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PhD position Computational synthetic living systems

  • Nieuwe Universiteitsgebouw (NU)
  • Amsterdam
  • 0.8 / 1
  • Faculty of Science
  • PhD
  • MSc
  • Closes on
    10-06-2025
  • Publishing date
    12-05-2025
Apply
Do you have an inquisitive mind and a passion for interdisciplinary science? Please apply for a PhD position at Vrije Universiteit Amsterdam.

Your function

The Department of Mathematics of Vrije Universiteit Amsterdam welcomes applications for a fully-funded, 4-year PhD position in computional modelling of synthetic living systems within the Amsterdam Center for Dynamics and Computation. We are an inclusive, interdisciplinary group, and diversity and internationalism is at the heart of our research principles, as well as our teaching practice. 

At the origin of life, chemical reaction networks of prebiotic compounds played an essential role. These networks likely began relatively simple but grew in complexity over time, forming dynamic molecular structures capable of essential functions of life such as self-replication, metabolism, and compartmentalization. Our understanding of how these functions emerged from prebiotic building blocks and their reactivity in different environmental conditions is only starting to unfold. While most biomolecules can now be synthesized under prebiotic conditions, organizing them into a self-sustaining, thermodynamically out-of-equilibrium living system poses a major challenge. This project aims to generate a synthetic living system that features multiple functions of life by modelling the emergence of metabolism and compartmentalization using a simple out-of-equilibrium peptide-based self-replicating system as a starting point. This position is part of the PRELIFE consortium. 

We are looking for a candidate with a master’s degree in (applied) mathematics, (bio)physics, (bio)chemistry, biomedical / life-sciences or a related field with a strong interest in computational modelling. The project will entail programming (scripting, Python etc.), solving coupled differential equations and carrying out molecular dynamics simulations on high-performance super-computers.  

You will be supervised by Bob Planqué (VU) and Patrick Onck (RUG). The first two years you will work in Groningen; the second two years in Amsterdam. 

The PRELIFE consortium 

The origin of life remains one of the greatest mysteries in science. While many theories have been proposed, no single explanation has yet gained universal agreement. That’s where the PRELIFE consortium comes in. PRELIFE unites experts across a wide range of disciplines from astronomy, biology, chemistry, computer science, earth and planetary sciences, education, mathematics, to physics. Together we will explore two fundamental questions: How did life emerge on Earth, and how common are the conditions elsewhere in the universe?  

We’re searching for answers to life’s biggest questions, and we need your help. As part of the PRELIFE program we offer 15 exciting research projects. Are you a student with deep expertise in your field and a passion for crossing disciplinary boundaries? Each project connects different scientific fields, working together to unlock the secrets of life’s origins and take the public along. Are you in?  

Application 

The preferred starting date is 01.09.2025 (or sooner). 

Applications from all groups currently under-represented in academic posts are especially encouraged. We particularly welcome applications from women and people with an ethnic minority background. 

Your duties 

  • doing research towards writing a PhD thesis 

  • teaching tasks (roughly 15% of your time), for instance supervising exercise classes 

Your profile

  • a (prospective) MSc. degree in (applied) mathematics, (bio)physics, (bio)chemistry, biomedical / life-sciences or a related field with a strong interest in computational modelling. 

  • good communication skills in English 

What do we offer?

A challenging position in a socially involved organization. On full-time basis the remuneration amounts to a minimum gross monthly salary of €2901 (at the start) and a maximum €3707 (in the fourth year). The job profile is based on the university job ranking system and is vacant for 0.8-1.0 FTE. 

The appointment will initially be for 1 year. After a satisfactory evaluation of the initial appointment, the contract will be extended for a further 3 years. Additionally, Vrije Universiteit Amsterdam offers excellent fringe benefits and various schemes and regulations to promote a good work/life balance, such as: 

  • 8% holiday allowance and 8.3% end-of-year bonus 
  • contribution to commuting expenses 
  • optional model for designing a personalized benefits package 
  • a maximum of 41 days of annual leave based on full-time employment 
  • good paid parental leave scheme 

About us

The Department of Mathematics 
The Department of Mathematics strives for excellence in research. The department balances pure mathematical research with mathematical research motivated by applications. Researchers in the department are on one hand active at a fundamental and theoretical level, and, on the other hand, work on applications with links to business, the sciences, and societal issues. The department has a strong international research staff with expertise in dynamical systems, topology, geometry and algebra, as well as in stochastics (statistics, data analytics, probability). 

