Between 1942 and 1944, Pen fled to Samarkand in Uzbekistan in order to avoid the German invasion. In 1951, a few years after his return to Russia, Pen earned his doctorate degree and began working as a professor of the Drawing Department at the Ilya Repin Leningrad Academy of Painting, Sculpture and Architecture. He spent 35 years as an educator at the Academy. Additionally, Pen became a member of the Leningrad Union of Artists.
