I think this is really a non-issue. Any decent search engine will return hits for your paper, even if one searches for *harmonisation* (the spelling more common in Britain) rather than *harmonization* (the spelling used in the USA, and also valid, though less common, in Britain) as long as a literal search isn't used.

[Example search][1].

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I'm amending my answer to address the part of your question about whether specific journals require certain spellings. A [Google search limited to the .edu domains](https://www.google.ca/webhp?sourceid=chrome-instant&ie=UTF-8&ion=1#bpcl=35466521&hl=en&q=site:edu+%22author+guidelines%22++british+spelling&safe=active) finds lots of author guidelines that address this issue to various degrees, but nothing shows me that there's a single way to go. 
 
  [1]: http://scholar.google.com/scholar?q=harmonisation%20murchan&btnG=&hl=en&as_sdt=0,5