materials & Surface Science for EUVL group at ARCNL, the Hybrid Nanosystems group at AMOLF, and the semiconductor equipment manufacturing company ASML. With guidance from these project partners, you will develop a research plan to resolve the atomic-scale details of light-induced modifications to thin films in the context of nanolithography and optical metrology. You will operate a state-of-the-art aberration corrected TEM with unique light incoupling and ultrafast time-resolution capabilities. You will have access to thin-film preparation and surface characterization facilities at ARCNL and AMOLF to fabricate thin layers and characterize their composition and structure. With the help of experts in the respective methods, you will grow layers for the TEM experiments and have the option to pre- and post-characterize them with several techniques such as atomic-force microscopy (AFM), optical microscopy, scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), and Raman spectroscopy.

Qualifications

• You have a PhD in Physics, Physical Chemistry, or Materials Science and hands-on experience with transmission electron microscopy.
• You are independent and have good project management skills.
• Good verbal and written communication skills (in English) are required.
• A background in light-matter interaction, laser spectroscopy, thin-film growth, or surface science is considered an advantage for the project.

Work environment
ARCNL performs fundamental research, focusing on the physics and chemistry involved in current and future key technologies in nanolithography, primarily for the semiconductor industry. While the academic setting and research style are geared towards establishing scientific excellence, the topics in ARCNL’s research program are intimately connected with the interests of the industrial partner ASML. The institute is located at Amsterdam Science Park and currently employs about 100 persons of which 65 are ambitious (young) researchers from all over the globe. www.arcnl.nl

Working conditions
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 2 years, with a salary in scale 10 (CAO-OI) and a range of employment benefits. ARCNL assists any new foreign Postdoc with housing and visa applications and compensates their transport costs and furnishing expenses.

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

Dr. Roland Bliem
Group leader for Materials and Surface Science for EUV Lithography
E-mail: r.bliem@arcnl.nl
Phone: +31- 20 851 7100

Dr. Wiebke Albrecht
Group leader for Hybrid Nanosystems
E-mail: W.Albrecht@amolf.nl
Phone: +31- 20 754 7100

Prof.dr. Paul Planken
Group leader for Light-Matter Interaction
E-mail: P.Planken@arcnl.nl
Phone: +31- 20 851 7100

Application
You can respond to this vacancy online on the ARCNL webpage.
Please send your:

• Resume;
• Motivation why you want to perform the outlined research (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 includes your motivation letter.

Online screening may be part of the selection.

Commercial activities in response to this ad are not appreciated.

Diversity code
ARCNL 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.

Commercial activities in response to this ad are not appreciated.

PhD: Charging and secondary electron emission for electron microscopy

Work Activities
The goal of the project is to better understand charging of surfaces and how it affects materials properties such as secondary electron emission in the context of scanning electron microscopy for metrology applications. The experiments on materials used in the semiconductor industry will be interpreted in the context of electron scattering simulations performed by collaboration partners. As a PhD student you will use state of the art electron spectroscopy and surface preparation tools to unravel the physical and chemical changes at surfaces induced by charging. You will determine how the secondary electron yields of surfaces are affected by the presence of excess charge, contamination, and defects.

This project is part of a larger KIC project, “Foundations for electron-beam metrology and inspection”, in which knowledge institutes Delft University of Technology and ARCNL are working together with high-tech company ASML. You will perform this project in close collaboration with a team of PhD students and postdocs working on this project at ARCNL and at Delft University of Technology, and with researchers at the Dutch semiconductor manufacturing equipment company ASML. At ARCNL you will be embedded in the Materials & Surface Science for EUVL group of dr. Roland Bliem and work closely together also with the Light/Matter Interaction group of Prof. dr. Paul Planken.

Qualifications
You have a university degree in physics, physical chemistry, or a related field that satisfies the Dutch university requirement to enter into a PhD program.

Good verbal and written communication skills (in English) are required.

Prior experience with surface science, ultra-high vacuum, and spectroscopy techniques is considered an advantage for the project.

Work environment
ARCNL performs fundamental research, focusing on the physics and chemistry involved in current and future key technologies in nanolithography, primarily for the semiconductor industry. While the academic setting and research style are geared towards establishing scientific excellence, the topics in ARCNL’s research program are intimately connected with the interests of the industrial partner ASML. The institute is located at Amsterdam Science Park and currently employs about 100 persons of which 65 are ambitious (young) researchers from all over the globe. www.arcnl.nl

Working conditions
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, with a starting salary of gross € 2,781 per month and a range of employment benefits. 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. A favorable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants. ARCNL 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:
dr. Roland Bliem
Group leader Materials and Surface Science for EUVL
E-mail: r.bliem@arcnl.nl
Phone: +31 (0)20-851 7100

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

Online screening may be part of the selection.

Diversity code
ARCNL 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.

Commercial activities in response to this ad are not appreciated.