particles/protein-folding.html at main · danlex/particles · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
<!DOCTYPE html>
<html lang="en">
<head>
  <meta charset="UTF-8">
  <meta name="viewport" content="width=device-width, initial-scale=1.0">
  <title>Protein Folding — Particles</title>
  <meta name="description" content="A protein chain folds from a straight backbone into alpha helices and beta sheets, then relaxes and refolds.">
  <meta name="author" content="Alexandru DAN">
  <meta name="theme-color" content="#050505">
  <link rel="canonical" href="https://particles.alexandrudan.com/protein-folding.html">
  <link rel="icon" type="image/svg+xml" href="favicon.svg">

  <!-- Open Graph -->
  <meta property="og:type" content="website">
  <meta property="og:url" content="https://particles.alexandrudan.com/protein-folding.html">
  <meta property="og:title" content="Protein Folding — Particles">
  <meta property="og:description" content="A protein chain folds from a straight backbone into alpha helices and beta sheets, then relaxes and refolds.">
  <meta property="og:image" content="https://particles.alexandrudan.com/og-image.svg">
  <meta property="og:site_name" content="Particles">

  <!-- Twitter -->
  <meta name="twitter:card" content="summary_large_image">
  <meta name="twitter:title" content="Protein Folding — Particles">
  <meta name="twitter:description" content="A protein chain folds from a straight backbone into alpha helices and beta sheets, then relaxes and refolds.">
  <meta name="twitter:image" content="https://particles.alexandrudan.com/og-image.svg">
  <style>
    * { margin: 0; padding: 0; box-sizing: border-box; }
    body { background: #000; overflow: hidden; font-family: 'Courier New', monospace; }
    canvas { display: block; }
    #controls {
      position: fixed;
      bottom: 24px;
      left: 50%;
      transform: translateX(-50%);
      display: flex;
      gap: 20px;
      background: rgba(0,0,0,0.6);
      backdrop-filter: blur(12px);
      border: 1px solid rgba(255,255,255,0.08);
      border-radius: 12px;
      padding: 14px 28px;
      z-index: 10;
      align-items: center;
    }
    .ctrl-group {
      display: flex; flex-direction: column; align-items: center; gap: 4px;
    }
    .ctrl-group label {
      color: rgba(255,255,255,0.4); font-size: 9px;
      text-transform: uppercase; letter-spacing: 1.5px;
    }
    .ctrl-group input[type="range"] {
      -webkit-appearance: none; width: 100px; height: 3px;
      background: rgba(255,255,255,0.15); border-radius: 2px; outline: none;
    }
    .ctrl-group input[type="range"]::-webkit-slider-thumb {
      -webkit-appearance: none; width: 12px; height: 12px;
      border-radius: 50%; background: #fff; cursor: pointer;
    }
    #info {
      position: fixed; top: 24px; left: 28px; z-index: 10;
    }
    #info h1 {
      color: rgba(255,255,255,0.7); font-size: 14px; font-weight: 400;
      letter-spacing: 3px; text-transform: uppercase;
    }
    #info p {
      color: rgba(255,255,255,0.25); font-size: 10px;
      margin-top: 6px; letter-spacing: 1px;
    }
    #fps {
      position: fixed; top: 24px; right: 28px;
      color: rgba(255,255,255,0.2); font-size: 10px;
      letter-spacing: 1px; z-index: 10;
    }
    #back {
      position: fixed; top: 24px; left: 50%; transform: translateX(-50%);
      z-index: 10;
    }
    #back a {
      color: rgba(255,255,255,0.2); font-size: 9px; text-decoration: none;
      letter-spacing: 2px; text-transform: uppercase;
      transition: color 0.3s;
    }
    #back a:hover { color: rgba(255,255,255,0.5); }
      .zoom-btn {
      width: 32px; height: 32px; border-radius: 50%;
      background: rgba(255,255,255,0.06); border: 1px solid rgba(255,255,255,0.12);
      color: rgba(255,255,255,0.5); font-size: 18px; cursor: pointer;
      display: flex; align-items: center; justify-content: center;
      transition: background 0.2s;
      font-family: monospace;
    }
    .zoom-btn:hover { background: rgba(255,255,255,0.12); }
  </style>
</head>
<body>
  <div id="info">
    <h1>Protein Folding</h1>
    <p id="particle-count"></p>
  </div>
  <div id="fps"></div>
  <div id="back"><a href="index.html">Gallery</a></div>
  <div id="controls">
    <div class="ctrl-group">
      <input type="range" id="speed" min="0.1" max="5" step="0.1" value="1">
      <label>Speed</label>
    </div>
    <div class="ctrl-group">
      <input type="range" id="bloom" min="0" max="3" step="0.1" value="0.4">
      <label>Bloom</label>
    </div>
    <div class="ctrl-group">
      <input type="range" id="size" min="0.5" max="4" step="0.1" value="1.0">
      <label>Size</label>
    </div>
    <div class="ctrl-group">
      <input type="range" id="hueShift" min="0" max="1" step="0.01" value="0">
      <label>Hue</label>
    </div>
    <button class="zoom-btn" id="zoomOut">−</button>
    <button class="zoom-btn" id="zoomIn">+</button>
  </div>

