T. Niina

The stoichiometric interaction model for mesoscopic molecular dynamics simulations of liquid-liquid phase separation

This paper introduces a new potential, the stoichiometric interaction potential, to improve mesoscopic simulations of liquid-liquid phase separation in multidomain proteins, achieving quantitative agreement with experimental data.

F0-F1 coupling and symmetry mismatch in ATP synthase resolved in every F0 rotation step

The paper uses molecular dynamics simulations and cryo-EM structures to analyze symmetry mismatch in ATP synthase during each rotation step, revealing mechanical couplings and structural adaptations.

Cooperation among c-subunits of FoF1-ATP synthase in rotation-coupled proton translocation

The paper investigates cooperation among c-subunits in FoF1-ATP synthase by analyzing ATP synthesis and proton pump activities with mutated cE56D subunits, showing decreased activity with increasing mutation separation.

Rigid-Body Fitting to Atomic Force Microscopy Images for Inferring Probe Shape and Biomolecular Structure

This paper develops a method to infer AFM probe shape and molecular structure from images by rigid-body fitting, showing that similarity scores vary depending on the target molecule.

The Particle Filter Method to Integrate High-Speed Atomic Force Microscopy Measurement with Biomolecular Simulations

The paper develops a particle filter method to integrate HS-AFM data with coarse-grained MD simulations, showing that more particles improve likelihood and enabling inference of true conditions from AFM movies.

Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations

This paper introduces a method to flexibly fit biomolecular structures to AFM images using biased molecular simulations, demonstrating its effectiveness with synthetic and real data.

Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motor

The paper uses molecular dynamics simulations to study proton-transfer coupled rotations in yeast mitochondrial ATP synthase FO motor, finding 36-degree steps per proton transfer and high efficiency.

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations

This study uses molecular simulations to show that nucleosome sliding depends on DNA sequence, with strong positioning sequences sliding in large jumps and uniform sequences sliding in a rotation-coupled manner.