arXiv subjects

Amir Barati Farimani

Publications and source records attributed to Amir Barati Farimani.

At least 19 recordsLinked to original sources

arXiv2026

CFD Forge: A Physics-Constrained Agentic Framework for Autonomous CFD

Setting up, running, and assessing a computational fluid dynamics (CFD) simulation requires substantial manual effort, from meshing and solver setup to diagnosis and interpretation, and repeating it across design variants slows engineering iteration. We present CFD Forge, an agentic framework built around OpenFOAM that carries an engineering request through case construction, meshing, solver execution, diagnostics, and reporting. A large language model interprets the request, reads the simulation evidence, identifies likely causes of problems, and proposes actions from a closed set. Automation is only useful if its results can be trusted, so acceptance is not left to the model: deterministic checks, registered for each type of flow, measure explicit criteria and decide. We demonstrate the framework on a converging-diverging nozzle and a two-dimensional forward-facing step, including geometry and operating changes requested in text. A turbulent cube, run outside the agent loop, shows why the checks matter: the solver completed and the mean drag settled, but the lateral-force oscillations were still growing, so a retrospective assessment withheld acceptance. To test this separation, we replayed 36 recorded simulation states, some with deliberately altered diagnostics, through the same model in two setups. Judging from the evidence without the check results, the model accepted 12 of the 13 detectable faults in all three repeats; with CFD Forge's checks deciding, none was accepted. The two setups also differ in prompting, and a fixed rule reached the same verdicts, so the model's value lies in the open-ended work rather than the verdict. Case files, recorded model calls, and decisions are retained for audit. A model that does the work, paired with checks that decide what is accepted, is a step toward automated CFD that can be trusted in high-throughput design and active-learning loops.

physics.flu-dyn↗

arXiv2026

Cross-Domain Pretraining for Steady-State Neural CFD Surrogates

Neural surrogates for computational fluid dynamics (CFD) have the potential to greatly enhance engineering innovation through accelerating simulation. However, the primary limitation for neural surrogates is the lack of generalization to geometries and applications beyond the training set, which is significant given the diversity of engineering scenarios. Currently, this is addressed by generating a new dataset for a specific application; however, this requires running costly numerical solvers. In this work, we take a step toward addressing this by studying neural surrogates trained across different geometries, boundary conditions, and fidelities. We find that cross-domain pretraining improves zero- and few-shot performance on held-out datasets relative to both training from scratch and transferring from domain-specific experts. In particular, finetuning a pretrained, cross-domain model can achieve 2-3x lower errors at the same sample size and use 8x fewer samples to achieve the same error, compared to training from scratch. This benefit is architecture agnostic and improves with model size and pretraining dataset diversity. Furthermore, we study how and why cross-domain pretraining works in CFD surrogates, and find that simply pooling steady-state datasets is both sufficient and effective. Given the high cost of generating CFD data, leveraging existing datasets through cross-domain pretraining will likely be a valuable strategy as future surrogates expand to tackle new problems and use cases.

cs.LG↗

arXiv2026

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

Molecular dynamics (MD) simulations are essential for understanding protein structure, dynamics, and function, but preparing, running, and analyzing simulations remains time-consuming and error-prone. We present an automated pipeline that combines large language model (LLM) agents with Python scripting and HTMD MCP tools to generate simulation-ready inputs for NAMD3/CHARMM, execute simulations, analyze outputs, and recover from build or runtime failures. The framework was evaluated across five biomolecular system classes: a protein-DNA complex (p53 DNA-binding domain bound to its response element), a protein-membrane system (M2 muscarinic receptor with iperoxo in a POPC/cholesterol bilayer), a protein-ligand series (five congeneric TYK2 inhibitors), a protein-water reference (ubiquitin), and a protein-protein complex (barnase-barstar). For the protein-DNA system, the automated workflow reproduced key metrics from an independent published benchmark. To distinguish framework performance from model-specific behavior, we repeated the complete protein-DNA study using three LLM orchestrators: Claude Opus-4.8, GPT-5.6 Sol, and Nemotron 3 Ultra. All three completed the workflow, but they differed in benchmark-ranking fidelity and by up to two orders of magnitude in token consumption and cost. Across all system classes, the agent recovered experimentally and computationally established behavior. Additional post-processing software was used to refine simulation outputs, enabling a complete and largely hands-free workflow. This approach reduces setup effort, limits manual errors, supports parallel handling of diverse biomolecular systems, and provides a robust, adaptable foundation for LLM-driven automation in computational structural biology.

