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After the German unification the Science Council evaluated the institutes of the former GDR Academy of Sciences. They concluded that there were most promising activities in the institutes of Physical Chemistry and Organic Chemistry in Berlin-Adlershof and of former Polymer Chemistry in Teltow that could be integrated into a prospective Max Planck Institute. This proposal was taken up by a committee of the Max Planck Society that realized a large potential and need for basic science in this area between physics, chemistry and biology. Hence the Max Planck Institute of Colloids and Interfaces was founded on 01.01.1992.

After founding the institute new buildings were anticipated. The groups with preliminary housing in Berlin-Adlershof and Teltow moved to the new location at the Potsdam-Golm Science Park in April 1999. An outstation in Freiberg, initially also set up was meanwhile moved to the TU there. The preliminary leadership was taken over by the Max Planck directors Prof. Kahlweit, Prof. Kampa and Prof. Spieß. Their main task was to build up the administration and the infrastructure and to decide on personnel because most of the 100 positions foreseen for the institute had to be filled as soon as possible. The preliminary leadership was supported by advice from Prof. Kretzschmar and Prof. Philipp who have been previously in leading positions at the two locations.

On 01.10.93 and 01.11.1993 the founding directors Prof. Markus Antonietti, Prof. Reinhard Lipowsky and Prof. Helmuth Möhwald took over the joint leadership of the institute and gave it its scientific directions and structure with the departments "Interfaces" (H. Möhwald), "Colloid Chemistry" (M. Antonietti) and "Theory" (R. Lipowsky). Since 01.02.2003 the forth department "Biomaterials" under Prof. Fratzl had been started. On 01.06.2008 the Institute could expand again: the department "Biomolecular Systems" (P. H. Seeberger) found an interim stay at the campus of the FU Berlin before it could move into the extension building at the Science Park Potsdam-Golm in 2015. The Department of Interfaces was closed on February 1st, 2014 with the retirement of Helmuth Möhwald. The field of physical chemistry of interfaces will be supported from 1 July 2014 by the Max Planck Research Group Mechano(Bio)Chemistry directed by Dr. Kerstin Blank.

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