Yuanqi Du

Maximilian Schebek, Jiajun He, Emil Hoffmann et al. · cambridge

The accurate estimation of free energy differences between two states is a long-standing challenge in molecular simulations. Traditional approaches generally rely on sampling multiple intermediate states to ensure sufficient overlap in phase space and are, consequently, computationally expensive. Several generative-model-based methods have recently addressed this challenge by learning a direct bridge between distributions, bypassing the need for intermediate states. However, it remains unclear which approaches provide the best trade-off between efficiency, accuracy, and scalability. In this work, we systematically review these methods and benchmark selected approaches with a focus on condensed-matter systems. In particular, we investigate the performance of discrete and continuous normalizing flows in the context of targeted free energy perturbation as well as FEAT (Free energy Estimators with Adaptive Transport) together with the escorted Jarzynski equality, using coarse-grained monatomic ice and Lennard-Jones solids as benchmark systems. We evaluate accuracy, data efficiency, computational cost, and scalability with system size. Our results provide a quantitative framework for selecting effective free energy estimation strategies in condensed-phase systems.

Yuanqi Du, Botao Yu, Tianyu Liu et al.

There has been unprecedented interest in developing agents that expand the boundary of scientific discovery, primarily by optimizing quantitative objective functions specified by scientists. However, for grand challenges in science , these objectives are only imperfect proxies. We argue that automating objective function design is a central, yet unmet requirement for scientific discovery agents. In this work, we introduce the Scientific Autonomous Goal-evolving Agent (SAGA) to amend this challenge. SAGA employs a bi-level architecture in which an outer loop of LLM agents analyzes optimization outcomes, proposes new objectives, and converts them into computable scoring functions, while an inner loop performs solution optimization under the current objectives. This bi-level design enables systematic exploration of the space of objectives and their trade-offs, rather than treating them as fixed inputs. We demonstrate the framework through a broad spectrum of applications, including antibiotic design, inorganic materials design, functional DNA sequence design, and chemical process design, showing that automating objective formulation can substantially improve the effectiveness of scientific discovery agents.