Physics-informed diffusion models for extrapolating crystal structures beyond known motifs

Andrij Vasylenko, Federico Ottomano, Christopher M. Collins, Rahul Savani, Matthew S. Dyer, Matthew J. RosseinskyarXiv 2025 · DOI

Introduction

The discovery of novel crystal structures with transformative properties—such as advanced battery electrolytes or superconductors—remains a primary objective in materials science. While generative AI has demonstrated significant potential in proposing new materials, current models often struggle with two fundamental challenges: distributional fidelity and physical plausibility. Most existing models are trained to mimic known databases, leading to "interpolation" (finding variations of known structures) rather than "extrapolation" (discovering entirely new structural motifs). Furthermore, AI-generated structures frequently suffer from physical inconsistencies, such as unrealistic atomic packing or "hallucinated" voids.

To address these limitations, this research introduces PIGEN (Physics-Informed GENerative model), a diffusion-based architecture designed to steer generative processes toward uncharted but physically plausible regions of chemical space.

Methodology

PIGEN builds upon denoising diffusion architectures by incorporating physics-informed constraints and novelty-targeting metrics directly into the generation loop. The framework utilizes two primary innovations to guide the model:

  1. Compactness ($C$) as a Physics-Informed Loss: The model integrates a compactness metric—defined as the ratio of atomic volume to unit cell volume—into the training loss. This serves as a computationally efficient proxy for energetic stability, forcing the model to internalize the principles of dense atomic packing.
  2. Local Environment Diversity ($M_{LED}$): To quantify structural novelty, the researchers developed $M_{LED}$. This metric uses Gaussian kernels to represent coordination motifs as smooth probability distributions. By conditioning generation on high $M_{LED}$ scores, the model is steered toward rare or previously unseen local environments.
Extracted figure from page 4 of Physics-informed diffusion models for extrapolating crystal structures beyond known motifs

The generation process employs Classifier-Free Guidance (CFG), allowing researchers to tune the output by specifying desired levels of compactness and diversity. Following generation, candidates undergo a five-stage validation pipeline that filters for structural validity, compositional novelty, and energetic stability before final verification via Density Functional Theory (DFT) and Crystal Structure Prediction (CSP).

Results and Discussion

PIGEN demonstrates a marked improvement over state-of-the-art baselines like MatterGen and DiffCSP. When conditioned on both diversity and compactness, PIGEN produced 42.0% valid, diverse candidates, more than doubling the performance of the base MatterGen model (17.8%).

Crucially, PIGEN excels at targeting novelty: 67% of its plausible structures did not match any of the top 100 most common prototypes in the Inorganic Crystal Structure Database (ICSD), whereas standard energy-guided models achieved only 42% novelty.

Extracted figure from page 4 of Physics-informed diffusion models for extrapolating crystal structures beyond known motifs

A key highlight of the study is the discovery of a novel stable framework for $Rb_2Er_4O_7$. The PIGEN-generated candidate, when subjected to global optimization via CSP, relaxed into a distinct, stable structure that was absent from all major materials databases. This result underscores the synergy between generative AI and traditional physics-based methods, where AI acts as an efficient "scout" for novel chemical regions.

Conclusion

PIGEN represents a significant shift from simple data imitation to targeted exploration in materials discovery. By embedding physical principles like compactness and structural diversity into the diffusion process, the model successfully navigates the trade-off between stability and novelty. Future work will focus on scaling these physics-informed constraints to larger, more complex systems, such as Metal-Organic Frameworks (MOFs) and macromolecular structures.

BibTeX
@misc{vasylenko2025physics,
  author = {Andrij Vasylenko and Federico Ottomano and Christopher M. Collins and Rahul Savani and Matthew S. Dyer and Matthew J. Rosseinsky},
  title = {{Physics-informed diffusion models for extrapolating crystal structures beyond known motifs}},
  year = {2025},
  eprint = {2510.23181},
  archivePrefix = {arXiv},
  url = {https://arxiv.org/abs/2510.23181},
}