v0.2.0: motion from physics + channelrhodopsin version 3

Motion from physics. Molecules now move as molecules, on one clock per film, at rates from the literature. Per-atom noise is gone.

Framework

• molanim.dynamics (new, tested) covers:
  • the film clock;
  • exposure-averaged Ornstein–Uhlenbeck processes with a box or triangle shutter;
  • Stokes–Einstein, Stokes–Einstein–Debye and Perrin diffusion;
  • tethered rigid-body Brownian motion;
  • anisotropic-network normal modes and side-chain χ turns;
  • worm-like-chain DNA bending and twist;
  • protein_motion, the whole recipe for any structure;
  • periodic processes, so loops close exactly.
• New geometry-node groups: dynamics, lipid_motion and chain_motion. Label passes can draw links between anchors, solid or dashed, with optional text.
• docs/motion.md is the motion schematic. Each row gives a physical value, its source, and how a film shows it.
• The project template now uses protein_motion on a 1 ns/s clock. It states the clock on screen and reports RMSF, bond strain and the loop seam in RESULT.
• pipeline.py preview --frames A-B renders a consecutive run of frames. pipeline.py motion warns on stepped previews, which cannot show a jerk that lasts one frame.

Case study. Channelrhodopsin version 3, "The twist that opens a pathway", 21 s, 1920×1080, 24 fps.

• 1 s of film = 1 ns.
• The protein moves in elastic-network normal modes, and side chains turn about their bonds.
• Lipids spin, wobble and flow as molecules, and Na⁺ diffuses.
• Against version 2's per-atom noise, the median bond stretch inside lipids fell from 0.62 to 0.04 Å.

Asset	Contents
channelrhodopsin-delivery.zip	Labelled and clean films (MP4 H.264 + WebM VP9) and three posters. Restore with python pipeline.py fetch channelrhodopsin
channelrhodopsin.mp4	The labelled film, for direct viewing

Reproducibility. python pipeline.py check channelrhodopsin renders frame 70 and matches the delivered poster: mean difference 0.000, max 1/255. Version 1 stays in release v0.1.0.

v0.1.0: framework + channelrhodopsin case study

First public release of the Molecular Animation framework.

Framework. molanim (pure-numpy science + Blender 5.2 helpers), pipeline.py (new, build, still, preview, render, deliver, motion, check, ...), a project template that turns any PDB entry into a studio shot, docs (workflow, principles, framework API, setup), tests and CI.

Case study. Channelrhodopsin C1C2, "The twist that opens a pathway", made from a brief for the 2026 Nobel Prize in Physiology or Medicine. A 21 s narrative, 1920×1080, 24 fps, built from PDB 9GO1/9GO2 with evidence levels on screen.

Asset	Contents
channelrhodopsin-delivery.zip	Labelled and clean films (MP4 H.264 + WebM VP9) and three posters. Restore with python pipeline.py fetch channelrhodopsin
channelrhodopsin.mp4	The labelled film, for direct viewing

Reproducibility: the case study rebuilds from its script. python pipeline.py check channelrhodopsin renders frame 70 and matches the delivered poster within 1/255.