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    Partly melted DNA conformations obtained with a probability peak finding method

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    Peaks in the probabilities of loops or bubbles, helical segments, and unzipping ends in melting DNA are found in this article using a peak finding method that maps the hierarchical structure of certain energy landscapes. The peaks indicate the alternative conformations that coexist in equilibrium and the range of their fluctuations. This yields a representation of the conformational ensemble at a given temperature, which is illustrated in a single diagram called a stitch profile. This article describes the methodology and discusses stitch profiles vs. the ordinary probability profiles using the phage lambda genome as an example.Comment: 11 pages, 9 figures; v3: major changes; v4: applications sectio

    Impact of a New Introductory Mathematical Modeling Course on Student Confidence in Mathematical Ability and Skills

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    Interdisciplinary mathematics and science courses are increasing in popularity. Faculty teaching these courses are given the opportunity to show how mathematics plays an important role in science and how it can be used to improve our understanding of mathematics and science. This paper discusses a new course in mathematical modeling that focuses on environmental issues. Course content and format are presented, as well as the results of a study on the changes in students’ perceptions of their mathematical abilities as a result of taking this new course
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