N. A. Denesyuk

Theory and simulations for crowding-induced changes in stability of proteins with applications to {lambda} repressor

The paper develops a theory and simulations showing that crowding particles increase protein stability, with applications to lambda repressor, and explains modest destabilization in cellular environments.

Shape changes and cooperativity in the folding of central domain of the 16S ribosomal RNA

The paper uses molecular simulations to study Mg2+-induced folding of the central domain of bacterial 16S rRNA, showing cooperative folding and heterogeneous structural assembly.

Ion Condensation onto Ribozyme is Site-Specific and Fold-Dependent

This study shows ion condensation on ribozymes is site-specific and fold-dependent, contrasting with uniform interactions on rigid charged rods.

Molecular Simulations of ion effects on the Thermodynamics of RNA Folding

The paper uses molecular simulations to study how ions affect RNA folding thermodynamics, showing a linear relationship between folding free energy and ion preferential coefficient.

Frictional effects on RNA folding: Speed limit and Kramers turnover

The paper investigates frictional effects on RNA folding rates using simulations, finding a maximum folding rate at moderate viscosity and a speed limit of 1-4 seconds at water viscosity.