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PhD Position in Algorithm Development / Image processing for Cryo-EM

misha-kudryashevgmail-com – Posted on October 11, 2017 at 4:58 am –

  • Job Type: PhD
  • Employer: Max Planck Institute for Biophysics
  • Location: Frankfurt on Main, Germany
  • Link:
  • Job Descriptions:

A PhD position is available in the group of Misha Kudryashev at the Max Planck Institute for
Biophysics (
www.biophys.mpg.de/en/kudryashev.html) and the Buchmann Institute for
Molecular Life Science (
www.bmls.de) at Goethe University, Frankfurt am Main, Germany.

The project focuses on a set of challenging problems in registration of noisy three-dimensional
data with anisotropic resolution. The data come from cryo electron tomograms and contain
important information about structure of important biological molecules. The developing
potential of cryo-EM is widely acknowledged, including the Noble Prize in 2017. The main
objective of the project is to set up the algorithmic and engineering workflow to extract maximum
information by subtomogram averaging from cryo electron tomograms. During the course of
the project the applicant will extend the GPU-based parallel computing approach using the
Matlab-based system
Dynamo (www.dynamo-em.org). Further development steps involve
algorithm design and implementation, construction of efficient OOP data structures to support
optimization in HPC environments, tuning data storage and accessing systems for
management and visualization of large sets of three-dimensional data, and enabling flexible
prototyping for fast testing of new algorithmic approaches. At the advanced stages of the project
application of modern methods for Computer Vision and Machine Learning will be explored.
The developed methods will be used for determination of structure of membrane proteins from
the human brain, which are important for neurological disorders. The initial contract duration is
3 years with an optional extension. Working language is English.

The candidate should have a Master/Diploma degree in Physics/Engineering/Mathematics or
a related discipline and programming skills with any of C++/Python/Matlab/CUDA. A
background in biology is not required. The successful candidate will take part in a PhD program.
The Max Planck Society aims at increasing the percentage of women in research positions and
strongly encourages women to apply. The Max Planck Society is an equal opportunity employer
and particularly welcomes applications from individuals with disabilities.

The Max Planck Institute for Biophysics in Frankfurt is one of the top places in the world to
study structure of membrane proteins. The institute departments combine cryo electron
microscopy, X-ray crystallography, biophysics and theoretical methods to gain insights into
structure and function of fundamentally important biological processes. The Kudryashev group
has access to excellent laboratory facilities, high-performance computing infrastructure (large
CPU and GPU-clusters) and high-end electron microscopes (2xFEI Titan Krios, Polara, F30
and JEOL 3200FSC) equipped with direct electron detectors.

Candidates should send a single pdf-file including a one-page motivation letter, the CV and the
names of two principal investigators from whom reference letters can be obtained. Please send
Informal inquiries are welcome.

Application deadline: Dec 1st 2017, early-bird applications are welcome, starting date is flexible. 

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