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The history of the Rijnhuizen Castle begins some eight hundred years ago when an originally wooden stronghold was first mentioned in the annals. Hardly two centuries later it was replaced by a brick building forming two fortified houses of 6 x 6 m2 connected together. During some turbulent centuries Rijnhuizen Castle was destroyed several times. In 1640 Sir Reinoud van Tuyll van Serooskerke rebuilt it into its present shape. In 1655 the De Geer family acquired Rijnhuizen that remained privately owned until the Foundation for Fundamental Research on Matter - FOM - bought it in 1958.

DIFFER is one of the three research institutes of the Foundation for fundamental research on matter (FOM), the funding organization for physics in the Netherlands. The primary goal of FOM is to promote fundamental research on matter for the advancement of science.

The high-quality scientific research takes place in four main departments.