Opening the lab notebook

For six years most of my thinking lived in places no one else could see: slide decks, half-finished Jupyter notebooks, and margins of printed papers. This notebook is an attempt to move some of it into the open.

What to expect

• Short daily notes. A plot that surprised me, a parameter that mattered, a paper worth reading. Some are three paragraphs long.
• Explainers. Longer pieces on methods I use all the time: Kirkwood–Buff theory, umbrella sampling, polarizable metal models, attention-based networks for materials.
• Behind the papers. The reasoning and dead ends that don’t fit in a methods section.
• Tool notes. Release notes and recipes for the software I build.

Why bother

Two reasons. Writing is the fastest way I know to find out whether I actually understand something. And most of what makes simulation work, like which force field to trust, how long to equilibrate, or why a free-energy profile looks wrong, is rarely written down anywhere useful.

If something here is wrong, or useful, I’d like to hear about it.