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  1. Article

    Open Access

    A steric gate controls P/E hybrid-state formation of tRNA on the ribosome

    The ribosome is a biomolecular machine that undergoes multiple large-scale structural rearrangements during protein elongation. Here, we focus on a conformational rearrangement during translocation, known as P...

    Mariana Levi, Kelsey Walak, Ailun Wang, Udayan Mohanty… in Nature Communications (2020)

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    Using SMOG 2 to Simulate Complex Biomolecular Assemblies

    Over the last 20 years, the application of structure-based (Gō-like) models has ranged from protein folding with coarse-grained models to all-atom representations of large-scale molecular assemblies. While the...

    Mariana Levi, Prasad Bandarkar, Huan Yang, Ailun Wang… in Biomolecular Simulations (2019)

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    Article

    Compact and ordered collapse of randomly generated RNA sequences

    As the raw material for evolution, arbitrary RNA sequences represent the baseline for RNA structure formation and a standard to which evolved structures can be compared. Here, we set out to probe, using physic...

    Erik A Schultes, Alexander Spasic, Udayan Mohanty… in Nature Structural & Molecular Biology (2005)

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    Chapter

    Polarization of Counterions in a Strongly Coupled Coulombic System: DNA

    Udayan Mohanty in Strongly Coupled Coulomb Systems (1998)

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    Article

    Bimodality and long-range order in ideal Bose systems

    The cluster expansion for the classical and the quantum canonical partition function are related to the Bell polynomials. This observation is exploited in derivation of a set of recursion relations that render...

    Udayan Mohanty, Biman Bagchi, Julian H. Gibbs in Journal of Statistical Physics (1982)