My Web Project: 3D Atom & Interactive Periodic Table

Crafting the Atom: A Deep Dive into Three.js

This was the most exciting and challenging part. How do you programmatically build an atom? I broke it down into three parts: the nucleus, the electron shells, and the electrons themselves.

The Nucleus: Protons and Neutrons

The nucleus is a cluster of protons and neutrons. Creating a single sphere in Three.js is easy. Creating up to 294 of them (for Oganesson) and arranging them in a somewhat spherical cluster without killing performance is hard. My first attempt, a simple loop creating new Mesh objects, was a disaster for performance. The solution? InstancedMesh. This powerful Three.js feature lets you render a huge number of identical objects with different positions and colors in a single draw call. I used one InstancedMesh for all the protons and another for the neutrons, dramatically improving frame rates.

The Shells and Electrons

For the electron shells, I opted for the classic Bohr model representation: simple circular orbits. I used a TorusGeometry for each shell, making them semi-transparent to maintain a clean look. The radius of each torus corresponds to the energy level of the shell.

The electrons are small spheres that need to animate along these orbital paths. This is where a little bit of trigonometry comes in handy. Inside the animation loop provided by React Three Fiber's useFrame hook, I update the position of each electron using sine and cosine functions:

useFrame((state, delta) => {
  // For each electron in its shell
  const angle = initialAngle + (speed * state.clock.elapsedTime);
  const x = orbitalRadius * Math.cos(angle);
  const z = orbitalRadius * Math.sin(angle);
  electronRef.current.position.set(x, 0, z);
});
        

By giving each electron a slightly different speed and initial angle, I could create a mesmerizing, dynamic dance that feels much more alive than any static diagram.

Overcoming Hurdles: Performance and Precision

As mentioned, performance was the biggest hurdle. Beyond using InstancedMesh, I implemented a few other optimizations:

• Geometry Sharing: All protons share a single SphereGeometry, as do all neutrons and electrons. This saves memory.
• Level of Detail (LOD): While not fully implemented yet, a future step is to simplify the model when it's viewed from a distance or on the main grid view, and only render the full, detailed atom when it's the main focus.
• Avoiding Unnecessary Re-renders: By using React.memo for UI components and carefully structuring my state, I ensured that only the necessary parts of the app re-render when the selected element changes.

Another challenge was scientific representation. The Bohr model is a simplification; in reality, electrons exist in complex probability clouds called orbitals. I made a conscious decision to stick with the Bohr model because it's more intuitive and visually clear for a general audience. I added a small disclaimer in the UI to acknowledge this, striking a balance between educational clarity and scientific accuracy.

Key Features and What I Learned

After weeks of coding, debugging, and tweaking, the project came together. The final product includes:

• A responsive, interactive periodic table with element filtering.
• A dynamic 3D viewer that constructs an atom for any selected element.
• Smooth animations for electrons orbiting the nucleus.
• A clean UI displaying essential data like atomic mass, electron configuration, and more.

This project was an incredible learning experience. My biggest takeaway was the power of declarative 3D with React Three Fiber. It completely changed my workflow for web-based 3D projects, making scene management feel as natural as building a web UI. I also gained a much deeper appreciation for performance optimization in WebGL. It’s not an afterthought; it has to be part of the design process from day one.

What's Next for This Atomic Explorer?

This project is by no means 'finished'. Science is about continuous exploration, and so is development. I have a list of features I'd love to add in the future:

• Orbital View: A mode to visualize the more accurate (and much more complex) s, p, d, and f electron orbitals.
• Isotopes: Allowing users to add or remove neutrons to see how isotopes are formed.
• Compound Builder: A far-future idea to let users combine atoms to see simple molecular structures.

Building this interactive atom viewer has been one of the most rewarding projects I've ever worked on. It's a perfect marriage of my interests in science, design, and technology. It transformed a static chart from my memory into a living, breathing digital playground. I hope it can serve as a small inspiration for how we can make learning more visual, interactive, and fun.

Feel free to check out the live project and dive into the source code on my GitHub. I'd love to hear your feedback!