PhD in Developing In Silico and In Vitro Methods for Thrombosis and Thrombus Formation

Organisation/Company

University of Amsterdam (UvA)

Research Field

Biological sciences » Biological engineering
Biological sciences » Biology
Computer science » Modelling tools
Computer science » Programming
Engineering » Biomedical engineering
Engineering » Simulation engineering

Researcher Profile

First Stage Researcher (R1)

Application Deadline

30 Apr 2026 - 21:59 (UTC)

Country

Netherlands

Type of Contract

Temporary

Job Status

Not Applicable

Hours Per Week

38.0

Is the job funded through the EU Research Framework Programme?

Not funded by a EU programme

Is the Job related to staff position within a Research Infrastructure?

No

Are you fascinated by the intersection of biology, physics, and computer science? Do you want to build "Digital Twins" that can save lives? If so, please continue reading!
Join Us!
The Computational Science Lab is looking for an ambitious PhD candidate to bridge the gap between computational modeling and experimental biomedicine. You will join ThromboRisk, a prestigious Marie Skłodowska-Curie Doctoral Network. Funded by the European Union, ThromboRisk brings together 17 leading universities, industry, hospitals and research institutes to train 18 Doctoral Candidates in a highly interdisciplinary and collaborative environment. This international consortium aims to revolutionize our understanding of thrombosis—from micro-scale mechanics to patient-specific prognosis.
If you are eager to combine state-of-the-art computational tools with advanced microscopy to solve the puzzle of blood clot fracture and embolization, this is your opportunity to work in a top-tier interdisciplinary setting.
This is what you will do
You will develop predictive computational models to capture the formation and heterogeneous structure of microthrombi, with a specific focus on predicting fracture and embolization risks.
Detached blood clots can block flow to critical organs, making the understanding of thrombus stability crucial for treatment planning. You will tackle this challenge by building a "virtual thrombus"—incorporating fluid mechanical effects, structural stresses, and agonist transport.
Your specific research challenges include:

• Building Digital Twins: You will use numerical tools, including COMSOL and the open-source HemoCell simulation package, to model cell-scale thrombus formation.
• Experimental Validation: You will not just code; you will validate. You will derive model parameters from experimental imaging and use inverse modeling techniques to measure microthrombi deformation under flow.
• Hybrid Research: You will study wall attachment using multiphoton microscopy, linking near-wall thrombus structure to flow embedding.

How do we support you? You will be embedded in the Computational Science Lab at the University of Amsterdam, but your work is inherently collaborative. You will spend a dedicated time at the Amsterdam Medical Center (AMC) with Prof. Ed van Bavel. There, you will learn to perform blood flow perfusion experiments in microfluidic chips and cannulated vessels, acquiring the data necessary to validate your models. Beyond this, you will be embedded in the ThromboRisk Doctoral Network with regular meetings, knowledge exchange, and tailored training events.
Tasks and responsibilities:

• Conducting independent research in computational biomedicine and experimentally validating your models;
• Collaborating within the ThromboRisk international consortium and attending network-wide training events;
• Writing academic publications for peer-reviewed international journals;
• Assisting in teaching courses and supervising Bachelor/Master theses within the department;
• Completing a PhD dissertation within four years.

What we ask of you
We are looking for a candidate with a "builder" mindset—someone who enjoys understanding how things work from the bottom up, whether it's code or biological structures.
Requirements:

• A Master’s degree in Computational Science, Biomedical Engineering, Biophysics, Physics, Applied Mathematics, or a related field;
• Strong programming skills (C++ or Python) and experience with numerical modeling (for instance, Finite Element Analysis or Computational Fluid Dynamics);
• A strong interest in—and willingness to learn and perform—biological experiments (microscopy, microfluidics);
• Excellent command of English, both written and spoken;
• A flexible, proactive attitude and the ability to work in an interdisciplinary team.
• MSCA Mobility Rule: You must not have resided or carried out your main activity (work, studies, etc.) in the Netherlands for more than 12 months in the 36 months immediately before the recruitment date;

It is a plus if you have any of the following:

• Prior experience with inverse modeling or parameter estimation.
• Experience in microscopy or microfluidic lab environments.
• Experience with open-source codes.
• Experience using supercomputers.

This is what we offer you
A temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). The preferred starting date is as soon as possible, but no later than 31 October 2026. This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.
The gross monthly salary, based on 38 hours per week and dependent on relevant experience, ranges between € 3,059 to € 3,881 (scale P). This does not include 8% holiday allowance and 8,3% year-end allowance. The UFO profile Promovendus is applicable. A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants. The Collective Labour Agreement of Universities of the Netherlands is applicable.
As an MSCA Fellow, you also benefit from:

• Access to the extensive ThromboRisk training network, including workshops and summer schools across Europe;
• A generous mobility allowance (and family allowance, if applicable) in accordance with Marie Skłodowska-Curie Actions rules.

Curious about our extensive secondary benefits package? You can read more about it here.
You will work in this team
The Faculty of Science has a student body of around 8,000, as well as 1,800 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works, be it elementary particles, the birth of the universe or the functioning of the brain.
The Computational Science Lab (CSL) is part of the Informatics Institute. We are a world-leading group in modeling and simulation, focusing on complex systems in biology, health, and sociology. You will be working in a team that values creativity, technical rigor, and interdisciplinary collaboration.
See more details about the team in the Lab: https://www.zavodszky.com/ .
Want to know more about our organisation? Read more about working at the University of Amsterdam.
If you feel the profile fits you, and you are interested in the job, we look forward to receiving your application. You can apply online via the button below. We accept applications until and including 30 April 2026. In case of high number of applications, we might start interviewing candidates before this date.
Applications should include the following information (all files besides your cv should be submitted in one single pdf file):

• a detailed CV including the months (not just years) when referring to your education and work experience;
• a letter of motivation explaining why you are interested in Digital Twins and Thrombosis;
• a list of publications (if applicable);
• the names and email addresses of two references who can provide letters of recommendation on request.

A knowledge security check can be part of the selection procedure.
(for details: national knowledge security guidelines )
Only complete applications received within the response period via the link below will be considered.
If you have any questions or do you require additional information? Please contact:

• Dr Gabor Zavodszky, g.zavodszky@uva.nl

Website

https://www.academictransfer.com/en/jobs/359563/phd-in-developing-in-silico-and…

Website for additional job details

https://www.academictransfer.com/359563/

Number of offers available

1

Company/Institute

UvA

Country

Netherlands

City

Amsterdam

Postal Code

1098XH

Street

Science Park 904

Geofield

City

Amsterdam

Website

http://www.uva.nl/

Street

Spui 21

Postal Code

1012 WX

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