  <script type="importmap">
  {
    "imports": {
      "three": "https://cdn.jsdelivr.net/npm/three@0.160.0/build/three.module.js",
      "three/addons/": "https://cdn.jsdelivr.net/npm/three@0.160.0/examples/jsm/"
    }
  }
  </script>
  <script type="module">
    import * as THREE from 'three';
    import { OrbitControls } from 'three/addons/controls/OrbitControls.js';
    import { EffectComposer } from 'three/addons/postprocessing/EffectComposer.js';
    import { RenderPass } from 'three/addons/postprocessing/RenderPass.js';
    import { UnrealBloomPass } from 'three/addons/postprocessing/UnrealBloomPass.js';
    import { GPUComputationRenderer } from 'three/addons/misc/GPUComputationRenderer.js';

    const WIDTH = 256;
    const PARTICLE_COUNT = WIDTH * WIDTH;

    // Scene
    const scene = new THREE.Scene();
    const camera = new THREE.PerspectiveCamera(60, innerWidth / innerHeight, 0.1, 2000);
    camera.position.set(0, 2, 20);

    const renderer = new THREE.WebGLRenderer({ antialias: false, powerPreference: 'high-performance' });
    renderer.setSize(innerWidth, innerHeight);
    renderer.setPixelRatio(1);
    document.body.appendChild(renderer.domElement);

    const orbitControls = new OrbitControls(camera, renderer.domElement);
    orbitControls.enableDamping = true;
    orbitControls.dampingFactor = 0.05;
    orbitControls.autoRotate = true;
    orbitControls.autoRotateSpeed = 0.5;

    // Post-processing
    const composer = new EffectComposer(renderer);
    composer.addPass(new RenderPass(scene, camera));
    const bloomPass = new UnrealBloomPass(
      new THREE.Vector2(innerWidth / 2, innerHeight / 2),
      0.4, 0.3, 0.85
    );
    composer.addPass(bloomPass);

    // GPU Computation
    const gpuCompute = new GPUComputationRenderer(WIDTH, WIDTH, renderer);
    const posTex0 = gpuCompute.createTexture();

    function seedTexture(tex) {
      const data = tex.image.data;
      for (let i = 0; i < PARTICLE_COUNT; i++) {
        const idx = i * 4;
        const along = i / PARTICLE_COUNT;
        // Start as a straight line
        data[idx]     = (along - 0.5) * 16.0;
        data[idx + 1] = 0;
        data[idx + 2] = 0;
        data[idx + 3] = along;
      }
    }

    seedTexture(posTex0);

    const positionShader = `
      uniform vec3 uMouse;
      uniform float uMouseActive;
      uniform float uDt;
      uniform float uSpeed;
      uniform float uFrame;
      uniform float uTime;

      #define PI 3.14159265359

      float hash(vec2 p) {
        vec3 p3 = fract(vec3(p.xyx) * 0.1031);
        p3 += dot(p3, p3.yzx + 33.33);
        return fract((p3.x + p3.y) * p3.z);
      }

      void main() {
        vec2 uv = gl_FragCoord.xy / resolution.xy;
        float idx = gl_FragCoord.y * resolution.x + gl_FragCoord.x;
        float total = resolution.x * resolution.y;

        float t = uTime * uSpeed;

        // Chain position (0 to 1 along the protein backbone)
        float along = idx / total;

        // Folding progress cycles
        float foldPhase = smoothstep(0.0, 0.6, fract(t * 0.08));
        float unfoldPhase = smoothstep(0.7, 1.0, fract(t * 0.08));
        float fold = foldPhase * (1.0 - unfoldPhase);

        // Unfolded: straight line
        float lineX = (along - 0.5) * 16.0;
        float lineY = 0.0;
        float lineZ = 0.0;

        // Folded: compact 3D structure
        // Alpha helix regions
        float helixFreq = 12.0;
        float helixR = 1.5;
        float helixPitch = 0.8;
        float helixAngle = along * helixFreq * 2.0 * PI;

