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Consider this example sentence from SPACEALC:

あなたがどうしているか気になっていた。 
"I was concerned about how you were."

What is the difference when 気にする is used instead? I.e.,

あなたがどうしているか気にしていた。

~なる seems to convey "spontaneity" or "arising from nowhere" while ~する seems to convey deliberate agency. Would ~する mean to be deliberately concerned about the person? The ~する version seems to be "more concerned" than the ~なる version because of explicit agency.

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up vote 6 down vote accepted

Yes, in that example, the only difference would be the deliberateness, and as a potential difference, the degree of the concern. 気にする is to be concerned about something to the point of being bothered/disturbed by it. 気になる could also mean the same, but not necessarily so. Depending on the context and tone, 気になっていた could be anywhere between lighthearted and grave.

Note that 気にする and 気になる are not always interchangeable. 気にする is to mind/care/worry as a generally negative emotion, while 気になる is broader and can be a neutral or positive feeling as well. So, when you are “interested by” rather than “concerned about” something, it is always 〜なる and never 〜する.

Here is an example that I think illustrates the different connotations. Let’s say you are talking about an artist who unveiled a new painting:

彼は自分の作品が人にどう思われるか気になっていた
“He wondered what people would think of his work.”

Similar to the usage of the word “wonder” in English, whether the artist is simply curious in what people would think, or whether he is somewhat worried about their opinion, is not apparent in this one sentence. It is context-dependent.

彼は自分の作品が人にどう思われるか気にしていた
“He was concerned with what people would think of his work.”

This, on the other hand, shows a value judgement of the effects of the artist’s interest in people’s opinions. You are saying that his interest affects him in a negative way. The extent of these negative effects can range anywhere from “it makes him a tiny bit anxious” to “he is preoccupied by it” to “he is destructively obsessed by it,” but in any case you have made a judgement that the effects on him are neither positive nor neutral.

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If you could provide example cases your answer would be much better. –  Flaw Dec 1 '11 at 14:19
    
I added an example. Hope that helps. I think that last paragraph pretty much sums it up for any situation. –  mirka Dec 5 '11 at 4:00
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