Scientific Internship: Simulation of multiplexing in immune cell receptors using eGFRD

Date posted December 3, 2020
Type Scientific Internships

When your body gets infected, the immune system rapidly spreads the message using small signaling molecules that bind to receptor molecules at the surface of the immune cells. Intriguingly, different types of signaling molecules can bind to the same set of receptors, and yet generate a specific response: immune cells can multiplex signals, akin to the transmission of information in telecommunication. How immune cells can transmit multiple messages through a common signaling pathway and yet respond specifically and reliably to each of them, is however not understood. 

Goal of the project
The goal of your project is to test the hypothesis that the distinct messages are encoded in the binding dynamics of the ligand molecules to the receptors. To this end, you will perform eGFRD simulations of the ligand-receptor binding dynamics. eGFRD is a highly efficient and exact scheme to simulate reaction-diffusion systems at the particle level. For more information, see
www.GFRD.org.

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.

This is a collaboration with the Physics of Cellular Interactions Group headed by Dr. Kristina Ganzinger, which conducts single-molecule experiments on the diffusion and interactions of membrane receptors in in-vitro systems using multi-color microscopy. These experiments will be used to develop the model, while the simulations will be used to propose new experiments.

Qualifications

You have a Bachelors degree in (bio)physics, physical chemistry or computer science and participate in a Master study in one of these areas. You have a nationality of an EU-member state and/or you are a student at a Netherlands University. (As from 01-01-2021 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 computational methods and an affinity with molecular simulations or modelling more broadly.

Terms of employment

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

Contact info

Prof. dr. Pieter Rein ten Wolde
Group leader Biochemical Networks Group
E-mail: tenwolde@amolf.nl
Phone: +31 (0)20-754 7100

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–  Resume;
–  List of followed courses plus grades.

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