We introduce ToPolyAgent, a multi-agent AI framework for performing coarse-grained molecular dynamics (MD) simulations of topological polymers through natural language instructions. By integrating large language models (LLMs) with domain-specific computational tools, ToPolyAgent supports both interactive and autonomous simulation workflows across diverse polymer architectures, including linear, ring, brush, and star polymers, as well as dendrimers. The system consists of four LLM-powered agents: a Config Agent for generating initial polymer-solvent configurations, a Simulation Agent for executing LAMMPS-based MD simulations and conformational analyses, a Report Agent for compiling markdown reports, and a Workflow Agent for streamlined autonomous operations. Interactive mode incorporates user feedback loops for iterative refinements, while autonomous mode enables end-to-end task execution from detailed prompts. We demonstrate ToPolyAgent's versatility through case studies involving diverse polymer architectures under varying solvent condition, thermostats, and simulation lengths. Furthermore, we highlight its potential as a research assistant by directing it to investigate the effect of interaction parameters on the linear polymer conformation, and the influence of grafting density on the persistence length of the brush polymer. By coupling natural language interfaces with rigorous simulation tools, ToPolyAgent lowers barriers to complex computational workflows and advances AI-driven materials discovery in polymer science. It lays the foundation for autonomous and extensible multi-agent scientific research ecosystems.

Simulations, although powerful in accurately replicating real-world systems, often remain inaccessible to non-technical users due to their complexity. Conversely, large language models (LLMs) provide intuitive, language-based interactions but can lack the structured, causal understanding required to reliably model complex real-world dynamics. We introduce our simulation agent framework, a novel approach that integrates the strengths of both simulation models and LLMs. This framework helps empower users by leveraging the conversational capabilities of LLMs to interact seamlessly with sophisticated simulation systems, while simultaneously utilizing the simulations to ground the LLMs in accurate and structured representations of real-world phenomena. This integrated approach helps provide a robust and generalizable foundation for empirical validation and offers broad applicability across diverse domains.

AI agents promise to change that. Think of them as AI models with a script and a purpose. They tend to come in one of two flavors. The first, called tool-based agents, can be coached using natural human language (rather than coding) to complete digital tasks for us. Anthropic released one such agent in October--the first from a major AI model-maker--that can translate instructions ("Fill in this form for me") into actions on someone's computer, moving the cursor to open a web browser, navigating to find data on relevant pages, and filling in a form using that data.

Led by Joon Sung Park, a Stanford PhD student in computer science, the team recruited 1,000 people who varied by age, gender, race, region, education, and political ideology. They were paid up to 100 for their participation. From interviews with them, the team created agent replicas of those individuals. As a test of how well the agents mimicked their human counterparts, participants did a series of personality tests, social surveys, and logic games, twice each, two weeks apart; then the agents completed the same exercises. The results were 85% similar.

While current deep learning systems excel at tasks such as object classification, language processing, and gameplay, few can construct or modify a complex system such as a tower of blocks. We hypothesize that what these systems lack is a "relational inductive bias": a capacity for reasoning about inter-object relations and making choices over a structured description of a scene. To test this hypothesis, we focus on a task that involves gluing pairs of blocks together to stabilize a tower, and quantify how well humans perform. We then introduce a deep reinforcement learning agent which uses object- and relation-centric scene and policy representations and apply it to the task. Our results show that these structured representations allow the agent to outperform both humans and more naive approaches, suggesting that relational inductive bias is an important component in solving structured reasoning problems and for building more intelligent, flexible machines.