arXiv subjects

Achuth Chandrasekhar

Publications and source records attributed to Achuth Chandrasekhar.

11 recordsLinked to original sources

arXiv2026

PolyJarvis: An LLM-Orchestrated Agent for Automated All-Atom Molecular Dynamics of Amorphous Homopolymers

All-atom molecular dynamics (MD) simulations can predict polymer properties from molecular structure, yet their execution requires specialized expertise in force field selection, system construction, equilibration, and property extraction. We present PolyJarvis, a platform in which a planning agent produces a validated run plan that deterministic stage scripts execute through established simulation toolkits, Enhanced Monte Carlo (EMC) for system construction and LAMMPS for molecular dynamics, exposed as Model Context Protocol (MCP) servers, with a recovery agent consulted only on structured failures and within a fixed decision budget. Given a repeat-unit SMILES string and target properties, PolyJarvis constructs the amorphous cell, equilibrates it under a mechanized convergence gate, and computes target properties. Validation is conducted on seven amorphous homopolymers, each run as three replicates that share a protocol frozen per system and use independent random seeds, namely polyethylene (PE), atactic polystyrene (aPS), syndiotactic poly(vinyl chloride) (sPVC), poly(L-lactic acid) (PLLA), poly(ethylene glycol) (PEG), poly(ether ether ketone) (PEEK), and polysulfone (PSU). Against experimental references, 13 of 19 graded comparisons meet the acceptance criteria (density 5 of 7, glass transition 4 of 7, bulk modulus 4 of 5). The failures are concentrated in the PCFF systems: under-density of aPS and PEG, overestimated glass transitions of the stiff PLLA and PEEK backbones, and an overstiff PEG bulk modulus.

cs.CL↗

arXiv2026

Catalyst-Agent: Autonomous heterogeneous catalyst screening with an LLM Agent

The discovery of catalysts for electrochemical applications such as the oxygen reduction reaction (ORR), nitrogen reduction reaction (NRR), and CO2 reduction reaction (CO2RR) remains a central challenge in chemistry and materials science. Machine-learning interatomic potentials (MLIPs) and graph neural network models now accelerate individual adsorption-energy calculations by orders of magnitude relative to density functional theory. However, true large-scale screening is still blocked by human decisions: selecting candidates, constructing slabs, enumerating adsorption sites, interpreting descriptor failures, and choosing follow-up modifications. Here, we introduce Catalyst-Agent, a Model Context Protocol (MCP) server-based, LLM-powered agent that autonomously coordinates closed-loop catalyst screening. Catalyst-Agent searches materials databases through OPTIMADE, constructs slabs, computes adsorption energies using Meta FAIRchem's UMA MLIP within AdsorbML, evaluates reaction-specific descriptors, and applies structural modifications to refine near-miss candidates. In ORR, NRR, and CO2RR campaigns, Catalyst-Agent demonstrates high performance and converges in 1.40-3.41 trials per successful material on average. It identified Sn3Sc, Sn3Y, Tl3La, Pb3Y and In3Y as CO2RR candidates for further validation that were not previously reported in the literature. DFT single-point checks confirmed screening outcomes for representative NRR and CO2RR candidates. Ablations show these gains arise from chemically informed candidate selection and feedback-directed modification rather than brute-force evaluation: fully randomized screening dropped to 13.3%, 16.7%, and 0% success for ORR, NRR, and CO2RR, respectively. These results show that tool-grounded LLM agents can shift catalyst screening from manual trial-and-error toward more autonomous, reproducible and adaptive workflows.

cs.CL↗

arXiv2026

Pepti-Agent: An AI Agent for Peptide Design and Optimization

Therapeutic peptides occupy a valuable design space between small molecules and biologics, but their development requires satisfying several competing constraints at once: solubility, hemolytic activity, and nonspecific surface fouling are governed by overlapping sequence features, so improving one property often degrades another. Computational design addresses this by pairing generative models with sequence-based property predictors, iteratively proposing and refining candidates. However, these components are typically wired together as monolithic scripts that are difficult to inspect, extend, or reuse, and they often refine sequences by natural-language reasoning rather than by tracking the evolving multi-property state of each candidate. We present Pepti-Agent, a closed-loop, peptide-specific framework that exposes generation, property prediction, and single-residue mutation as independently inspectable Model Context Protocol (MCP) tools. A large language model controller invokes these tools and consults live predictor output between calls, so refinement is guided by each sequence's current property profile rather than by language reasoning alone. Task-specific PeptideGPT models generate candidates, ProtBERT-based classifiers score solubility, hemolysis, and non-fouling, and two interchangeable mutation operators propose sequence edits. By recording a per-step trace of controller decisions, predictor outputs, and accepted mutations, Pepti-Agent offers a reproducible substrate for benchmarking multi-objective design strategies and for prioritizing candidates for experimental validation.

cs.CL↗

arXiv2026

Material Database Agent: A Multimodal Agentic Framework for Scientific Literature Mining

