On-going research

notebooks (private) Experimetal notebooks for on-going studies

MDToolbox.jl A Julia package for molecular dynamics trajectories analysis and modeling of biomolecules

differentiable test-bed for differeitiable physical parameter optimization

afm (private) AFM data (inc. Myosin-V) and some analysis codes

t1r (private) Taste receptor studies

vhh (private) VHH (nanobody) studies

fugaku (private) Files used on Fugaku supercomputer

capsid Virus capsid studies

fret (private) FRET data analysis and integrative modeling

Tutorials and lectures

tutorial on analyzing MD data Tutorial on analyzing MD data

tutorial on hidden Markov modeling Tutorial on hidden Markov modeling

lecture on Machine Learning with Python Notebooks used in the lecture on machine learning

lecture on Machine Learning with Julia Old notebooks used in the lecture on machine learning

lecture on Operations Research Notebooks used in the lecture on operations research

lecture on Ordinary Differential Equations Notebooks used in ODE lecture

Papers

differentiable blind tip reconstruction Differentiable BTR for AFM images

paper_mbar MBAR

paper_ogane2022 HMM of HS-AFM data

paper_higashida2021 gREST of VHH