Daily Papers

Generative models have advanced significantly in sampling material systems with continuous variables, such as atomistic structures. However, their application to discrete variables, like atom types or spin states, remains underexplored. In this work, we introduce a Boltzmann generator built on discrete flow matching, specifically tailored for systems with discrete phase-space coordinates (e.g., the Ising model or crystalline compounds). This approach enables a single model to sample free energy surfaces over a wide temperature range with minimal training overhead. In addition, the model generation is scalable to larger lattice sizes than those in the training set. We demonstrate the effectiveness of our approach on the 2D Ising model, showing efficient and reliable free energy sampling. This framework provides a scalable and computationally efficient solution for discrete coordinate systems and can be extended to sample the alchemical degrees of freedom in crystalline compounds.

Drug-protein binding and dissociation dynamics are fundamental to understanding molecular interactions in biological systems. While many tools for drug-protein interaction studies have emerged, especially artificial intelligence (AI)-based generative models, predictive tools on binding/dissociation kinetics and dynamics are still limited. We propose a novel research paradigm that combines molecular dynamics (MD) simulations, enhanced sampling, and AI generative models to address this issue. We propose an enhanced sampling strategy to efficiently implement the drug-protein dissociation process in MD simulations and estimate the free energy surface (FES). We constructed a program pipeline of MD simulations based on this sampling strategy, thus generating a dataset including 26,612 drug-protein dissociation trajectories containing about 13 million frames. We named this dissociation dynamics dataset DD-13M and used it to train a deep equivariant generative model UnbindingFlow, which can generate collision-free dissociation trajectories. The DD-13M database and UnbindingFlow model represent a significant advancement in computational structural biology, and we anticipate its broad applicability in machine learning studies of drug-protein interactions. Our ongoing efforts focus on expanding this methodology to encompass a broader spectrum of drug-protein complexes and exploring novel applications in pathway prediction.

Information on liquid jet stream flow is crucial in many real world applications. In a large number of cases, these flows fall directly onto free surfaces (e.g. pools), creating a splash with accompanying splashing sounds. The sound produced is supplied by energy interactions between the liquid jet stream and the passive free surface. In this investigation, we collect the sound of a water jet of varying flowrate falling into a pool of water, and use this sound to predict the flowrate and flowrate trajectory involved. Two approaches are employed: one uses machine-learning models trained using audio features extracted from the collected sound to predict the flowrate (and subsequently the flowrate trajectory). In contrast, the second method directly uses acoustic parameters related to the spectral energy of the liquid-liquid interaction to estimate the flowrate trajectory. The actual flowrate, however, is determined directly using a gravimetric method: tracking the change in mass of the pooling liquid over time. We show here that the two methods agree well with the actual flowrate and offer comparable performance in accurately predicting the flowrate trajectory, and accordingly offer insights for potential real-life applications using sound.