Y. Matsunaga

Representation of Protein Dynamics Disentangled by Time-structure-based Prior

The paper introduces two methods with a time-structure-based prior to disentangle protein dynamics from MD simulations, improving the representation of conformational transitions.

End-to-End Differentiable Blind Tip Reconstruction for Noisy Atomic Force Microscopy Images

This paper introduces an end-to-end differentiable method for blind tip reconstruction in AFM images, showing robustness to noise and accurate surface geometry reconstruction.

Hidden Markov Modeling of Molecular Orientations and Structures from High-Speed Atomic Force Microscopy Time-Series Images

This paper introduces a hidden Markov model to estimate molecular orientations from HS-AFM time-series data, showing improved robustness compared to frame-by-frame analysis.

Conformational changes in twitchin kinase in vivo revealed by FRET imaging of freely moving C. elegans

This study uses FRET imaging in C. elegans to show stretch-induced conformational changes in twitchin kinase during muscle activity.

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.

Energetics and Conformational Pathways of Functional Rotation in the Multidrug Transporter AcrB

This study calculates the minimum free energy pathway of functional rotation in AcrB, linking it to proton translocation and drug transport at the atomic level.