Opportunity for a Ph.D. student in quantitative biochemistry to probe the dynamics of eukaryotic DNA replication

Job description

We are looking to an ourstanding experimentalist for this exciting NWO-funded project at the interface of biochemistry and biophysics that has as its goals to understand the dynamics of eukaryotic DNA replication.

What are you going to do?

In this fully-funded project, you will:

• acquire skills in protein purification and sample preparation for ensemble biochemistry and single-molecule biophysics studies;
• develop an interdisciplinary skillset by using ensemble biochemistry and single-molecule biophysics to study and the prepared proteins to study DNA replication;
• come with suggestions to expand the interdisciplinary skillset as necessary for the benefit of the project;
• employ or develop simulations and data analysis routines to analyze acquired data;
• be embedded in an scientifically outstanding and warmly communicative interdisciplinary team at TU Delft;
• publish your results together with biochemists and biophysicists on the team;
• have the opportunity to obtain teaching experience and improve your leadership skills while guiding undergraduate students;

About the project

During our lifetimes, we copy approximately a lightyear’s worth of DNA, and how the different components of the molecular machinery (the replisome) work together to achieve this successfully is an area of highly active research.  Here, you will take on the exciting challenge of understanding the dynamics of DNA replication by purifying, reconstituting, and studying the activity of eukaryotic replisome at the single-molecule level. You will examine replisome composition, replisome motion dynamics, and the interplay between these two quantities; and examine how these change in the context of chromatin or obstacles on the DNA. To do so, you will employ a combination of biochemical approaches (protein purification, biochemical assays, DNA sequencing) and novel biophysical instrumentation (e.g. fluorescence imaging, single-molecule force spectroscopy, microfluidics, cryo-electron microscopy). You will analyze the resulting datasets using biophysical modelling, interact with collaborators in molecular biology and biochemistry in the United Kingdom (involving extensive visits), and in doing so, publish high-quality scientific papers to advance this exciting field.

For this innovative, interdisciplinary, and NWO-funded project, we are looking a quantitative biochemist, with:

• a completed M.Sc. in molecular biology, biochemistry, or biophysics;
• practical experience in the above areas are desired, preferably including protein purification;
• a strong motivation to develop a combined biochemistry/biophysics skillset (protein biochemistry and protein biophysics, single-molecule kinetics), and an interest in interdisciplinary research;
• an independent, well-organized, and reliable work style together with an ability and interest in working in a small team;
• good interpersonal communication skills and a strong interest in the broader field of biophysics, thereby contributing to our interactive lab culture.
• doing a PhD at TU Delft requires English proficiency at a certain level to ensure that the candidate is able to communicate and interact well, participate in English-taught Doctoral Education courses, and write scientific articles and a final thesis. For more details please check the Graduate Schools Admission Requirements .

We look for friendly and driven colleagues of all kinds to enrich our team. We would like to welcome our new colleague as soon as possible in 2023.

TU Delft offers PhD-candidates a 4-year contract, with an official go/no go progress assessment after one year. Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities, increasing from € 2541 per month in the first year to € 3247 in the fourth year. As a PhD candidate you will be enrolled in the TU Delft Graduate School. The TU Delft Graduate School provides an inspiring research environment with an excellent team of supervisors, academic staff and a mentor. The Doctoral Education Programme is aimed at developing your transferable, discipline-related and research skills.

The TU Delft offers a customisable compensation package, discounts on health insurance and sport memberships, and a monthly work costs contribution. Flexible work schedules can be arranged. For international applicants we offer the Coming to Delft Service and Partner Career Advice to assist you with your relocation.

Delft University of Technology is built on strong foundations. As creators of the world-famous Dutch waterworks and pioneers in biotech, TU Delft is a top international university combining science, engineering and design. It delivers world class results in education, research and innovation to address challenges in the areas of energy, climate, mobility, health and digital society. For generations, our engineers have proven to be entrepreneurial problem-solvers, both in business and in a social context. At TU Delft we embrace diversity and aim to be as inclusive as possible (see our Code of Conduct ). Together, we imagine, invent and create solutions using technology to have a positive impact on a global scale.

Challenge. Change. Impact! 

Faculty of Applied Sciences

With more than 1,000 employees, including 135 pioneering principal investigators, as well as a population of about 3,400 passionate students, the Faculty of Applied Sciences is an inspiring scientific ecosystem. Focusing on key enabling technologies, such as quantum- and nanotechnology, photonics, biotechnology, synthetic biology and materials for energy storage and conversion, our faculty aims to provide solutions to important problems of the 21st century. To that end, we train students in broad Bachelor's and specialist Master's programmes with a strong research component. Our scientists conduct ground-breaking fundamental and applied research in the fields of Life and Health Science & Technology, Nanoscience, Chemical Engineering, Radiation Science & Technology, and Engineering Physics. We are also training the next generation of high school teachers and science communicators.

Click here  to go to the website of the Faculty of Applied Sciences.

Department Bionanoscience

The Department of Bionanoscience focuses on the fundamental understanding of biological processes, from the level of single molecules to the full complexity of living cells. This research provides fascinating insight in the molecular mechanisms that lead to cellular function. Furthermore it enables the in vitro bottom-up construction of cellular machinery and it impacts applications ranging from biomolecular diagnostics to novel antibiotics and targeted nanomedicine. The department features a strongly multidisciplinary and international team of scientists, whose research areas include single-molecule biophysics, synthetic biology, as well as (quantitative) cell biology.

Who are we?

The Nynke Dekker Lab (http://nynkedekkerlab.tudelft.nl/ ) is a highly successful single-molecule biophysics research lab within the Department of Bionanoscience at the TU Delft. The lab focuses its studies on understanding DNA and RNA replication from a quantitative perspective both in vitro and in vivo. The lab employs state-of-the-art biophysical techniques (e.g. advanced single-molecule fluorescence, optical and magnetic tweezers) together with in-house molecular biology and biochemistry. Studying the dynamics of DNA and RNA replication at the single-molecule level requires broad and integrated expertise; as such, we employ outstanding international scientists trained in biophysics, biochemistry, and cell biology who work together enthusiastically as a multidisciplinary team. You will be part of this group and will interact actively with current members.

Are you interested in this vacancy? Please apply before 15 April 2023 via the application button or by sending an email to [email protected] .

Applications should include a motivated cover letter of application, a detailed CV, and the names and contact information of three references. Applications will be evaluated on a first-come, first-serve basis.

When applying for this position, please refer to vacancy number.

For more information about this position, please contact Prof. Nynke Dekker, phone: +31 (0)15-2783219, e-mail: [email protected] .

• A pre-employment screening can be part of the selection procedure.
• Applying for an exemption for specific research and educational areas is an obligatory part of the selection procedure for this vacancy. This exemption must be obtained from the Ministry of Education, Culture and Science (OCW) before an employment contract is agreed upon. Click here  for more information.
• Acquisition in response to this vacancy is not appreciated.