Currently, two mainstream GNN-based methods have been developed for constructing force fields: group theory-based methods and direction-based methods.

Systems of interacting objects often evolve under the influence of field effects that govern their dynamics, yet previous works have abstracted away from such effects, and assume that systems evolve in a vacuum. In this work, we focus on discovering these fields, and infer them from the observed dynamics alone, without directly observing them.

Accurate prediction of likely 3D geometries of flexiblemolecules is along standing goal of computational chemistry, with broad implications for drug design, biopolymer research, and QSAR analysis.

We propose a novel neural network-based approach to modeling protein dynamics using an implicit representation of a protein's surface in 3D and time.

Classical Hamiltonian mechanics has been widely used in machine learning in the form of Hamiltonian Monte Carlo for applications with predetermined force fields. In this paper, we explore the potential of deliberately designing force fields for Hamiltonian systems, introducing Hamiltonian velocity predictors (HVPs) as a core tool for constructing energy-based and generative models. We present two innovations: Hamiltonian Score Matching (HSM), which utilizes score functions to augment data by simulating Hamiltonian trajectories, and Hamiltonian Generative Flows (HGFs), a novel generative model that encompasses diffusion models and OT-flow matching as HGFs with zero force fields. We showcase the extended design space of force fields by introducing Oscillation HGFs, a generative model inspired by harmonic oscillators. Our experiments demonstrate that HSM and HGFs rival leading score-matching and generative modeling techniques.

Machine learning force fields (MLFFs) have instigated a groundbreaking shift in molecular dynamics (MD) simulations across a wide range of fields, such as physics, chemistry, biology, and materials science. Incorporating higher order many-body interactions can enhance the expressiveness and accuracy of models. Recent models have achieved this by explicitly including up to four-body interactions. However, five-body interactions, which have relevance in various fields, are still challenging to incorporate efficiently into MLFFs. In this work, we propose the quintuple network (QuinNet), an end-to-end graph neural network that efficiently expresses many-body interactions up to five-body interactions with \emph{ab initio} accuracy. By analyzing the topology of diverse many-body interactions, we design the model architecture to efficiently and explicitly represent these interactions. We evaluate QuinNet on public datasets of small molecules, such as MD17 and its revised version, and show that it is compatible with other state-of-the-art models on these benchmarks.

Force field-based molecular dynamics (MD) simulations are indispensable for probing the structure, dynamics, and functions of biomolecular systems, including proteins and protein-ligand complexes. Despite their broad utility in drug discovery and protein engineering, the technical complexity of MD setup, encompassing parameterization, input preparation, and software configuration, remains a major barrier for widespread and efficient usage. Agentic LLMs have demonstrated their capacity to autonomously execute multi-step scientific processes, and to date, they have not successfully been used to automate protein-ligand MD workflows. Here, we present DynaMate, a modular multi-agent framework that autonomously designs and executes complete MD workflows for both protein and protein-ligand systems, and offers free energy binding affinity calculations with the MM/PB(GB)SA method. The framework integrates dynamic tool use, web search, PaperQA, and a self-correcting behavior. DynaMate comprises three specialized modules, interacting to plan the experiment, perform the simulation, and analyze the results. We evaluated its performance across twelve benchmark systems of varying complexity, assessing success rate, efficiency, and adaptability. DynaMate reliably performed full MD simulations, corrected runtime errors through iterative reasoning, and produced meaningful analyses of protein-ligand interactions. This automated framework paves the way toward standardized, scalable, and time-efficient molecular modeling pipelines for future biomolecular and drug design applications.