In 1992, Zakharov became a professor of mathematics at the University of Arizona, and in 2004 he became the director of the Mathematical Physics Sector at the Lebedev Physical Institute.
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He was a lead scientist of the failed Mars missions, Mars 96 and Fobos-Grunt.
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In 1999, he became a project scientist on the feasibility of the Fobos-Grunt sample return mission.
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However with an agreement for cooperation with the European Space Agency on ExoMars had been reached, the space agency chose to focus on that program instead, but not ruled out any possible future Phobos sample return mission.
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Zakharov will be attending the Asia Oceania Geosciences Society AGU (WPGM) Joint Assembly from 13 to 17 August 2012 at Resorts World Sentosa, Singapore for the presentation on Mars Science and Exploration.
On January 2012 following the reentry of the Fobos-Grunt spacecraft, Zeleny proposed a repeat mission called Fobos-Grunt 2, on behalf of mission scientist Alexander Zakharov.