Faculty of Science 
Researchers and students at VU Amsterdam’s Faculty of Science tackle fundamental and complex scientific problems to help pave the way for a sustainable and healthy future. From forest fires to big data, from obesity to malnutrition, and from molecules to the moon: we cover the full spectrum of the natural sciences. Our teaching and research have a strong experimentally technical, computational and interdisciplinary nature. 

We work on new solutions guided by value-driven, interdisciplinary methodologies. We are committed to research, valorisation and training socially engaged citizens of the world who will make valuable contributions to a sustainable, healthy future. 

Are you interested in joining the Faculty of Science? You will join undergraduate students, PhD candidates and researchers at the biggest sciences faculty in the Netherlands. You will combine a professional focus with a broad view of the world. We are proud of our collegial working climate, characterised by committed staff, a pragmatic attitude and engagement in the larger whole. The faculty is home to over 11,000 students enrolled in 40 study programmes. It employs over 1,600 professionals spread across 10 academic departments. 

Vrije Universiteit Amsterdam 
Vrije Universiteit Amsterdam stands for values-driven education and research. We are open-minded experts with the ability to think freely. - a broader mind. Maintaining an entrepreneurial perspective and concentrating on diversity, significance and humanity, we work on sustainable solutions with social impact. By joining forces, across the boundaries of disciplines, we work towards a better world for people and planet. Together we create a safe and respectful working and study climate, and an inspiring environment for education and research.  

We are located on one physical campus, in the heart of Amsterdam's Zuidas business district, with excellent location and accessibility.  Over 6,150 staff work at the VU and over 31,000 students attend academic education. 

Diversity 
Diversity is the driving force of the VU. The VU wants to be accessible and receptive to diversity in disciplines, cultures, ideas, nationalities, beliefs, preferences and worldviews. We believe that trust, respect, interest and differences lead to new insights and innovation, to sharpness and clarity, to excellence and a broader understanding. 

We stand for an inclusive community and believe that diversity and internationalisation contribute to the quality of education, research and our services. Therefore, we are always searching for people whose backgrounds and experience contribute to the diversity of the VU community. 

Interested

Are you interested in this position? Please apply via the application button by 10.06.2025 and upload: a cover letter, a CV, a list of courses and grades at the MSc level, a (draft) MSc thesis if available, and the names and e-mail addresses of two references.

Applications received by e-mail will not be considered.

Your function

The Department of Mathematics of Vrije Universiteit Amsterdam welcomes applications for a fully-funded, 4-year PhD position in computional modelling of synthetic living systems within the Amsterdam Center for Dynamics and Computation. We are an inclusive, interdisciplinary group, and diversity and internationalism is at the heart of our research principles, as well as our teaching practice. 

At the origin of life, chemical reaction networks of prebiotic compounds played an essential role. These networks likely began relatively simple but grew in complexity over time, forming dynamic molecular structures capable of essential functions of life such as self-replication, metabolism, and compartmentalization. Our understanding of how these functions emerged from prebiotic building blocks and their reactivity in different environmental conditions is only starting to unfold. While most biomolecules can now be synthesized under prebiotic conditions, organizing them into a self-sustaining, thermodynamically out-of-equilibrium living system poses a major challenge. This project aims to generate a synthetic living system that features multiple functions of life by modelling the emergence of metabolism and compartmentalization using a simple out-of-equilibrium peptide-based self-replicating system as a starting point. This position is part of the PRELIFE consortium. 

We are looking for a candidate with a master’s degree in (applied) mathematics, (bio)physics, (bio)chemistry, biomedical / life-sciences or a related field with a strong interest in computational modelling. The project will entail programming (scripting, Python etc.), solving coupled differential equations and carrying out molecular dynamics simulations on high-performance super-computers.  

You will be supervised by Bob Planqué (VU) and Patrick Onck (RUG). The first two years you will work in Groningen; the second two years in Amsterdam. 

The PRELIFE consortium 

The origin of life remains one of the greatest mysteries in science. While many theories have been proposed, no single explanation has yet gained universal agreement. That’s where the PRELIFE consortium comes in. PRELIFE unites experts across a wide range of disciplines from astronomy, biology, chemistry, computer science, earth and planetary sciences, education, mathematics, to physics. Together we will explore two fundamental questions: How did life emerge on Earth, and how common are the conditions elsewhere in the universe?  

