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Exner comes from one of the most important university families of the Austrian-Hungarian empire. The same Exner family includes Adolf Exner, Karl Exner, Sigmund Exner, and Marie von Frisch. Exner the youngest of five children of parents Franz Serafin Exner and Charlotte Dusensy. His father Franz Serafin was, from 1831 to 1848, a professor for philosophy in Prague and 1848 onwards was on the Board of Education in Vienna and an influential reformer of Austrian university education. He began his physics study in Vienna in 1867 and attained a doctorate after an academic year in Zurich under August Kundt, also working with Wilhelm Conrad Röntgen, in the year 1871 in Vienna to towards the DPhil. The largest influence on his training was Viktor von Lang for his habilitation one year later with a work entitled "over diffusion by liquid lamellas." In 1879 he tool up an appointment as extra full professor and in 1891 this was renamed to full professor of the chemico-physical institute, 1902 to "second physical Institut", as a successor to Johann Josef Loschmidt, who had always worried about the "Exner children" as a close friend of family after the early death of his parents. When Exner was appointed 1908 as chancellor of the University of Vienna, he was at the pinnacle of his scientific activities.

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