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 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.

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. Our method utilizes the zero-level set of signed distance functions (SDFs) to represent protein surfaces, enabling temporally and spatially continuous representations of protein dynamics. Our experimental results demonstrate that our model accurately captures protein dynamic trajectories and can interpolate and extrapolate in 3D and time. Importantly, this is the first study to introduce this method and successfully model large-scale protein dynamics. This approach offers a promising alternative to current methods, overcoming the limitations of first-principles-based and deep learning methods, and provides a more scalable and efficient approach to modeling protein dynamics. Additionally, our surface representation approach simplifies calculations and allows identifying movement trends and amplitudes of protein domains, making it a useful tool for protein dynamics research. Codes are available at https://github.com/Sundw-818/DSR,

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.

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.