Jul 2026· Journal of Chemical Theory and Computation· 0 citations· 26 references
Medicine
Abstract
Gas adsorption in porous materials is naturally modeled in the grand-canonical ensemble. We give a compact, self-contained derivation of Metropolis-Hastings acceptance criteria for insertion, deletion, and displacement moves, including nonuniform insertion proposals based on a mixture of Gaussians (MoG) matched to pore geometry. We clarify where indistinguishability and the de Broglie wavelength enter, and show how observables map to adsorption isotherms, isosteric heats, number-fluctuation compressibilities, and the grand potential Ω. Beyond the formulas, we provide a computationally efficient, differentiable reference implementation in JAX and JAX molecular dynamics (JAX-MD), featuring periodic boundaries, cutoff-shifted Lennard-Jones interactions, and static, mask-based arrays amenable to just-in-time compilation (jit) and vectorized mapping (vmap) calculations. We include pragmatic diagnostics (autocorrelation-aware uncertainties, effective sample sizes, acceptance ratios), per-pore and voxel-resolved estimators, visualizations of pores and configurations. The open-source implementation is available online. The full source code, scripts, RASPA2 input files, CIFs, and raw benchmark JSON outputs are accessible at the link above.
Diffusion quantum Monte Carlo (DMC) and coupled cluster theory [CCSD(T)] are widely used benchmark methods for noncovalent interactions (NCIs). However, recent studies have reported notable discrepancies for several hydrogen-bonded and dispersion-dominated systems, raising questions about the accuracy of the approximat...
Kousuke Nakano, B. X. Shi, D. Alfé et al.· Journal of Chemical Physics· 1 citation
Molecular dynamics is widely used to predict ionic conductivity in solid electrolytes, but the reliability of these predictions is often difficult to assess. Our analysis identifies finite trajectory length, limited cell size, and insufficient sampling as intrinsic limitations of finite atomistic ion-transport calculat...
Yi-Wei You, Shao-Fei Chen, Zhi-Feng Wu et al.· 0 citations
Classical density-functional theory (cDFT) predicts fluid adsorption in nanoporous solids at a fraction of the cost of molecular simulation, yet most implementations are one-dimensional, assume a rigid host, or are hard-wired to a single fluid and interaction model. We present porecdft, a modular, host- and fluid-agn...
Anupom Roy, Laveen Mathanamohan, Song-Hao Bao et al.· Journal of Physical Chemistr...· 0 citations
This work introduces NS-Flows: a single conditional normalizing flow, conditioned on the NS energy bound and trained on a sliding window of recent live sets, that replaces MCMC by direct parallel draws corrected by importance-weighted rejection resampling, allowing flow training without structured priors or a pre-exist...
A. Coretti, N. Unglert, Sebastian Falkner et al.· 0 citations
JANUS is a multimodal neural sampler that couples continuous and masked discrete diffusion through an equivariant graph neural network trained directly from energy evaluations, without pre-generated equilibrium data, providing a foundation for thermodynamic sampling, characterization and inverse design of chemically di...
Denis Blessing, Mou-Yang Cheng, M. Schebek et al.· 2 citations
Metal surfaces undergo structural, compositional, and morphological changes in response to their chemical environment. Tuning the surfaces'function and stability for a given application correspondingly necessitates an understanding of how this surface evolution couples to external conditions. Here, we demonstrate the f...
F. Riccius, Karsten Reuter, H. Heenen et al.· 1 citation
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