Materials science workflows rely on structured and unstructured data from the vast body of available scientific literature. However, most of the experimental details remain buried in text, tables, graphs and figures. Thus, constructing databases that incorporate this data is a manual, time-consuming, and hard-to-scale process. Multimodal large language models have made it feasible to extract information from text and scientific figures with high speed and accuracy. This opens the possibility of an AI system that can create production-scale material databases. Material Database Agent (MDA) is a modular, multi-agent system architecture for converting research literature into structured databases. MDA accepts article PDFs as input, which are subsequently processed in parallel into markdown files and figures. Multiple sub-agents read these markdown files and figures in parallel to assemble sub-databases for each paper. These sub-databases are then compiled into a single tabular database by an agent. As opposed to using either a rule-based approach or a single-pass pipeline for extracting information, MDA is a specialized architecture for transforming the literature into a database in the field of materials science. More generally, this study provides a basis for positioning multimodal agentic information extraction as a viable means for constructing next-generation scientific databases from the primary literature.

cs.CL↗

arXiv2026

Polymer-Agent: Large Language Model Agent for Polymer Design

On-demand Polymer discovery is essential for various industries, ranging from biomedical to reinforcement materials. Experiments with polymers have a long trial-and-error process, leading to use of extensive resources. For these processes, machine learning has accelerated scientific discovery at the property prediction and latent space search fronts. However, laboratory researchers cannot readily access codes and these models to extract individual structures and properties due to infrastructure limitations. We present a closed-loop polymer structure-property predictor integrated in a terminal for early-stage polymer discovery. The framework is powered by LLM reasoning to provide users with property prediction, property-guided polymer structure generation, and structure modification capabilities. The SMILES sequences are guided by the synthetic accessibility score and the synthetic complexity score (SC Score) to ensure that polymer generation is as close as possible to synthetically accessible monomer-level structures. This framework addresses the challenge of generating novel polymer structures for laboratory researchers, thereby providing computational insights into polymer research.

cs.CL↗

arXiv2026

Agentic Additive Manufacturing Alloy Evaluation

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 selection and evaluation 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 thermophysical property diagram calculations and lack of fusion process map generation. In addition, the multi-agent system can effectively reason through complex user prompts and provide analysis on the lack of fusion process window of common alloys such as SS316L and IN718 along with proposed composition variants of known 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 showcase the benefits of adopting a LLM enabled multi-agent system to automate and accelerate the task of evaluating proposed additive manufacturing alloys, both novel and known.

cs.AI↗

arXiv2025

Large Language Model Agent for Modular Task Execution in Drug Discovery

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, literature-grounded question answering via retrieval-augmented generation, molecular generation, multi-property prediction, property-aware molecular refinement, and 3D protein-ligand structure generation. 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 75 properties, including ADMET-related and general physicochemical descriptors, 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.

cs.LG↗

arXiv2025

Text to Band Gap: Pre-trained Language Models as Encoders for Semiconductor Band Gap Prediction

We investigate transformer-based language models, including RoBERTa, T5, Llama-3, and MatSciBERT, for predicting the band gaps of semiconductor materials directly from textual descriptions. The inputs encode key material features, such as chemical composition, crystal system, space group, and other structural and electronic properties. Unlike shallow machine learning models, which require extensive feature engineering, or Graph Neural Networks, which rely on graph representations derived from atomic coordinates, pretrained language models can process textual inputs directly, eliminating the need for manual feature preprocessing or structure-based encoding. Material descriptions were constructed in two formats: structured strings with a consistent template and natural language narratives generated via the ChatGPT API. Each model was augmented with a custom regression head and finetuned for band gap prediction task. Language models of different architectures and parameter sizes were all able to predict band gaps from human-readable text with strong accuracy, achieving MAEs in the range of 0.25-0.33 eV, highlighting the success of this approach for scientific regression tasks. Finetuned Llama-3, with 1.2 billion parameters, achieved the highest accuracy (MAE 0.248 eV, R2 0.891). MatSciBERT, pretrained on materials science literature, reached comparable performance (MAE 0.288 eV, R2 0.871) with significantly fewer parameters (110 million), emphasizing the importance of domain-specific pretraining. Attention analysis shows that both models selectively focus on compositional and spin-related features while de-emphasizing geometric features, reflecting the difficulty of capturing spatial information from text. These results establish that pretrained language models can effectively extract complex feature-property relationships from textual material descriptions.

cs.CL↗

arXiv2025

Automating MD simulations for Proteins using Large language Models: NAMD-Agent

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.

cs.CL↗

arXiv2025

NANOGPT: A Query-Driven Large Language Model Retrieval-Augmented Generation System for Nanotechnology Research

This paper presents the development and application of a Large Language Model Retrieval-Augmented Generation (LLM-RAG) system tailored for nanotechnology research. The system leverages the capabilities of a sophisticated language model to serve as an intelligent research assistant, enhancing the efficiency and comprehensiveness of literature reviews in the nanotechnology domain. Central to this LLM-RAG system is its advanced query backend retrieval mechanism, which integrates data from multiple reputable sources. The system retrieves relevant literature by utilizing Google Scholar's advanced search, and scraping open-access papers from Elsevier, Springer Nature, and ACS Publications. This multifaceted approach ensures a broad and diverse collection of up-to-date scholarly articles and papers. The proposed system demonstrates significant potential in aiding researchers by providing a streamlined, accurate, and exhaustive literature retrieval process, thereby accelerating research advancements in nanotechnology. The effectiveness of the LLM-RAG system is validated through rigorous testing, illustrating its capability to significantly reduce the time and effort required for comprehensive literature reviews, while maintaining high accuracy, query relevance and outperforming standard, publicly available LLMS.

cs.CL↗

arXiv2024

AMGPT: a Large Language Model for Contextual Querying in Additive Manufacturing

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.

cs.CL↗