Scientific Internship: The stochastic thermodynamics of gene expression

Date posted April 8, 2022
Type Scientific Internships

A hallmark of living systems is the ability to produce copies of information-carrying molecules such as DNA and mRNA. These molecules are polymers, and the ordering of the monomers, the polymer sequence, encodes the information for the creation of complex molecules vital to cellular function. In the cell, during gene expression, the sequence of the gene on the DNA is copied into mRNA, which is then further copied into a protein, a complex polymer whose form and function is entirely dependent on the information contained within its sequence.

Goal of the project

Making simple models of copying systems which can be solved analytically allows us to develop our understanding of the fundamental physics of polymer copying. They enable us to understand how copy speed and copy accuracy, both vital for cell functionality, trade off against energy dissipation, and, more generally, how efficiently a cell uses its resources. In this project you will build models with different types of copy-template interactions to develop this understanding. While in previous work we considered minimal models with only correct and incorrect interactions between the monomers of the template and the copy (Poulton, Ten Wolde, Ouldridge, PNAS, 2019), you will develop more realistic models of transcription and translation. These models include the different types of base-pairing in transcription, and the fact that in translation one amino-acid of the protein is encoded by three bases of the mRNA.

About the group

The Biochemical Networks Group combines analytical theory with innovative computational techniques to elucidate general design principles of cell signaling. To this end, it uses ideas from statistical physics and measures from information theory. For more information, see www.amolf.nl.

Qualifications

You have a Bachelors degree in physics or chemistry and participate in a Master study in one of these areas during the entire internship period. The internship must be a mandatory part of your curriculum. You have a nationality of an EU-member state and/or you are a student at a Netherlands University. Please note: As of January 2021 the UK is no longer an EU member state. You must be available for at least 6 months.
We are looking for an enthusiastic student with a strong background in statistical physics and an interest in non-equilibrium thermodynamics, and an experience in building models in c++, python or julia.

Terms of employment

At the start of the traineeship your trainee plan will be set out, in consultation with your AMOLF supervisor.

Contact info

Dr. Jenny Poulton
Postdoc Biochemical Networks Group
E-mail: j.poulton@amolf.nl
Phone: +31 (0)20-754 7100

You can respond to this vacancy online via the button below.
Please annex your:
–  Resume;
–  List of followed courses plus grades.

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.

AMOLF is highly committed to an inclusive and diverse work environment. Hence, we greatly encourage candidates from any personal background and perspective to apply.

Commercial activities in response to this ad are not appreciated.