Is it appropriate (as an undergraduate) to email an academic with a question on their publication? I am currently studying a published article as part of an undergraduate research project I am doing. I am having difficulty understanding specific parts as the article is quite dense and makes some leaps in logic that I am having trouble following. The article is of a mathematical/computer science nature and suppresses many details.

I would like to email the article's author to ask a question or two, and I am wondering, is this appropriate? If I were a post-doc or something I would not hesitate. My concern is that as an undergraduate, perhaps my questions will be silly and/or a waste of time for the author. Or worse yet, I am concerned that it is inappropriate for an undergraduate to email at all. Can anyone offer some comments on this?
Some relevant info: 
- I have studied the problem and am unable to answer the questions thus far. 
- My supervisor does not know the answer either and would have to study the paper (my job) to determine the answer.  As noted, this is nearly identical to a question asked by a Masters student, but I feel it justifies its own responses. My concern here is that I may be asking questions that would be obvious to a Master's student.
It is definitely appropriate. Further, I wouldn't even tell the author that you are an undergraduate. Just tell them you read their paper as part of a research project and had a few questions. Should be as simple as that.