https://github.com/elkins/synth-afm
Differentiable High-Speed AFM (HS-AFM) simulation for protein structures. JAX-powered toolkit for generating synthetic movies with realistic tip-dilation and scanning lag.
https://github.com/elkins/synth-afm
afm-analysis biophysics computational-biology differentiable-physics high-speed-afm hs-afm jax protein-dynamics simulation structural-biology
Last synced: 2 days ago
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Differentiable High-Speed AFM (HS-AFM) simulation for protein structures. JAX-powered toolkit for generating synthetic movies with realistic tip-dilation and scanning lag.
- Host: GitHub
- URL: https://github.com/elkins/synth-afm
- Owner: elkins
- Created: 2026-05-28T02:05:20.000Z (7 days ago)
- Default Branch: master
- Last Pushed: 2026-05-28T02:32:02.000Z (7 days ago)
- Last Synced: 2026-05-28T04:07:56.010Z (7 days ago)
- Topics: afm-analysis, biophysics, computational-biology, differentiable-physics, high-speed-afm, hs-afm, jax, protein-dynamics, simulation, structural-biology
- Language: Python
- Homepage: https://elkins.github.io/synth-afm/
- Size: 38.1 KB
- Stars: 1
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
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README
# 🧬 synth-afm: Differentiable HS-AFM Simulation
[](https://github.com/elkins/synth-afm)
[](https://github.com/elkins/synth-afm)
[](https://github.com/elkins/synth-afm/actions/workflows/test.yml)
[](https://github.com/elkins/synth-afm)
[](https://opensource.org/licenses/MIT)
[](https://github.com/google/jax)
[](https://github.com/psf/black)
`synth-afm` is a JAX-powered toolkit for generating synthetic High-Speed Atomic Force Microscopy (HS-AFM) images and movies from atomistic protein structures.
Built with the **differentiable biophysics** philosophy, every step—from coordinate rotation to tip-collision height mapping—is end-to-end differentiable.
---
### 🧪 For Structural Biologists
HS-AFM provides a unique look at "proteins at work," but interpreting noisy movies is challenging. `synth-afm` helps you bridge the resolution gap:
* **Realistic Tip Physics:** Uses a spherical-tip dilation model to account for the broadening effect of the AFM probe.
* **Atomic Rigor:** Automatically assigns van der Waals radii based on element (Bondi, 1964) for accurate topography.
* **Temporal Distortion:** Models **Scanning Lag**, simulating how protein dynamics during a scan cause the "shear" artifacts seen in real HS-AFM movies.
* **Force Maps:** Go beyond height-maps with experimental support for tip-sample repulsion (deflection) modeling.
### 🤖 For Machine Learning Geeks
`synth-afm` treats the entire AFM scanning process as a differentiable operator $\mathcal{H}: \mathbb{R}^{N \times 3} \rightarrow \mathbb{R}^{H \times W}$:
* **End-to-End Differentiable:** Built entirely in JAX, allowing you to flow gradients from an experimental AFM image $\mathbf{I}_{exp}$ back to atomic coordinates $\mathbf{X}$.
* **Flexible Fitting:** Enable gradient-based optimization of molecular structures using experimental AFM data as a loss term: $\mathcal{L} = \|\mathcal{H}(\mathbf{X}) - \mathbf{I}_{exp}\|^2$.
* **Synthetic Benchmarking:** Generate large-scale, ground-truth datasets of "corrupted" AFM movies (with lag, noise, and dilation) to train denoising or state-detection models.
---
## 🚀 Key Features
* **Differentiable Height Mapping:** Efficient Log-Sum-Exp collision detection for sub-nanometer topography.
* **Scanning Lag Simulation:** Models the line-by-line temporal delay inherent in pixel-by-pixel acquisition.
* **Flexible Tip Geometries:** Supports spherical and parabolic tip-shape dilation.
* **Integration:** Reads PDB/mmCIF files via `biotite` and integrates with `synth-pdb` and `resonance-flow`.
## 📦 Installation
```bash
pip install synth-afm
```
## 📖 Tutorials
Get started immediately with our interactive Jupyter notebooks:
* **[Quick Start: Differentiable HS-AFM Simulation](examples/quickstart_afm.ipynb)**: Learn how to generate height maps with tip dilation and scanning lag.
[](https://colab.research.google.com/github/elkins/synth-afm/blob/master/examples/quickstart_afm.ipynb)
## 🛠Quick Start
```python
import jax.numpy as jnp
from synth_afm.simulator import AFMSimulator
from synth_afm.io import load_coords_and_radii
# 1. Load your structure (N, 3) and radii (N,)
coords, radii = load_coords_and_radii("molecule.pdb")
# 2. Initialize simulator (1A pixel size, 2nm tip radius)
sim = AFMSimulator(pixel_size=1.0, tip_radius=20.0)
# 3. Generate height map (Differentiable!)
height_map = sim.scan(coords, radii)
```
## 🧪 Scientific Validation
The height-mapping kernels are validated against the standard Villarrubia algorithm and verified to preserve atomic heights within 0.01 Ã… precision. The temporal lag simulation correctly reproduces the stroboscopic shearing effects documented in high-speed biological AFM (Ando et al., 2011).
## 📜 License
Distributed under the MIT License. See `LICENSE` for more information.