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Upon returning home, Bohr was given an assistant professorship at the University of Copenhagen and the chance to lecture on the mechanical foundations of thermodynamics. But he was also eager to return to his research on atoms. He continued to correspond with Rutherford, who offered constructive criticism and helped Bohr prepare his work for publication. This work included the Trilogy of articles that established Bohr's reputation. Soon the university would ask Bohr to submit an application for appointment as professor of theoretical physics. But before any action had been formally completed, Rutherford, in search of an original young mind, wrote to Bohr inviting him to accept a readership at Manchester. Bohr could not turn this opportunity down, and he asked the university to grant him leave.

After preparing for the trip back to England, Bohr decided to take a walking trip through the Austrian Alps with his brother. Their timing could not have been worse, for as they relaxed in the peace of the mountains, Archduke Franz Ferdinand was assassinated, and longstanding tensions soon reached their climax. The brothers managed to catch one of the last trains to cross the border, and as Denmark came to grips with its vulnerable position, Bohr faced the equally difficult predicament of whether to continue on to England. The dangers posed by conflicts in the sea made the journey especially questionable, but Bohr and his wife made it safely.

At Manchester, Bohr had the opportunity to work closely with H. G. J. Moseley, who had been studying X rays. Using X rays and photographic plates, Moseley was soon able to confirm Bohr's hypothesis that adding individual electrons formed the basis for a table of elements. Moseley was later killed in a war-related incident—a death that shocked Bohr and the entire scientific community. The war itself remained constantly in the back of Bohr's mind. When it finally ended, he believed, like many others, that war must never occur again. In a letter to Rutherford, he expressed the sincere hope that Germany would not be allowed to dissipate into anarchy, recognizing that stable peace could be achieved only through a substantial revision of international relations.

Meanwhile, coping with the calamity of his colleague's death and the constant pressures created by the war, Bohr had to frequently revise and refine his atomic model in light of new discoveries. One significant paper, "On the Quantum Theory of Radiation and the Structure of the Atom," added more specific details about atomic states. For example, Bohr had earlier made the argument that electrons could jump from one orbit to another as energy was emitted or absorbed. In this paper, he theorized that an atom possesses stationary states in which energy was neither emitted nor absorbed. Any emission or absorption that did occur—such as might induce an electron to jump—would correspond to the transition between two stationary states.

Already having asked for an extension on his leave, Bohr was scheduled to return in 1916 to a newly created post of professor of theoretical physics. He would return to establish his own base at Copenhagen, but the influence of Manchester and Rutherford would remain with him. Manchester had been an ideal setting, offering a well-equipped laboratory and brilliant colleagues from around the world. At the same time, Rutherford had shown Bohr the value of an effective leader that encouraged and directed his scientists in their independent but integrated pursuits. Thus he returned to Copenhagen with clear models to follow.

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