Achuth Chandrasekhar

Achuth Chandrasekhar, Jonathan Chan, Francis Ogoke et al.

Generalized large language models (LLMs) such as GPT-4 may not provide specific answers to queries formulated by materials science researchers. These models may produce a high-level outline but lack the capacity to return detailed instructions on manufacturing and material properties of novel alloys. Enhancing a smaller model with specialized domain knowledge may provide an advantage over large language models which cannot be retrained quickly enough to keep up with the rapid pace of research in metal additive manufacturing (AM). We introduce "AMGPT," a specialized LLM text generator designed for metal AM queries. The goal of AMGPT is to assist researchers and users in navigating the extensive corpus of literature in AM. Instead of training from scratch, we employ a pre-trained Llama2-7B model from Hugging Face in a Retrieval-Augmented Generation (RAG) setup, utilizing it to dynamically incorporate information from $\sim$50 AM papers and textbooks in PDF format. Mathpix is used to convert these PDF documents into TeX format, facilitating their integration into the RAG pipeline managed by LlamaIndex. Expert evaluations of this project highlight that specific embeddings from the RAG setup accelerate response times and maintain coherence in the generated text.

Janghoon Ock, Radheesh Sharma Meda, Srivathsan Badrinarayanan et al.

We present a modular framework powered by large language models (LLMs) that automates and streamlines key tasks across the early-stage computational drug discovery pipeline. By combining LLM reasoning with domain-specific tools, the framework performs biomedical data retrieval, domain-specific question answering, molecular generation, property prediction, property-aware molecular refinement, and 3D protein-ligand structure generation. In a case study targeting BCL-2 in lymphocytic leukemia, the agent autonomously retrieved relevant biomolecular information, including FASTA sequences, SMILES representations, and literature, and answered mechanistic questions with improved contextual accuracy compared to standard LLMs. It then generated chemically diverse seed molecules and predicted 67 ADMET-related properties, which guided iterative molecular refinement. Across two refinement rounds, the number of molecules with QED > 0.6 increased from 34 to 55. The number of molecules satisfying empirical drug-likeness filters also rose; for example, compliance with the Ghose filter increased from 32 to 55 within a pool of 100 molecules. The framework also employed Boltz-2 to generate 3D protein-ligand complexes and provide rapid binding affinity estimates for candidate compounds. These results demonstrate that the approach effectively supports molecular screening, prioritization, and structure evaluation. Its modular design enables flexible integration of evolving tools and models, providing a scalable foundation for AI-assisted therapeutic discovery.

Achuth Chandrasekhar, Amir Barati Farimani

Molecular dynamics simulations are an essential tool in understanding protein structure, dynamics, and function at the atomic level. However, preparing high quality input files for MD simulations can be a time consuming and error prone process. In this work, we introduce an automated pipeline that leverages Large Language Models (LLMs), specifically Gemini 2.0 Flash, in conjunction with python scripting and Selenium based web automation to streamline the generation of MD input files. The pipeline exploits CHARMM GUI's comprehensive web-based interface for preparing simulation-ready inputs for NAMD. By integrating Gemini's code generation and iterative refinement capabilities, simulation scripts are automatically written, executed, and revised to navigate CHARMM GUI, extract appropriate parameters, and produce the required NAMD input files. Post processing is performed using additional software to further refine the simulation outputs, thereby enabling a complete and largely hands free workflow. Our results demonstrate that this approach reduces setup time, minimizes manual errors, and offers a scalable solution for handling multiple protein systems in parallel. This automated framework paves the way for broader application of LLMs in computational structural biology, offering a robust and adaptable platform for future developments in simulation automation.

Peter Pak, Achuth Chandrasekhar, Amir Barati Farimani

Agentic systems enable the intelligent use of research tooling, augmenting a researcher's ability to investigate and propose novel solutions to existing problems. Within Additive Manufacturing (AM), alloy discovery remains a complex challenge, often requiring expertise in the various domains of materials science, thermodynamic simulations, and experimental analysis. Large Language Model (LLM) enabled agents can facilitate this endeavor by utilizing their extensive knowledge base to dispatch tool calls via Model Context Protocol (MCP) to perform actions such as Thermo-Calc property diagram calculations and lack of fusion process map generation. In addition, the multi-agent system developed in this work is able to effectively reason through complex user prompts and provide analysis on the printability of proposed alloys. These agents can dynamically adjust their task trajectory to the outcomes of tool call results, effectively enabling autonomous decision-making in practical environments. This work aims to utilize LLM enabled agents to automate and accelerate the task of alloy discovery within the field of additive manufacturing and showcase the benefits of adopting this multi-agent system.