Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Journal of Chemical Physics  

To analyze hydration effects on macromolecular diffusion, the friction coefficients of macromolecules were examined using molecular dynamics simulations with an all-atom model. In the present study, a method was introduced to decompose the molecular friction coefficient into the contributions for each site on the macromolecule. The method was applied to several fullerenols in ambient water. The friction coefficients for the hydrophilic part, such as the OH group, were larger than those for the hydrophobic part, such as the C. The hydration effect did not depend only on the kind of functional group but also on the surface roughness. This approach would be useful in explaining the experimentally observed large changes in diffusion coefficients of proteins that were accompanied by conformation changes.

DOI： 10.1063/5.0241914

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PubMed

Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Chemical Physics Letters  

Yeh and Hummer's simplified estimation method has often been adopted to obtain diffusion coefficients for solute molecules using molecular dynamic simulation. However, the simplified formula is not necessarily valid when a small basic cell is used. Therefore, we conducted molecular dynamics simulations of aqueous protein solution to estimate the diffusion coefficient for the infinite dilution limit. We confirmed a deviation from the simplified formula in the simulation data and rationalized the discrepancy based on the unsimplified formula.

DOI： 10.1016/j.cplett.2022.140096

Web of Science

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