N. Hori

Salt-dependent self-association of trinucleotide repeat RNA sequences

The paper shows that salt concentration affects RNA self-association rates and yields through changes in free energy gaps, with implications for repeat RNA aggregation.

Competition between stacking and divalent cation mediated electrostatic interactions determines the conformations of short DNA sequences

The paper develops a computational model to study ion-DNA interactions and shows it accurately predicts experimental results without parameter tuning.

Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time

The paper uses molecular simulations to study how Mg2+ ions influence the folding and misfolding kinetics of the Azoarcus ribozyme, revealing diverse folding pathways and the role of energetic and topological frustration.

Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation

The paper shows that odd-even differences in RNA repeat sequences affect phase separation propensity through free energy gaps between ground and slipped hairpin states.

Condensates in RNA Repeat Sequences are Heterogeneously Organized and Exhibit Reptation-like Dynamics

This study uses a coarse-grained model to simulate RNA repeat sequences, showing that condensates exhibit reptation-like dynamics and complex intermolecular networks.

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.

Folding RNA in mixtures of monovalent and divalent cations: Theory and simulations

This paper develops a theory and simulation approach to accurately predict RNA folding in mixed ion solutions, showing good agreement with experimental data.

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.

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.

Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA

The paper develops a TIS model for DNA that accurately reproduces experimental data on melting temperatures, ssDNA size, and persistence lengths without parameter tuning.

Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot

This study investigates how monovalent ions affect the folding pathways of an RNA pseudoknot, showing that salt concentration modulates the flux between parallel folding pathways.

Protein Collapse is Encoded in the Folded State Architecture

The paper develops a polymer physics-based theory to assess protein collapsibility using contact maps, showing that beta-sheet proteins are more collapsible than alpha-helical ones and explaining the origin of multi-domain proteins.