arXiv:2410.20317v2 Announce Type: replace Abstract: Molecular dynamics (MD) simulations are a principled but computationally expensive approach for studying protein conformational variability, making...
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. 15309v1 Announce Type: cross Abstract: Proteins function through coordinated motion across multiple spatial and temporal scales, underpinning processes such as ligand binding, allostery, and catalysis.
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.
The paper presents a closed‑loop molecule generation pipeline that iteratively retrains on new quantum‑chemical simulation data, overcoming limitations of static generative models. This approach produces molecules whose properties extend up to 0.44 standard deviations beyond the training set and improves out‑of‑distribution classification accuracy by 79%. By conditioning on thermodynamic stability during the loop, the method yields a 3.5‑fold increase in the proportion of stable, potentially synthesizable molecules.
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:2607. 09998v1 Announce Type: new Abstract: Macrocyclic peptides are an increasingly important therapeutic modality, but existing computational methods for modeling their structures and properties are limited in scope and do not generalize well across the synthetically accessible chemical space.
arXiv:2606. 01628v1 Announce Type: cross Abstract: Biomolecules such as proteins and small-molecule ligands play a central role in biological systems, arising from the tight interplay between sequence and three-dimensional structure.
arXiv:2607. 10887v1 Announce Type: cross Abstract: Machine learning interatomic potentials (MLPs) have revolutionized atomistic modeling, offering the potential to replace traditional methods like Density Functional Theory (DFT).
The paper introduces Orbformer, a transferable wavefunction model that uses deep neural networks to pretrain on 22,000 equilibrium and dissociating molecular structures. Fine‑tuning Orbformer on unseen molecules achieves an accuracy‑cost ratio comparable to classical multireference methods, consistently reaching chemical accuracy (1 kcal/mol) on standard benchmarks, challenging bond dissociations, and Diels‑Alder reactions. This demonstrates that amortizing the cost of solving the Schrödinger equation across many molecules is feasible in quantum chemistry.
arXiv:2608. 06956v1 Announce Type: new Abstract: Generative models for matter are often evaluated as samplers over output representations, and their latent spaces are commonly used as proxies for navigating chemical space.
The article reviews modern machine learning techniques for estimating the committor and related kinetic statistics from molecular dynamics simulations. It emphasizes self‑supervised methods that solve the underlying dynamical equations instead of relying on labeled data, and unifies various approaches—generator‑based PDEs, variational principles, Markov state models, dynamical Galerkin approximation, and neural networks—under a common operator framework. The review also discusses practical guidance for handling non‑Markovian effects, sampling strategies, and outlines future research directions such as connections to reinforcement learning and generative modeling.