What are effective strategies for increasing concentration and motivation when doing seemingly passive activities such as reading journal articles?
Increasing Concentration

A method that is geared espeacially towards reading scientific texts is SQ3R. SQ3R is short for survey, question, read, recite and review. So instead of "just reading" a text, one is supposed to 


survey it first to grasp the basic outline by reading the abstract, introduction or table of contents
formulate questions as to what it is that one learns from the text


After these two steps you start "really reading" the text, which is the 3R- part of the method. After reading a passage, pause and summarize what you have learned. You can be critical and evaluate the things with respect to a certain criteria (e.g.: how much evidence does the author provide?).

Maybe you don't even have to take this method too literally. You might want to switch the order of the steps a little, or only do some of the things mentioned. Thinking about my way of reading papers, I often do some of the things, but not all of them. But that is of course just my personal experience.

Increasing Motivation

This is maybe the harder part of your question. Goal Setting Theory (Locke &amp; Latham, 2002) might work. According to the theory, setting a specific and challenging goal leads to better performance than a vage and easy goal. In addition, setting a proximal learning goals is recommended, when "the knowledge or skill for attaining a goal is unknown" (Latham &amp; Locke, 2007, p.293). This could be appropriate for a student reading papers, as he is probably not already familiar with the material. Setting a proximal goal also goes well with the notion of reading only a small protion of the text and then summarizing it (the 3R- part from above) as opposed to a more distal goal like: "I want to understand this paper". Using Goal Setting Theory amounts to a form of extrinisc motivation. It does not necessarily get you into a flow. So maybe this is not what you wanted when you asked the question. But after all, having to read a lot of papers as a student is an externally prescribed task. 

References:

Latham, G. P., &amp; Locke, E. A. (2007). New developments in and directions for goal-setting research. European Psychologist, 12(4), 290-300. PDF
Locke, E. A., &amp; Latham, G. P. (2002). Building a practically useful theory of goal setting and task motivation: A 35-year odyssey. American psychologist, 57(9), 705. HTML