Polymer AR Lab

Draw a molecule on paper, and watch it pop into 3-D — even in augmented reality on your desk. You can also look up real molecules, snap them together into long polymer chains, and save a file that lets scientists' software "relax" the shape. It all runs in your web browser on a phone or a computer — nothing to download.

For education only: Polymer AR Lab is a teaching demonstration. Molecular recognition, generated structures, UFF-style parameters, and simulation schedules are approximate. The app is not validated for production engineering, safety decisions, or research conclusions.

▶️ Open it here

• App: https://kenichinomura.github.io/PolymerARLab/
• Illustrated guide: https://kenichinomura.github.io/PolymerARLab/tutorial.html

📱 On a phone, you scan drawings with the camera. 🖥️ On a computer, you upload a photo instead. Both work the same after that.

---

What can it do?

1. 📷 Scan a hand-drawn Lewis structure — take a photo of your drawing and get a 3-D molecule.
2. 🧬 Build a polymer chain — take one small molecule and repeat it into a long chain.
3. 🔎 Load real molecules — type a name like caffeine, a PubChem CID, or a SMILES string such as CC(=O)O.
4. 💾 Save a science file — export a file that the simulation program LAMMPS can open to tidy up the shape.
5. 🥽 Augmented reality — stand the molecule up on your real desk through the camera.

---

The buttons

• Camera — turns on the camera to scan a drawing. Once it's on, tap the frame on the screen to take the picture (drag the frame's edges to make it bigger or smaller, drag the middle to move it).
• Reset view — recenters the molecule if it drifts off screen.
• Clear — removes the molecule so you can start over.
• AR View — (on iPhone/iPad) places the molecule in the real world.
• Edit ✏️ — opens the molecule panel (load PubChem/SMILES, upload a sketch, toggle labels).
• Polymer 🔗 — opens the polymer builder (choose a curing mechanism, load monomers, grow a chain).
• Status ⓘ — shows how many atoms and bonds the molecule has.
• Tutorial 📖 — opens the picture guide.
• Save ⬇ — downloads the LAMMPS files for the current structure.

---

Guide 1 — Scan a drawing and see it in AR

1. Draw a molecule on paper — clear lines and letters work best (try water, CO₂, or ethanol).
2. Take the picture.
   • 📱 Phone: tap Camera, line the drawing up inside the on-screen frame, then tap the frame.
   • 🖥️ Computer: tap Edit → Upload sketch and pick a photo.
   • A flash and a spinning "Recognizing…" circle appear, then your 3-D molecule shows up.
3. Look around — drag to spin it, scroll or pinch to zoom. In Edit you can turn on Atom labels (C1, C2, …) and Show hydrogens.
4. See it in AR — put the molecule on your real desk:
   • 📱 iPhone/iPad: tap the AR View button, wait until it glows, tap again, then point at your paper.
   • 🤖 Android: tap START AR (top-right), point at your desk, and tap the screen — the molecule appears on that spot.

(AR needs a back camera and a secure page. If your device can't do AR, you can still spin the molecule in 3-D.)

---

Guide 2 — Build a polymer and save it for LAMMPS

1. Open the polymer builder. Tap the Polymer 🔗 icon and choose Addition cure or Condensation cure. Edit and Polymer cannot be open together; changing panels clears the previous working scene.
2. Choose the input source. Tap the database icon for a PubChem name/CID or the smile icon for SMILES, enter the molecule, and press Load. PubChem is selected by default. SMILES is case-sensitive: uppercase C is aliphatic carbon and lowercase c is aromatic carbon.
3. Try isoprene 1,4-addition. In SMILES mode, load C=C(C=C)C (an ordering that keeps the diene backbone labelled C1–C4), select terminal atoms C1 and C4, and choose Cis or Trans. The two original double bonds become single bonds and a new C2=C3 double bond remains: C1=C2–C3=C4 → –C1–C2=C3–C4–.
4. Press Make repeat unit, then drag the Repeats slider. If you change Cis/Trans after building, the app returns to the monomer; press Make repeat unit again to build the newly selected geometry.

Cis and trans polyisoprene: cis-1,4-polyisoprene models natural rubber, while trans-1,4-polyisoprene models gutta-percha. The cis chain generally crystallizes less readily when unstretched; the trans chain packs and crystallizes more readily. Natural rubber can still crystallize under strain or suitable low-temperature conditions, so it is not correct to say that cis-polyisoprene never crystallizes.

Condensation polymers: the app uses a simplified teaching model in which forming a new bond releases H₂O from a carboxylic acid or HCl from an acyl chloride. To try it:

1. In the polymer builder, choose Condensation cure and load a monomer with the right ends, e.g. lactic acid.
2. The app suggests the −COOH carbon and the −OH oxygen as anchors (you can re-pick them; a wrong pick shows an error explaining what can react).
3. Press Make repeat unit — the chain forms and little byproduct molecules float away. They are a teaching visual and are excluded from AR and LAMMPS exports.
4. For PET, load ethylene glycol into slot A and pick its two alcohol oxygens. Load terephthalic acid into slot B and pick its two carboxyl carbons. The new ester bonds form between those oxygens and carbons. In the simplified net reaction, the alcohol oxygen remains in the ester linkage; the acid −OH and alcohol H form water. Industrial PET production is more involved: initial direct esterification forms water, while later melt polycondensation commonly removes ethylene glycol.
5. Press the Save LAMMPS (UFF) download icon in the bottom-left dock. It downloads two files: <name>.data (the molecule) and in.relax (the instructions).
6. If you use LAMMPS, run lmp -in in.relax. It performs overlap relief, FIRE minimization, and 10 ps of NVT at 300 K, then saves one XYZ trajectory (.xyz) and the final shape (.relaxed.data). This short, finite-chain vacuum run demonstrates geometry relaxation; it cannot establish bulk crystallinity or research-quality material properties.

💡 Keep Show hydrogens turned on before you save, so the file has every atom.

---

Tips

• Draw clearly with good lighting — the scanner is making its best guess. Tap the Status ⓘ button to see what it found, and redraw if it looks wrong.
• Reset view just recenters the camera; Clear removes the molecule completely.
• Some molecules use elements the app doesn't support — if a lookup fails, try a simpler molecule.

---

Are you a teacher or developer who wants to run, host, or change the app? See the Developer guide.