        // Different secondary structures along the chain
        float region = floor(along * 5.0); // 5 structural regions
        float localAlong = fract(along * 5.0);
        float regionHash = hash(vec2(region, 0.0));

        float foldX, foldY, foldZ;

        if (regionHash < 0.5) {
          // Alpha helix
          foldX = helixR * cos(helixAngle);
          foldY = along * helixPitch * 10.0 - 4.0;
          foldZ = helixR * sin(helixAngle);
          // Offset each helix region
          foldX += (region - 2.0) * 3.0;
          foldZ += sin(region * 1.5) * 2.0;
        } else {
          // Beta sheet (flat zigzag)
          foldX = (localAlong - 0.5) * 4.0 + (region - 2.0) * 2.0;
          foldY = sin(localAlong * 8.0 * PI) * 0.5 + (region - 2.0) * 1.5;
          foldZ = (region - 2.0) * 2.5;
        }

        // Compact the folded form
        foldX *= 0.8; foldY *= 0.8; foldZ *= 0.8;

        // Interpolate between unfolded and folded
        float x = mix(lineX, foldX, fold);
        float y = mix(lineY, foldY, fold);
        float z = mix(lineZ, foldZ, fold);

        // Slight thickness (not a 1D line)
        float spread = 0.15;
        x += (hash(vec2(idx, 1.0)) - 0.5) * spread;
        y += (hash(vec2(idx, 2.0)) - 0.5) * spread;
        z += (hash(vec2(idx, 3.0)) - 0.5) * spread;

        // Mouse attraction
        if (uMouseActive > 0.01) {
          vec3 toMouse = uMouse - vec3(x, y, z);
          float mouseDist = length(toMouse);
          float mouseForce = uMouseActive * 0.3 / (mouseDist * mouseDist + 1.0);
          x += toMouse.x * mouseForce * uDt;
          y += toMouse.y * mouseForce * uDt;
          z += toMouse.z * mouseForce * uDt;
        }

        gl_FragColor = vec4(x, y, z, along);
      }
    `;

    const posVar = gpuCompute.addVariable('texturePosition', positionShader, posTex0);
    gpuCompute.setVariableDependencies(posVar, [posVar]);

    posVar.material.uniforms.uDt = { value: 0.03 };
    posVar.material.uniforms.uSpeed = { value: 1.0 };
    posVar.material.uniforms.uFrame = { value: 0.0 };
    posVar.material.uniforms.uTime = { value: 0.0 };
    posVar.material.uniforms.uMouse = { value: new THREE.Vector3(0, 0, -1000) };
    posVar.material.uniforms.uMouseActive = { value: 0.0 };

    posVar.wrapS = THREE.RepeatWrapping;
    posVar.wrapT = THREE.RepeatWrapping;

    const err = gpuCompute.init();
    if (err !== null) console.error('GPU Computation init error:', err);

    // Particle Rendering
    const vertexShader = `
      uniform sampler2D uPositionTexture;
      uniform float uHueShift;
      uniform float uPointSize;
      uniform float uScale;
      uniform float uFold;
      attribute vec2 aTexCoord;
      varying vec3 vColor;

      vec3 hsl2rgb(float h, float s, float l) {
        float c = (1.0 - abs(2.0 * l - 1.0)) * s;
        float h6 = h * 6.0;
        float x = c * (1.0 - abs(mod(h6, 2.0) - 1.0));
        float m = l - c * 0.5;
        vec3 rgb;
        if (h6 < 1.0) rgb = vec3(c, x, 0.0);
        else if (h6 < 2.0) rgb = vec3(x, c, 0.0);
        else if (h6 < 3.0) rgb = vec3(0.0, c, x);
        else if (h6 < 4.0) rgb = vec3(0.0, x, c);
        else if (h6 < 5.0) rgb = vec3(x, 0.0, c);
        else rgb = vec3(c, 0.0, x);
        return rgb + m;
      }

      void main() {
        vec4 posData = texture2D(uPositionTexture, aTexCoord);
        vec3 pos = posData.xyz * uScale;
        float along = posData.w;

        // Color: position along chain -> rainbow (N-terminus to C-terminus)
        float hue = fract(along + uHueShift);
        float saturation = 0.6 + uFold * 0.2;
        float lightness = 0.12 + uFold * 0.15;

        vColor = hsl2rgb(hue, saturation, lightness);

        vec4 mvPosition = modelViewMatrix * vec4(pos, 1.0);
        gl_PointSize = uPointSize * (55.0 / -mvPosition.z);
        gl_PointSize = max(gl_PointSize, 0.3);
        gl_Position = projectionMatrix * mvPosition;
      }
    `;

    const fragmentShader = `
      varying vec3 vColor;
      void main() {
        float d = length(gl_PointCoord - 0.5) * 2.0;
        if (d > 1.0) discard;
        // Soft gaussian falloff with bright core
        float glow = exp(-d * d * 3.0);
        float core = exp(-d * d * 12.0);
        float alpha = (glow * 0.15 + core * 0.3);
        // Slight color boost at core (hotter center)
        vec3 col = vColor + core * 0.15;
        gl_FragColor = vec4(col, alpha);
      }
    `;

