PhD Student

Job description

Within the framework of an ERC Consolidator Grant (PASTIME project), we are seeking a motivated PhD students in biophysical modeling. The students will perform theoretical and computational research using simulations at the molecular scale.

In the PASTIME project, we search for methodologies to study the kinetics of drug transport. Since experiments often are too expensive or lack sufficient detail, molecular simulations can give insight in the dynamics of drug binding to proteins, or the permeation kinetics of those drug molecules through membranes. While such computational methodologies exist, new fundamental developments are needed to understand the ‘time’ aspects and to make the computations feasible with present-day computational power.

The student will make developments in the path sampling methodology for accurate kinetics predictions. The project has multiple parts, on which the team is working:
(A) Developing new methods for simulations of drug transport through cell membranes, building up from membrane permeability calculations, for instance by reducing memory in the simulations.
(B) Developing new methods for screening of the binding kinetics of candidate cancer drugs to protein binding sites, with application in precision medicine, where drugs are tailored to the specific DNA of the patient.
(C) Improving the path sampling methodology to incorporate nonequilibrium kinetics, which is especially relevant for understanding cell death caused by a photoporation treatment.


The student will be embedded in the Biophysical Models for Medical Applications (BioMMedA, https://biommeda.ugent.be) research group, which creates a motivating environment to perform research. BioMMedA is part of the Institute of Biomedical Technology (IBiTech), which is a hub of biophysicists and engineers working on biomedical research questions.

The PhD student will work towards a doctoral degree through the doctoral schools program of Ghent University under the supervision of Prof. An Ghysels. A contribution to teaching can also be part of the job content. This research is performed in close collaboration with international groups (e.g. the group of Prof. Titus van Erp at NTNU in Trondheim, Norway). Locally, collaborations within the Cancer Research Institute Ghent network (CRIG, Ghent, Belgium) are encouraged, especially for experimental validation of the research results, and international collaborations with other research groups are also possible.

We offer:

• We offer a full-time position as a doctoral fellow, consisting of an initial period of 12 months, which - after a positive evaluation, will be extended to a total maximum of 48 months.
• Your contract will start on 01/02/2025 at the earliest.
• You will be working in the friendly and dynamic BioMMedA group. You will have the opportunity to collaborate with experts in molecular simulations through our international network. Locally, you will be able to interact with experts in cancer research and experimental partners, thus allowing to validate your simulation results. You will have access to state-of-the-art research infrastructure at the Flemish High-Performance Computing Centre (VSC), allowing for high-level scientific training at a top-ranked university.
• You will have the opportunity to attend international conferences, publish your results in high-profile journals and visit relevant research institutes.
• All Ghent University staff members enjoy a number of benefits, such as a wide range of training and education opportunities, 36 days of holiday leave (on an annual basis for a full-time job) supplemented by annual fixed bridge days, bicycle allowance and eco vouchers. Click here for a complete overview of all the staff benefits.
• Ghent is a vibrant, safe, cultural, and welcoming university city allowing great quality of life.

Job profile

(1) You have excellent skills in physics/mathematics (for method development) and you enjoy abstract thinking.
(2) You are skilled in scientific programming, data analysis, and dealing with large data (computational tools for generating and analyzing data of complex molecular systems), for instance with Python (or equivalent).
(3) Ideally, you have also knowledge in statistical physics, biophysics or material physics, programming, scientific communication. Ideally, you have already some experience with molecular simulations. Knowledge of biology or chemistry is a strong point, but not necessary at the start of the PhD.
(4) You have a problem-solving, analytical mind, dedicated to overcoming technical challenges.
(5) You have an open attitude towards learning, and are driven, hard-working, committed to obtaining a PhD.
(6) You have good oral and written communication skills, with fluency in English.

How to apply

Hiring will occur on a ongoing basis, so do not hesitate to apply before the deadline.

• Your application must be in English and consist of the following:

1. A motivation letter
2. A curriculum vitae
3. Copies of the relevant diplomas
4. Grade lists (transcript of records of Bachelor and Master courses)
5. Optionally: a sample part of your master thesis or other problem solving accomplishment

• The curriculum vitae should also mention a list of two professors with their institute and contact details, who have supervised you in your Bachelor and/or Master research project and who are willing to provide a letter of recommendation (not now yet, but later in the application process).
• The curriculum vitae should mention the dates (month and year) and locations (city and country) when you describe studies, positions, etc.
• The application should be sent to PASTIME.vacancy@ugent.be using the following subject line: "PhD: predicting kinetics with molecular simulations, LAST NAME, FIRST NAME”.
  Only complete applications will be considered. From all applications, a short-list of candidates will be made, who will be contacted for an interview (possibly over Zoom/Teams).