cs.CL↗

arXiv2026

RheOFormer: A generative transformer model for simulation of complex fluids and flows

The ability to model mechanics of soft materials under flowing conditions is key in designing and engineering processes and materials with targeted properties. This generally requires solution of internal stress tensor, related to the deformation tensor through nonlinear and history-dependent constitutive models. Traditional numerical methods for non-Newtonian fluid dynamics often suffer from prohibitive computational demands and poor scalability to new problem instances. Developments in data-driven methods have mitigated some limitations but still require retraining across varied physical conditions. In this work, we introduce Rheological Operator Transformer (RheOFormer), a generative operator learning method leveraging self-attention to efficiently learn different spatial interactions and features of complex fluid flows. We benchmark RheOFormer across a range of different viscometric and non-viscometric flows with different types of viscoelastic and elastoviscoplastic mechanics in complex domains against ground truth solutions. Our results demonstrate that RheOFormer can accurately learn both scalar and tensorial nonlinear mechanics of different complex fluids and predict the spatio-temporal evolution of their flows, even when trained on limited datasets. Its strong generalization capabilities and computational efficiency establish RheOFormer as a robust neural surrogate for accelerating predictive complex fluid simulations, advancing data-driven experimentation, and enabling real-time process optimization across a wide range of applications.

cs.LG↗

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

AI Agentic Selective Laser Sintering Process Optimization

Agentic systems enable the intelligent automation of complex workflows, specific to additive manufacturing this is applicable for complex tasks such as process parameter optimization for mechanical properties. This work investigates the AI enabled agentic process optimization within Selective Laser Sintering (SLS) to iteratively improve the tensile and flexural properties of 3 different materials on the Inova Mk1. These materials include PA12 GF, PA11 Onyx, and PA12 Blend (volume mixture of 25% PA12 GF and 75% PA12 White) and with using knowledge from previous builds and minimal guidance from the user, the agentic system was able to optimize process parameters over a small number of iterations to achieve comparable TDS specified mechanical properties. This work showcases the ability for an agentic system to continually learn from updated data, enabling the intelligent automation of complex tasks such as process parameter optimization for selective laser sintering.

cs.MA↗

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

AgentsCAD: Automated Design for Manufacturing of FDM Parts via Multi-Agent LLM Reasoning and Geometric Feature Recognition

Parts manufactured with Fused Deposition Modeling (FDM) often require Design for Additive Manufacturing (DFAM) modifications to ensure printability, structural integrity, and reduced post-processing. Current slicers identify defects such as steep overhangs but are unable to modify the underlying geometry. This work presents AgentsCAD, a multi-agent system that bridges raw boundary-representation (B-Rep) geometry and Large Language Model (LLM) reasoning to automate targeted DFM. The workflow begins by parsing a STEP file. The agentic system detects overhangs above a 45°threshold, constructs a face-adjacency topology graph, and optionally injects semantic feature labels from a GraphSAGE model trained on MFCAD++ (59,665 parts), before dispatching a Claude Sonnet design-reasoning agent that recommends reorientations, fillets, chamfers, and similar modifications. A GPT-4o vision-language verifier inspects rendered views to confirm geometric integrity. Outputs include a modified STEP file and a human-readable report. A test case on a birdhouse model demonstrates that the system correctly diagnoses overhangs, selects appropriate defect mitigation strategies, and proposes physically valid corrections, partially solving the geometry-to-language translation problem central to LLM-driven CAD modification.

