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PhD Position in Computational Biophysics
A PhD position on modeling cell mechanics and its relation to fluctuation measurements is available at the Theoretical Soft Matter and Biophysics group, Institute of Complex Systems (ICS-2) of Forschungszentrum Jülich, Germany. Our group works at the interface between physics, biology, and chemistry using computer simulations and analytical theory.
The observation of cell flickering (a visible vibration motion of cell membrane) is a standard experimental technique to measure mechanical properties of a cell. Cell membrane fluctuations are directly associated with the cell's characteristics and properties of cytosol and suspending medium. However, the interpretation of experimental measurements still remains difficult, and existing theoretical models provide the understanding and quantification only for a limited number of cases including simple geometries (e.g., planar, spherical) and certain membrane properties (e.g., bending rigidity, membrane tension). It remains unclear whether it would be possible to quantify a number of cell parameters simultaneously from a single experimental measurement. Also, it is not clear to which extent different cell properties can be separately identified. Finally, in addition to thermal fluctuations, there exists a contribution of active processes (so-called active flickering) arising in experimental measurements, which may occur due to metabolic processes in a biological cell [Turlier, Fedosov et al., Nature Physics 12, 513 (2016)].
The new team member will be investigating flickering of a cell membrane using mesoscopic simulations. The model is based on the dissipative particle dynamics (DPD) method, a mesoscale hydrodynamic simulation technique, and is implemented within a highly parallelized code. The main aim is to understand the contribution of different factors to membrane flickering, in particular cell shape, elastic and viscous properties of a cell, and potential metabolic activities. We will focus first on a red blood cell membrane, which includes a non-spherical biconcave shape, membrane elasticity and viscosity, as well as possible active membrane processes. Furthermore, we plan to investigate the effect of cell adhesion to a substrate and of solid-like intra-cell inclusions on membrane fluctuations, which are present in certain diseases, such as malaria and sickle-cell anemia. Finally, membrane fluctuations of more complex cells, which possess internal bulk cytoskeleton, will be studied.
- Strong motivation to study and model cell mechanics, and to develop new algorithms.
- A master's degree or diploma in physics, biophysics, applied mathematics, chemistry, or a relevant engineering discipline.
- Good programming skills and experience with numerical modeling and particle-based methods.
- Experience with parallel programming using MPI and high-performance computing resources is advantageous, but not necessary.
- Experienced and friendly international research team with a strong background in biophysics and modeling cell mechanics.
- Cutting-edge computational facilities including the on-site top European supercomputers.
- Collaboration with the world's leading experimental groups on cell mechanics.
- Three-year PhD program including a competitive salary and social benefits.
- To take part in the International Helmholtz Research School of Biophysics and Soft Matter with a highly multidisciplinary environment.
April 2017 or later. Applications will be accepted until the position is filled.
How to apply
Please send your application by email to Dr. Dmitry Fedosov (firstname.lastname@example.org) including
- Curriculum Vitae.
- Motivation letter (a one page statement of your background and research interests).
- Copies of your university degree/s and grades.
- Contact information of at least two references.
Dr. Dmitry Fedosov
Institute of Complex Systems (ICS-2)