arXiv:2605. 00337v2 Announce Type: replace Abstract: Sampling the distribution of collective variables (CVs) and estimating the associated free energy surface are crucial problems in statistical physics, as they underpin a better understanding of chemical reactions and conformational transitions.
arXiv:2602. 16634v2 Announce Type: replace-cross Abstract: The rare-event sampling problem has long been the central limiting factor in molecular dynamics (MD), especially in biomolecular simulation.
arXiv:2605. 31498v2 Announce Type: replace Abstract: A long standing challenge in computational chemistry and biophysics is efficiently sampling the Boltzmann distribution of molecules.
arXiv:2603. 23398v3 Announce Type: replace-cross Abstract: Generative modeling of discrete data, such as graphs, underpins many scientific and industrial applications, including molecular discovery and materials design.
Path sampling methods generate ensembles of reactive trajectories connecting metastable states, but extracting mechanistic insight from these data remains nontrivial. We introduce Flux Matching, a framework that learns two complementary objects directly from reactive trajectory data: a current velocity $u(z)$, whose streamlines trace the dominant reaction pathways, and a scalar potential $h(z)$, obtained from a weighted Helmholtz-Hodge decomposition of the reactive current, that serves as a data-driven reaction coordinate.
arXiv:2608. 07648v1 Announce Type: cross Abstract: Sampling high-dimensional probability distributions is a central task in scientific computing, with applications ranging from Bayesian inference to statistical physics and molecular simulation.
arXiv:2606. 04100v1 Announce Type: new Abstract: Machine learning interatomic potentials (MLIPs) enable efficient and accurate atomistic simulations but depend critically on the quality and diversity of the training data.
arXiv:2606. 06295v1 Announce Type: new Abstract: Path sampling methods generate ensembles of reactive trajectories connecting metastable states, but extracting mechanistic insight from these data remains nontrivial.
arXiv:2608. 18004v1 Announce Type: new Abstract: Probabilistic modeling of physical fields benefits from both a data-driven prior and known physical structure such as the governing equations.
arXiv:2607. 03513v1 Announce Type: cross Abstract: We present AquaGen, the first all-atom, explicit solvent, periodic-boundary-condition-aware generative model that produces molecular configurations from the Boltzmann distribution at a fraction of the cost of molecular dynamics (MD).
arXiv:2607. 07519v1 Announce Type: new Abstract: We address the problem of efficiently sampling multimodal probability distributions, where standard Markov Chain Monte Carlo methods often suffer from poor mixing and mode trapping.
arXiv:2510. 08906v2 Announce Type: replace-cross Abstract: Training set sampling methods are used to improve model performance and lower data costs in machine learning problems relevant to chemistry.
arXiv:2602. 24007v3 Announce Type: replace-cross Abstract: Protein function relies on dynamic conformational ensembles, yet current generative models like AlphaFold3 often fail to produce ensembles that match experimental data.