S. Fuchigami

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.

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.