cs.MA↗

arXiv2026

RocketSmith: Agentic Additive Manufacturing of High-Powered Rockets

RocketSmith is an agentic system which intelligently automates the DFAM process for the development of high powered rockets suitable for launch. The system utilizes a large language model to orchestrate the execution of software tools to validate design characteristics such as flight stability and generate the parametric design components for the rocket assembly. A collection of subagents and skills enable optimization workflows of flight parameters via iteration in both zero-shot and human-in-the-loop workflows. With this system, four distinct high power rockets with various motor and assembly configurations were developed utilizing the unique design capabilities of additive manufacturing. These assembly components were fabricated using various FDM printers, manually evaluated for flight readiness, and flight tested at a launch event. From these tests, all rockets achieved a stable launch and two of the four rockets were successfully recovered in reflyable condition. The altimeter data validated that the rockets achieved an altitude 80% of the expected apogee predicted by the agentic system, establishing consistency between simulation and experimentation.

cs.RO↗

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

Domain Adapted Large Language Models for Additive Manufacturing

This work presents a collection of multi-modal domain adapted large language models built upon the instruction tuned variants of open weight models (Gemma 3, Qwen 3, Gemma 4) using a relatively small dataset of around 50 million tokens. The dataset consists of open-access additive manufacturing journal articles with data extracted for the domain adaptive pretraining and visual instruction tuning processes. Various stages of the developed model are evaluated with the Additive-Manufacturing-Benchmark which consists of additive manufacturing domain specific tasks compiled published resources. Domain adapted and instruction tuned models exhibit proficiency in both language and vision based tasks, achieving accuracies upwards of 90% in general additive manufacturing knowledge. This domain adaptive pretraining and instruction tuning strategy outline an accessible specialization method for large language models to a domain such as additive manufacturing.

cs.LG↗

arXiv2026

LLM Trainer: Automated Robotic Data Generation via Demonstration Augmentation using LLMs

We present LLM Trainer, a fully automated pipeline that leverages the world knowledge of Large Language Models (LLMs) to transform a small number of human demonstrations (as few as one) into a large robot dataset for imitation learning. Our approach decomposes demonstration generation into two steps: (1) offline demonstration annotation that extracts keyframes, salient objects, and pose-object relations; and (2) online keypose retargeting that adapts those keyframes to a new scene, given an initial observation. Using these modified keypoints, our system warps the original demonstration to generate a new trajectory, which is then executed, and the resulting demo, if successful, is saved. Because the annotation is reusable across scenes, we use Thompson sampling to optimize the annotation, significantly improving generation success rate. We evaluate our method on a range of tasks, and find that our data annotation method consistently outperforms expert-engineered baselines. We further show an ensemble policy that combines the optimized LLM feed-forward plan with a learned feedback imitation learning controller. Finally, we demonstrate hardware feasibility on a Franka Emika Panda robot. For additional materials and demonstration videos, please see the project website: https://sites.google.com/andrew.cmu.edu/llm-trainer

cs.RO↗

arXiv2026

Generative Neural Operators through Diffusion Last Layer

Neural operators provide a powerful framework for learning discretization invariant mappings between function spaces, but standard deterministic models do not capture predictive uncertainty. We introduce diffusion last layer (DLL), a modular probabilistic output head for neural operator backbones. DLL represents target fields through an input dependent low rank expansion inspired by the Karhunen-Loéve expansion and learns a conditional diffusion model over the corresponding coefficient space. This design enables efficient distributional modeling while preserving the structural advantages of operator learning. On stochastic PDE benchmarks with random forcing, DLL achieves strong distributional fidelity and performs competitively with pixel space and conventional latent diffusion baselines. In deterministic long horizon rollout tasks, DLL improves rollout stability over the underlying backbone and provides useful estimates of predictive uncertainty under compounding autoregressive errors. These results suggest that diffusion modeling in learned coefficient spaces offers a practical route to uncertainty aware neural operators.

cs.LG↗

arXiv2026

SMDD-Bench: Can LLMs Solve Real-World Small Molecule Drug Design Tasks?

