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Advertising division: IBG-1 - Biotechnology
Reference number: D074/2018, Experimental physics, chemistry, engineering

Master Project: Microfluidic measurements of diffusion in crowded environments

Background
Biochemistry of life, on the cellular level, is driven by two elementary physical phenomena: Diffusion of enzymes and metabolites and enzyme-catalyzed conversion of metabolites. The cytoplasm, the cellular interior where diffusion and reactions take place, is overcrowded with molecules, hence physicochemical conditions inside the cells differ significantly from what is used in a typical laboratory system. In particular, self diffusion coefficients of both enzymes and metabolites decrease substantially, and the diffusion process can anomalously slow-down under certain conditions. Since diffusion determines essentially the kinetics of many cellular processes, its study is of vital importance for life sciences and biotechnological applications.

Typically such studies are conducted by using Fluorescence Correlation Spectroscopy (FCS) or Fluorescent Recovery After Photobleaching (FRAP). However, their drawbacks are that the diffusion coefficients are extracted from fluorescent signals of labelled macromolecules by fitting them to an autocorrelation function, which is known only approximately. In addition, FCS and FRAP probe collective diffusion, rather than self-diffusion, since sufficiently many labelled macromolecules are needed to obtain measurable signals.

Project description
The MSc thesis will focus on diffusion of proteins in a crowded environment of other proteins. In this explorative study a microfluidic H-cell will be tested as a tool to study macromolecular diffusion in crowded environments. The H-cell consists of two inlets and two outlets, with the macromolecules under study entering the H-cell from one inlet only. The method is based on concentration measurements at the H-cell’s two outlets and thus does not require fluorescent labelling of macromolecules. The study will be conducted with artificial crowders. The work will be done in collaboration with Prof. Svyatoslav Kondrat from the Institute of Physical Chemistry in Warsaw, who will contribute theoretical analysis and guidance for experimental design.

What we offer.
We offer a motivated and interdisciplinary research environment where chemists, biologists, mathematicians and physicists work closely together. Forschungszentrum Jülich is situated between Cologne and Aachen in Germany, and is one of the largest research centers in Europe.

Requirements
We are looking for an enthusiastic and motivated master’s student with a background in experimental physics, chemistry, engineering or related fields of study, in their final year. Experience in microfluidics and/or mass spectrometry is desirable, as well as good communication skills and strong interest in multidisciplinary research.

Contacts
Dr. Eric von Lieres (e.von.lieres@fz-juelich.de)
IBG-1: Biotechnology
Forschungszentrum Jülich
http://www.fz-juelich.de/ibg/ibg-1

and Prof. Svyatoslav Kondrat (skondrat@ichf.edu.pl, svyatoslav.kondrat@gmail.com).