    const geometry = new THREE.BufferGeometry();
    const texCoords = new Float32Array(PARTICLE_COUNT * 2);
    for (let j = 0; j < WIDTH; j++) {
      for (let i = 0; i < WIDTH; i++) {
        const idx = (j * WIDTH + i) * 2;
        texCoords[idx]     = (i + 0.5) / WIDTH;
        texCoords[idx + 1] = (j + 0.5) / WIDTH;
      }
    }
    const dummyPositions = new Float32Array(PARTICLE_COUNT * 3);
    geometry.setAttribute('position', new THREE.BufferAttribute(dummyPositions, 3));
    geometry.setAttribute('aTexCoord', new THREE.BufferAttribute(texCoords, 2));

    const material = new THREE.ShaderMaterial({
      vertexShader,
      fragmentShader,
      uniforms: {
        uPositionTexture: { value: null },
        uHueShift: { value: 0.0 },
        uPointSize: { value: 1.0 },
        uScale: { value: 1.2 },
        uFold: { value: 0.0 },
      },
      transparent: true,
      blending: THREE.AdditiveBlending,
      depthWrite: false,
    });

    const points = new THREE.Points(geometry, material);
    const pivot = new THREE.Group(); pivot.add(points); scene.add(pivot);

    // UI
    document.getElementById('particle-count').textContent =
      `${PARTICLE_COUNT.toLocaleString()} particles — fully GPU computed`;

    const speedSlider = document.getElementById('speed');
    const bloomSlider = document.getElementById('bloom');
    const sizeSlider = document.getElementById('size');
    const hueSlider = document.getElementById('hueShift');
    const fpsEl = document.getElementById('fps');

    document.getElementById('zoomIn').addEventListener('click', () => {
      material.uniforms.uScale.value *= 1.15;
    });
    document.getElementById('zoomOut').addEventListener('click', () => {
      material.uniforms.uScale.value *= 0.85;
    });

    // Mouse interaction
    const mouse = new THREE.Vector2();
    const mouse3D = new THREE.Vector3();
    const raycaster = new THREE.Raycaster();
    let mouseActive = false;

    renderer.domElement.addEventListener('mousemove', (e) => {
      mouse.x = (e.clientX / innerWidth) * 2 - 1;
      mouse.y = -(e.clientY / innerHeight) * 2 + 1;
      mouseActive = true;
      raycaster.setFromCamera(mouse, camera);
      mouse3D.copy(raycaster.ray.direction).multiplyScalar(15).add(camera.position);
    });
    renderer.domElement.addEventListener('mouseleave', () => { mouseActive = false; });

    // Animation Loop
    let lastTime = performance.now();
    let frameCount = 0;

    function animate(now) {
      requestAnimationFrame(animate);

      frameCount++;
      if (now - lastTime >= 1000) {
        fpsEl.textContent = `${frameCount} FPS`;
        frameCount = 0;
        lastTime = now;
      }

      const speed = parseFloat(speedSlider.value);
      posVar.material.uniforms.uSpeed.value = speed;
      posVar.material.uniforms.uFrame.value += 1.0;
      posVar.material.uniforms.uTime.value += 0.016 * speed;
      bloomPass.strength = parseFloat(bloomSlider.value);
      material.uniforms.uHueShift.value = parseFloat(hueSlider.value);
      material.uniforms.uPointSize.value = parseFloat(sizeSlider.value);

      // Compute fold state for vertex shader saturation/lightness
      const t = posVar.material.uniforms.uTime.value * speed;
      const foldPhase = Math.min(Math.max((t * 0.08 % 1) / 0.6, 0), 1);
      const unfoldPhase = Math.min(Math.max(((t * 0.08 % 1) - 0.7) / 0.3, 0), 1);
      material.uniforms.uFold.value = foldPhase * (1 - unfoldPhase);

      // Update mouse uniforms
      if (mouseActive) {
        posVar.material.uniforms.uMouse.value.copy(mouse3D);
        posVar.material.uniforms.uMouseActive.value = 1.0;
      } else {
        posVar.material.uniforms.uMouseActive.value *= 0.95;
      }

      gpuCompute.compute();

      material.uniforms.uPositionTexture.value =
        gpuCompute.getCurrentRenderTarget(posVar).texture;

      pivot.rotation.x += 0.0008;
      orbitControls.update();
      composer.render();
    }

    animate(performance.now());

    // Resize
    window.addEventListener('resize', () => {
      camera.aspect = innerWidth / innerHeight;
      camera.updateProjectionMatrix();
      renderer.setSize(innerWidth, innerHeight);
      composer.setSize(innerWidth, innerHeight);
    });
  </script>
<script src="shared-ui.js"></script>
</body>
</html>