LLM agents have incredible potential for scientific discovery applications. However, the performance of LLM agents on real-world, small molecule drug design (SMDD) tasks across diverse chemistries and targets is unclear. Current evaluation methods are either ad hoc, too simple for real-world discovery, limited in scale, or restricted to single-turn question answering. In effort to standardize the evaluation of LLM agents on small molecule design, we introduce SMDD-Bench, a challenging, multi-turn, long-horizon agentic benchmark consisting of 502 guaranteed-solvable task instances spanning 5 task types: 2D Pharmacophore Identification, Interaction Point Discovery, Scaffold Hopping, Lead Optimization, and Fragment Assembly. SMDD-Bench tasks span a wide region of chemical space and involve 102 unique protein targets. Completely solving the benchmark would require having strong chemical and biological reasoning and 3D intuition, understanding specialized tool use, and displaying planning expertise over a limited number of oracle calls. We benchmark 7 frontier open and closed source LLMs and find even the most performant LLM, GPT5.4, solves only 40.2\% of tasks. We hope SMDD-Bench provides a standardized testbed to invigorate the field towards training and evaluating LLM agents for fully autonomous computational drug design. We host a public leaderboard at smddbench.com .

cs.AI↗

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

CADSmith: Multi-Agent CAD Generation with Programmatic Geometric Validation

Existing methods for text-to-CAD generation either operate in a single pass with no geometric verification or rely on lossy visual feedback that cannot resolve dimensional errors. We present CADSmith, a multi-agent pipeline that generates CadQuery code from natural language. It then undergoes an iterative refinement process through two nested correction loops: an inner loop that resolves execution errors and an outer loop grounded in programmatic geometric validation. The outer loop combines exact measurements from the OpenCASCADE kernel (bounding box dimensions, volume, solid validity) with holistic visual assessment from an independent vision-language model Judge. This provides both the numerical precision and the high-level shape awareness needed to converge on the correct geometry. The system uses retrieval-augmented generation over API documentation rather than fine-tuning, maintaining a current database as the underlying CAD library evolves. We evaluate on a custom benchmark of 100 prompts in three difficulty tiers (T1 through T3) with three ablation configurations. Against a zero-shot baseline, CADSmith achieves a 100% execution rate (up from 95%), improves the median F1 score from 0.9707 to 0.9846, the median IoU from 0.8085 to 0.9629, and reduces the mean Chamfer Distance from 28.37 to 0.74, demonstrating that closed-loop refinement with programmatic geometric feedback substantially improves the quality and reliability of LLM-generated CAD models.

cs.AI↗

arXiv2026

Image2Gcode: Image-to-G-code Generation for Additive Manufacturing Using Diffusion-Transformer Model

Mechanical design and manufacturing workflows conventionally begin with conceptual design, followed by the creation of a computer-aided design (CAD) model and fabrication through material-extrusion (MEX) printing. This process requires converting CAD geometry into machine-readable G-code through slicing and path planning. While each step is well established, dependence on CAD modeling remains a major bottleneck: constructing object-specific 3D geometry is slow and poorly suited to rapid prototyping. Even minor design variations typically necessitate manual updates in CAD software, making iteration time-consuming and difficult to scale. To address this limitation, we introduce Image2Gcode, an end-to-end data-driven framework that bypasses the CAD stage and generates printer-ready G-code directly from images and part drawings. Instead of relying on an explicit 3D model, a hand-drawn or captured 2D image serves as the sole input. The framework first extracts slice-wise structural cues from the image and then employs a denoising diffusion probabilistic model (DDPM) over G-code sequences. Through iterative denoising, the model transforms Gaussian noise into executable print-move trajectories with corresponding extrusion parameters, establishing a direct mapping from visual input to native toolpaths. By producing structured G-code directly from 2D imagery, Image2Gcode eliminates the need for CAD or STL intermediates, lowering the entry barrier for additive manufacturing and accelerating the design-to-fabrication cycle. This approach supports on-demand prototyping from simple sketches or visual references and integrates with upstream 2D-to-3D reconstruction modules to enable an automated pipeline from concept to physical artifact. The result is a flexible, computationally efficient framework that advances accessibility in design iteration, repair workflows, and distributed manufacturing.

cs.LG↗

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↗