We’re searching for answers to life’s biggest questions, and we need your help. As part of the PRELIFE program we offer 15 exciting research projects. Are you a student with deep expertise in your field and a passion for crossing disciplinary boundaries? Each project connects different scientific fields, working together to unlock the secrets of life’s origins and take the public along. Are you in?  

Application 

The preferred starting date is 01.09.2025 (or sooner). 

Applications from all groups currently under-represented in academic posts are especially encouraged. We particularly welcome applications from women and people with an ethnic minority background. 

Your duties 

  • doing research towards writing a PhD thesis 

  • teaching tasks (roughly 15% of your time), for instance supervising exercise classes 

Your profile

  • a (prospective) MSc. degree in (applied) mathematics, (bio)physics, (bio)chemistry, biomedical / life-sciences or a related field with a strong interest in computational modelling. 

  • good communication skills in English 

What do we offer?

A challenging position in a socially involved organization. On full-time basis the remuneration amounts to a minimum gross monthly salary of €2901 (at the start) and a maximum €3707 (in the fourth year). The job profile is based on the university job ranking system and is vacant for 0.8-1.0 FTE. 

The appointment will initially be for 1 year. After a satisfactory evaluation of the initial appointment, the contract will be extended for a further 3 years. Additionally, Vrije Universiteit Amsterdam offers excellent fringe benefits and various schemes and regulations to promote a good work/life balance, such as: 

  • 8% holiday allowance and 8.3% end-of-year bonus 
  • contribution to commuting expenses 
  • optional model for designing a personalized benefits package 
  • a maximum of 41 days of annual leave based on full-time employment 
  • good paid parental leave scheme 

About us

The Department of Mathematics 
The Department of Mathematics strives for excellence in research. The department balances pure mathematical research with mathematical research motivated by applications. Researchers in the department are on one hand active at a fundamental and theoretical level, and, on the other hand, work on applications with links to business, the sciences, and societal issues. The department has a strong international research staff with expertise in dynamical systems, topology, geometry and algebra, as well as in stochastics (statistics, data analytics, probability). 

Faculty of Science 
Researchers and students at VU Amsterdam’s Faculty of Science tackle fundamental and complex scientific problems to help pave the way for a sustainable and healthy future. From forest fires to big data, from obesity to malnutrition, and from molecules to the moon: we cover the full spectrum of the natural sciences. Our teaching and research have a strong experimentally technical, computational and interdisciplinary nature. 

We work on new solutions guided by value-driven, interdisciplinary methodologies. We are committed to research, valorisation and training socially engaged citizens of the world who will make valuable contributions to a sustainable, healthy future. 

Are you interested in joining the Faculty of Science? You will join undergraduate students, PhD candidates and researchers at the biggest sciences faculty in the Netherlands. You will combine a professional focus with a broad view of the world. We are proud of our collegial working climate, characterised by committed staff, a pragmatic attitude and engagement in the larger whole. The faculty is home to over 11,000 students enrolled in 40 study programmes. It employs over 1,600 professionals spread across 10 academic departments. 

Vrije Universiteit Amsterdam 
Vrije Universiteit Amsterdam stands for values-driven education and research. We are open-minded experts with the ability to think freely. - a broader mind. Maintaining an entrepreneurial perspective and concentrating on diversity, significance and humanity, we work on sustainable solutions with social impact. By joining forces, across the boundaries of disciplines, we work towards a better world for people and planet. Together we create a safe and respectful working and study climate, and an inspiring environment for education and research.  

We are located on one physical campus, in the heart of Amsterdam's Zuidas business district, with excellent location and accessibility.  Over 6,150 staff work at the VU and over 31,000 students attend academic education. 

Diversity 
Diversity is the driving force of the VU. The VU wants to be accessible and receptive to diversity in disciplines, cultures, ideas, nationalities, beliefs, preferences and worldviews. We believe that trust, respect, interest and differences lead to new insights and innovation, to sharpness and clarity, to excellence and a broader understanding. 

We stand for an inclusive community and believe that diversity and internationalisation contribute to the quality of education, research and our services. Therefore, we are always searching for people whose backgrounds and experience contribute to the diversity of the VU community. 

Questions about the vacancy?

Please contact

Bob Planqué

Associate professor

Interested

Are you interested in this position? Please apply via the application button by 10.06.2025 and upload: a cover letter, a CV, a list of courses and grades at the MSc level, a (draft) MSc thesis if available, and the names and e-mail addresses of two references.

Applications received by e-mail will not be considered.

Questions about the vacancy?

Please contact

Bob Planqué

Associate professor

Application procedure

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