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📻 diff-epr: Differentiable EPR/DEER Simulation in JAX\n\n[![Tests](https://github.com/elkins-lab/diff-epr/actions/workflows/test.yml/badge.svg)](https://github.com/elkins-lab/diff-epr/actions/workflows/test.yml)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n[![JAX](https://img.shields.io/badge/backend-JAX-9cf.svg)](https://github.com/google/jax)\n\n**diff-epr** provides differentiable kernels for simulating EPR distance distributions (DEER/PELDOR) from structural ensembles and spin-label rotamers.\n\n---\n\n## 🎯 Features\n\n- **Spin-Label Modeling:** Differentiable distance calculations between paramagnetic centers.\n- **Orientation Selection:** Support for the **Polyhach 5-angle formula** (Polyhach et al., 2007) to model relative domain orientations.\n- **Time-Domain Simulation:** Simulate DEER modulation traces $V(t)$ with parameterizable background decay and modulation depth.\n- **Rotamer Library Integration:** Support for weighted rotamer averages in distance distribution calculations.\n- **Hardware Acceleration:** GPU-optimized distance kernels via JAX.\n\n---\n\n## 📚 Tutorials\n\nExperience **diff-epr** directly in your browser:\n\n- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/elkins-lab/diff-epr/blob/main/examples/interactive_tutorials/deer_spectroscopy_tutorial.ipynb) **DEER Spectroscopy Simulation** — Learn how to simulate time-domain traces from distance distributions and rotamer clouds.\n\n---\n\n## 🏗️ Technical Architecture\n\n- **Backend:** JAX (XLA-compiled).\n- **Physics:** Dipolar coupling frequency ($\\omega$) based kernels.\n- **Performance:** $O(N)$ scaling for distance distribution integration.\n\n---\n\n## 🚀 Roadmap\n\n- [x] Core DEER trace simulation kernels.\n- [x] Background decay and modulation depth parameters.\n- [ ] Integration with MMM (Multi-Scale Modeling of Macromolecules) rotamer libraries.\n- [ ] Full orientation-dependence support.\n\n---\n\n## 🚀 Installation\n\n```bash\npip install diff-epr\n```\n\n## 🧪 Scientific Validation\n\n- **Dipolar Frequency Parity:** Coupling frequencies verified against the Pake pattern $1/r^3$ dependence.\n- **Time-Domain Accuracy:** DEER traces validated for parity against standard simulation tools (e.g., DeerAnalysis/MMM).\n- **Auto-Diff Gradients:** Differentiable distance-to-signal kernels verified with JAX `grad`.\n\n---\n\n## 🔗 Related Projects\n\ndiff-epr is part of the **differentiable biophysics** ecosystem:\n\n- [diff-biophys](https://github.com/elkins-lab/diff-biophys) — Core differentiable biophysics engine.\n- [diff-hdx](https://github.com/elkins-lab/diff-hdx) — Differentiable HDX-MS prediction.\n- [diff-fret](https://github.com/elkins-lab/diff-fret) — Differentiable FRET modeling.\n- [synth-nmr](https://github.com/elkins-lab/synth-nmr) — NMR observable simulation.\n\n---\n\n## 📖 Citation\n\n```bibtex\n@software{diff_epr,\n  author  = {Elkins, George},\n  title   = {diff-epr: Differentiable EPR/DEER simulation in JAX},\n  year    = {2026},\n  url     = {https://github.com/elkins-lab/diff-epr},\n  version = {0.1.2}\n}\n```\n\n## ⚖️ License\n\nMIT\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Felkins-lab%2Fdiff-epr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Felkins-lab%2Fdiff-epr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Felkins-lab%2Fdiff-epr/lists"}