arXiv subjects

Harry W. Sullivan

Publications and source records attributed to Harry W. Sullivan.

4 recordsLinked to original sources

arXiv2026

MolCrystalFlow: Molecular Crystal Structure Prediction via Flow Matching

Molecular crystal structure prediction represents a grand challenge in computational chemistry due to large sizes of constituent molecules and complex intra- and intermolecular interactions. While generative modeling has revolutionized structure discovery for molecules, inorganic solids, and metal-organic frameworks, extending such approaches to fully periodic molecular crystals is still elusive. Here, we present MolCrystalFlow, a flow-based generative model for molecular crystal structure prediction. The framework disentangles intramolecular complexity from intermolecular packing by embedding molecules as rigid bodies and jointly learning the lattice matrix, molecular orientations, and centroid positions. Centroids and orientations are represented on their native Riemannian manifolds, allowing geodesic flow construction and graph neural network operations that respects geometric symmetries. We benchmark our model against a state-of-the-art generative model (MOFFlow) for large-size periodic crystals and a rule-based structure generation method (Genarris) on two open-source molecular crystal datasets. MolCrystalFlow outperforms MOFFlow while achieving competitive performance against Genarris. We also demonstrate an integration of MolCrystalFlow model with universal machine learning potential to accelerate molecular crystal structure prediction, paving the way for data-driven generative discovery of molecular crystals.

cs.LG↗

arXiv2026

Physics-Informed Gaussian Process Inference of Liquid Structure from Scattering Data

We present a nonparametric Bayesian framework to infer radial distribution functions from experimental scattering measurements with uncertainty quantification using non-stationary Gaussian processes. The Gaussian process prior mean and kernel functions are designed to mitigate well-known numerical challenges with the Fourier transform, including discrete measurement binning and detector windowing, while encoding fundamental yet minimal physical knowledge of liquid structure. We demonstrate uncertainty propagation of the Gaussian process posterior to unmeasured quantities of interest. Experimental radial distribution functions of liquid argon and water with uncertainty quantification are provided as both a proof of principle for the method and a benchmark for molecular models. The full implementation is available on GitHub at: https://github.com/hoepfnergroup/LiquidStructureGP-Sullivan.

physics.chem-ph↗

arXiv2025

Experimental Evidence of Quantum Drude Oscillator Behavior in Liquids Revealed with Probabilistic Iterative Boltzmann Inversion

The first experimental evidence of quantum Drude oscillator behavior in liquids is determined using probabilistic machine learning-augmented iterative Boltzmann inversion applied to noble gas radial distribution functions. Furthermore, classical force fields for noble gases are shown to be reduced to a single parameter through simple empirical relations linked to atomic dipole polarizability. These findings highlight how neutron scattering data can inspire innovative force field design and offer insight into interatomic forces to advance molecular simulations.

physics.chem-ph↗

arXiv2024

Bayesian Analysis Reveals the Key to Extracting Pair Potentials from Neutron Scattering Data

The inverse problem of statistical mechanics is an unsolved, century-old challenge to learn classical pair potentials directly from experimental scattering data. This problem was extensively investigated in the 20th century but was eventually eclipsed by standard methods of benchmarking pair potentials to macroscopic thermodynamic data. However, it is becoming increasingly clear that existing force field models fail to reliably reproduce fluid structures even in simple liquids, which can result in reduced transferability and substantial misrepresentations of thermophysical behavior and self-assembly. In this study, we revisited the structure inverse problem for a classical Mie fluid to determine to what extent experimental uncertainty in neutron scattering data influences the ability to recover classical pair potentials. Bayesian uncertainty quantification was used to show that structure factors with random noise smaller than 0.005 to $\sim30$ A$^{-1}$ are required to accurately recover pair potentials from neutron scattering. Notably, modern neutron instruments can achieve this precision to extract classical force models to within approximately $\pm$ 1.3 for the repulsive exponent, $\pm$ 0.068 A$^{-1}$ for atomic size, and 0.024 kcal/mol in the potential well-depth with 95\% confidence. Our results suggest the exciting possibility of improving molecular simulation accuracy through the incorporation of neutron scattering data, advancement in structural modeling, and extraction of model-independent measurements of local atomic forces in real fluids.

cond-mat.stat-mech↗