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Jiri Sponer et al.
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Alan A. Chen et al.
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Alan A. Chen et al.
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In Suk Joung et al.
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Gregory R. Bowman et al.
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Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin
Angel E. Garcia et al.
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EJ Sorin et al.
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P Várnai et al.
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SY Ponomarev et al.
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HW Horn et al.
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YP Pan et al.
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A Laio et al.
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A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions
MW Mahoney et al.
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