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Full-Text Articles in Physical Sciences and Mathematics
Why Protein Conformers In Molecular Dynamics Simulations Differ From Their Crystal Structures: A Thermodynamic Insight, Fi̇li̇ppo Pullara, Mao Wenzhi, Mert Gür
Why Protein Conformers In Molecular Dynamics Simulations Differ From Their Crystal Structures: A Thermodynamic Insight, Fi̇li̇ppo Pullara, Mao Wenzhi, Mert Gür
Turkish Journal of Chemistry
Conformers generally deviate structurally from their starting X-ray crystal structures early in molecular dynamics (MD) simulations. Studies have recognized such structural differences and attempted to provide an explanation for and justify the necessity of MD equilibrations. However, a detailed explanation based on fundamental physics and validation on a large ensemble of protein structures is still missing. Here we provide the first thermodynamic insights into the radically different thermodynamic conditions of crystallization solutions and conventional MD simulations. Crystallization solution conditions can lead to nonphysiologically high ion concentrations, low temperatures, and crystal packing with strong specific protein--protein interactions, not present under physiological …
Pore Length- And Ion Concentration-Dependent Ionic Current In Cylindrical Nanopores: An Atomistic Molecular Dynamics Study, Nazar İleri̇ Ercan
Pore Length- And Ion Concentration-Dependent Ionic Current In Cylindrical Nanopores: An Atomistic Molecular Dynamics Study, Nazar İleri̇ Ercan
Turkish Journal of Chemistry
The sensing of individual molecules as they pass through nanopores under an external field is a popular research field. The approach is simply based on the detectable temporary blockades in the ionic current as the molecules pass through the nanopores. These signatures of the current have been shown to be a function of nanoparticle and nanopore size and geometry as well as the external electric field. However, models developed in this context fail to predict the experimentally observed behavior in technologically important shorter nanopores. Here we present atomistic molecular dynamics simulation results from colloidal nanoparticle translocation through mid-to-low aspect ratio …