Double Space

I Built My Own Cube Timer

Mon, 20 Apr 2026 01:00:00 +0000

Existing apps weren't smooth enough, so I built my own cube timer with a little help from AI.

SCA/HPCAsia: My First Time Computational Conference

Sun, 01 Feb 2026 23:00:00 +0000

Low labor cost, high performance computing, and a lot of random parameters.

Presentation List

Mon, 19 Jan 2026 00:00:00 +0000

Invited Talks

Modulation of Structure and Dynamics in Biomolecular Condensates Revealed by Large-Scale Molecular Dynamics Simulations.
The 63rd Annual Meeting of the Biophysical Society of Japan (Symposium: Towards the Elucidation of Structure of Meso-entangled Bodies through the Integration of Computational and Experimental Approaches), Nara, Japan
Thr, Sep 25, 2025

Publication List

Sun, 18 Jan 2026 00:00:00 +0000

Journal Articles

Selected Papers

GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems.
Jaewoon Jung,$^{\star}$ Cheng Tan,$^{\star}$ and Yuji Sugita.
Nature Communications 15, 1 (2024): 3370. ($\star$ co-first author)

2025 Annual Summary

Wed, 31 Dec 2025 23:00:00 +0000

A personal review of 2025, and a very slow reading progress.

Using Azure AI Services for Productivity Boosts (TTS, STT, and Translation)

Sun, 25 Aug 2024 12:00:00 +0000

Let me share some fun tools I've recently created using Azure AI. It's a good way to embrace the convenience that AI brings.

Cover Image Designs for the GENESIS 2.1 Paper

Tue, 30 Apr 2024 23:00:00 +0000

A showcase of the rejected cover image designs prepared for the GENESIS 2.1 paper.

eTechou PDF Planner has been open sourced!

Fri, 04 Mar 2022 12:00:00 +0000

I have deployed my LaTeX pdf planner (e手帳) on Github.

PDF Planner 2021 (for iPad + apple pencil)

Tue, 12 Jan 2021 12:00:00 +0000

A pdf planner (手帳 in Japanese) created with LaTeX.

COVID19 Time-Dependent Distribution in Japan

Sat, 14 Mar 2020 12:00:00 +0000

I made a gif showing the distribution of infections in Japan from Jan-16 to March-13.

Proof without words: trigonometric differentiation

Tue, 10 Mar 2020 22:00:00 +0000

This is an idea of showing all the basic trigonometric functions and their derivatives in one figure. I spent some time plotting it with TikZ.

LaTeX Typesetting Chinese Character and PinYin Box

Sun, 02 Feb 2020 02:00:00 +0000

I made a template for teaching my daughter Chinese characters.

New Year and New Document

Mon, 13 Jan 2020 23:41:00 +0000

I am writing a new document for CG models with LaTeX.

Maxima cheat sheet

Fri, 08 Mar 2019 20:38:00 +0000

Cheat sheet for Maxima 5.42 typeset with LaTeX.

CG Arts of Sox2 Binding on Nucleosome

Fri, 15 Feb 2019 16:06:00 +0000

I was asked to make some fancy pictures about our current work. So I made these...

Julia cheat sheet v1.0

Sun, 10 Feb 2019 22:22:00 +0000

Cheat sheet for Julia 1.0.3 typeset with LaTeX.

I Found Something Funny

Thu, 31 Jan 2019 21:31:00 +0000

I found a new language that can break my head.

Coarse-grained simulation of protein solvation in explicit water (fake)

Sun, 10 Jun 2018 10:10:00 +0000

Protein solvation studied with computer simulations. Details at the molecular level are revealed.

LaTeX Template for My Notes in 2018

Tue, 30 Jan 2018 12:20:00 +0000

I made a template for all my LaTeX notes in 2018.

LaTeX math cheat sheet

Tue, 25 Jul 2017 12:10:00 +0000

A simple cheat sheet for math in LaTeX produced with LaTeX.

Personal Chatting Bot for Wechat

Sun, 02 Oct 2016 11:10:00 +0000

Use wxBot to build a Chatting bot for Wechat.

First try of git-svn on CafeMol

Thu, 15 Sep 2016 20:25:00 +0000

An example of using git-svn for CafeMol.

Typesetting Lyrics of Japanese/Chinese Songs with LuaTeX

Tue, 02 Aug 2016 11:17:00 +0000

A simple example of typesetting Japanese Lyrics with translations.

A Short Example of Using Ledger with Emacs Org-mode

Thu, 28 Jul 2016 12:19:00 +0000

Use ledger in Emacs as personal bookkeeping.

About

Thu, 28 Jul 2016 00:00:00 +0000

I joined the Computational Biophysics Research Team at RIKEN Center for Computational Science in May 2019, where I currently work. One of my primary responsibilities is to develop code for molecular dynamics software GENESIS (and CafeMol in my last job). My research interests in computational biophysics are:

Install Dokuwiki + apache2 + php on macOS

Sat, 23 Jul 2016 16:41:00 +0000

Notes of installing Dokuwiki + apache2 + php.

Vocabulary Builder Employing StarDict Dictionaries

Fri, 20 May 2016 15:01:00 +0000

A stupid dictionary writen in python with regexp supporting.

Deploying Pelican Blogs on VPS with Git

Tue, 26 Apr 2016 18:05:00 +0000

Build simple blogs with pelican on VPS with git.

Jupyter/IPython Notebook Theme and Chinese Fonts

Sun, 25 Oct 2015 10:10:00 +0000

A theme for Jupyter Notebook, including Chinese font settings.

Local Network IRC Server + Web IRC Client + IRC Bot

Sat, 10 Oct 2015 10:10:00 +0000

One simple way to build local IRC chatting server.

Chinese 12-Year-Cycle Animals as Org-mode Heading Icons

Sun, 27 Sep 2015 20:00:00 +0000

Use emoji for Emacs Org-mode heading icons.

Pocket Cube: Corners of the Last Layer

Sun, 16 Aug 2015 17:15:00 +0000

CLL algorithms for Pocket Cube.

Rubik's Cube: Orientation of the Last Layer

Sat, 15 Aug 2015 22:22:00 +0000

OLL algorithms for Rubik's cube.

Diagram of Nucleic Acids

Mon, 03 Aug 2015 10:01:00 +0000

A chart of basic nucleic acids.

Chart of Amino Acids

Thu, 30 Jul 2015 20:01:00 +0000

A table of amino acids.

A LaTeX Note Template

Wed, 19 Nov 2014 17:26:00 +0000

A simple template for notes taken with LaTeX.