The paper introduces a data-driven effective model for stochastic chemical reaction networks that bypasses the high computational cost of the Stochastic Simulation Algorithm (SSA). By approximating the finite-time transition kernel of the SSA-induced continuous-time Markov chain with a generative machine learning model, the method operates on a user-defined coarse time step independent of microscopic reaction events. Using a conditional normalizing flow as the stochastic propagator, the trained model recursively generates statistically consistent trajectories, achieving significant computational savings while maintaining accuracy, as demonstrated through numerous numerical examples.
By Yuan Chen, Weize Mao, Dongbin Xiu
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.
By Joanna Zou, Fraser Birks, Dallas Foster, Youssef Marzouk
arXiv:2601. 22123v4 Announce Type: replace Abstract: Simulating the long-time evolution of Hamiltonian systems is limited by the small timesteps required for stable numerical integration.
By Winfried Ripken, Michael Plainer, Gregor Lied, Thorben Frank, Oliver T. Unke, Stefan Chmiela, Frank No\'e, Klaus-Robert M\"uller
arXiv:2604. 02121v2 Announce Type: replace-cross Abstract: Stochastic kinetic models are ubiquitous in physics, yet inferring their parameters from experimental data remains challenging.
By Ludwig Burger, Annalena Kofler, Lukas Heinrich, Ulrich Gerland
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.
By Marylou Gabri\'e
MAELLE is a mechanistic reaction prediction framework that models chemical reactions as discrete flow matching over graph-structured electron occupation vectors. It formulates the reactant-to-product mapping as a Continuous-time Markov Chain on electron sites and uses Optimal Transport to generate mechanistically interpretable edit trajectories without elementary step annotations. The method achieves competitive accuracy on the USPTO-480K benchmark, remains robust in out-of-distribution scenarios, and can recover mechanistic pathways that align with known chemistry and predict side products.
By Nguyen Xuan-Vu, Octavian Susanu, Daniel Armstrong, Philippe Schwaller
arXiv:2608. 13800v1 Announce Type: new Abstract: Transition path sampling (TPS) aims to efficiently generate rare molecular transition trajectories between metastable states and is essential for understanding biomolecular mechanisms.
By Jingqian Liu, Yu-Hsiang Wang, Yanru Qu, Ge Liu
arXiv:2606. 14498v1 Announce Type: cross Abstract: Predicting the Kohn-Sham Hamiltonian with machine learning can accelerate density functional theory while retaining access to molecular orbitals, energy levels, and electronic-structure observables that energy-only surrogates cannot resolve.
By Yunhong Lou, Xihang Yue, Xinran Wei, Tianqi Deng, Linchao Zhu
The review explores how control theory, optimal transport, probabilistic inference, non‑equilibrium thermodynamics, and machine learning are interconnected through the optimization of free‑energy‑like functionals under dynamical or statistical constraints. It presents a conceptual thread linking these five fields and illustrates the ideas with applications in reinforcement learning, variational inference, and generative modeling. The article is written for readers without prior familiarity, beginning with physics principles.
By Emmy Blumenthal, Nikolas Claussen, Benjamin Eysenbach, Catherine Ji, Gautam Reddy, Colin Scheibner, Benjamin Sorkin
arXiv:2607. 09582v1 Announce Type: cross Abstract: We present a physics-constrained machine learning framework for accelerating the direct numerical simulation (DNS) of turbulent reacting flows.
By Okezzi Ukorigho, Opeoluwa Owoyele
arXiv:2603. 11249v4 Announce Type: replace Abstract: Accurate prediction of phase equilibria remains a central challenge in chemical engineering.
By Karim K. Ben Hicham, Moreno Ascani, Jan G. Rittig, Alexander Mitsos
ReCurveflow is a flow‑matching framework that learns to predict transition state geometries by training on continuously curved reference paths derived from full NEB bands, rather than straight linear paths. It introduces an off‑path correction mechanism that generates corrective velocity fields when the model encounters geometries off the training path, improving resistance to exposure bias and TS prediction accuracy. Across multiple data splits and evaluation metrics, ReCurveflow outperforms seven baselines and produces reaction trajectories whose energy profiles closely follow the reference NEB path, aiding NEB optimization and demonstrating effective corrective behavior.
By Seungheun Baek, Mogan Gim, Jaewoo Kang