Particle Smoother to Assimilate Asynchronous Movie Data of High-Speed AFM with MD Simulations

End-to-end differentiable blind tip reconstruction for noisy atomic force microscopy images

(2023) Yasuhiro Matsunaga et al.   Scientific Reports

An ultrafast piezoelectric Z-scanner with a resonance frequency above 1.1 MHz for high-speed atomic force microscopy

(2022) Masahiro Shimizu et al.   REVIEW OF SCIENTIFIC INSTRUMENTS

Inferring Conformational State of Myosin Motor in an Atomic Force Microscopy Image via Flexible Fitting Molecular Simulations

(2022) Sotaro Fuchigami et al.   Frontiers in Molecular Biosciences

Faster high-speed atomic force microscopy for imaging of biomolecular processes

(2021) Shingo Fukuda et al.   REVIEW OF SCIENTIFIC INSTRUMENTS

Case Report: Bayesian Statistical Inference of Experimental Parameters via Biomolecular Simulations: Atomic Force Microscopy

(2021) Sotaro Fuchigami et al.   Frontiers in Molecular Biosciences

Localization atomic force microscopy

(2021) George R. Heath et al.   NATURE

Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy

(2021) Hiroki Koide et al.   PLoS Computational Biology

Architecture of zero-latency ultrafast amplitude detector for high-speed atomic force microscopy

(2021) Kenichi Umeda et al.   APPLIED PHYSICS LETTERS

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

(2020) Toru Niina et al.   Journal of Chemical Theory and Computation

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

(2020) Sotaro Fuchigami et al.   Journal of Chemical Theory and Computation

Structural and dynamics analysis of intrinsically disordered proteins by high-speed atomic force microscopy

(2020) Noriyuki Kodera et al.   Nature Nanotechnology

Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models

(2020) Xiaowei Wang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

High-speed atomic force microscopy

(2019) Toshio Ando   CURRENT OPINION IN CHEMICAL BIOLOGY

Advances in high-speed atomic force microscopy (HS-AFM) reveal dynamics of transmembrane channels and transporters

(2019) George R Heath et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Force-induced conformational changes in PIEZO1

(2019) Yi-Chih Lin et al.   NATURE

Applications of high-speed atomic force microscopy to real-time visualization of dynamic biomolecular processes

(2018) Takayuki Uchihashi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Markov State Models: From an Art to a Science

(2018) Brooke E. Husic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dynamic structural states of ClpB involved in its disaggregation function

(2018) Takayuki Uchihashi et al.   Nature Communications

Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning

(2018) Yasuhiro Matsunaga et al.   eLife

Direct visualization of glutamate transporter elevator mechanism by high-speed AFM

(2017) Yi Ruan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy

(2017) Mikihiro Shibata et al.   Nature Communications

Functional extension of high-speed AFM for wider biological applications

(2016) Takayuki Uchihashi et al.   ULTRAMICROSCOPY

Cofilin-induced unidirectional cooperative conformational changes in actin filaments revealed by high-speed atomic force microscopy

(2015) Kien Xuan Ngo et al.   eLife

Filming Biomolecular Processes by High-Speed Atomic Force Microscopy

(2014) Toshio Ando et al.   CHEMICAL REVIEWS

Coarse-grained modeling of DNA curvature

(2014) Gordon S. Freeman et al.   JOURNAL OF CHEMICAL PHYSICS

Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains

(2014) W. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DockAFM: benchmarking protein structures by docking under AFM topographs

(2013) Rui C. Chaves et al.   BIOINFORMATICS

Characterization of the motion of membrane proteins using high-speed atomic force microscopy

(2012) Ignacio Casuso et al.   Nature Nanotechnology

Computational Reconstruction of Multidomain Proteins Using Atomic Force Microscopy Data

(2012) Minh-Hieu Trinh et al.   STRUCTURE

Multiscale Ensemble Modeling of Intrinsically Disordered Proteins: p53 N-Terminal Domain

(2011) Tsuyoshi Terakawa et al.   BIOPHYSICAL JOURNAL

CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

(2011) Hiroo Kenzaki et al.   Journal of Chemical Theory and Computation

High-Speed Atomic Force Microscopy Reveals Rotary Catalysis of Rotorless F1-ATPase

(2011) T. Uchihashi et al.   SCIENCE

Video imaging of walking myosin V by high-speed atomic force microscopy

(2010) Noriyuki Kodera et al.   NATURE

High-speed atomic force microscopy for nano-visualization of dynamic biomolecular processes

(2008) Toshio Ando et al.   PROGRESS IN SURFACE SCIENCE