Mohammad Atif

Mohammad Atif, Pulkit Dubey, Pratik P. Aghor et al.

High-fidelity direct numerical simulation of turbulent flows for most real-world applications remains an outstanding computational challenge. Several machine learning approaches have recently been proposed to alleviate the computational cost even though they become unstable or unphysical for long time predictions. We identify that the Fourier neural operator (FNO) based models combined with a partial differential equation (PDE) solver can accelerate fluid dynamic simulations and thus address computational expense of large-scale turbulence simulations. We treat the FNO model on the same footing as a PDE solver and answer important questions about the volume and temporal resolution of data required to build pre-trained models for turbulence. We also discuss the pitfalls of purely data-driven approaches that need to be avoided by the machine learning models to become viable and competitive tools for long time simulations of turbulence.

Mohammad Atif, Kriti Chopra, Ozgur Kilic et al.

Next-generation High Energy Physics (HEP) experiments will generate unprecedented data volumes, necessitating High Performance Computing (HPC) integration alongside traditional high-throughput computing. However, HPC adoption in HEP is hindered by the challenge of porting legacy software to heterogeneous architectures and the sparse documentation of these complex scientific codebases. We present CelloAI, a locally hosted coding assistant that leverages Large Language Models (LLMs) with retrieval-augmented generation (RAG) to support HEP code documentation and generation. This local deployment ensures data privacy, eliminates recurring costs and provides access to large context windows without external dependencies. CelloAI addresses two primary use cases, code documentation and code generation, through specialized components. For code documentation, the assistant provides: (a) Doxygen style comment generation for all functions and classes by retrieving relevant information from RAG sources (papers, posters, presentations), (b) file-level summary generation, and (c) an interactive chatbot for code comprehension queries. For code generation, CelloAI employs syntax-aware chunking strategies that preserve syntactic boundaries during embedding, improving retrieval accuracy in large codebases. The system integrates callgraph knowledge to maintain dependency awareness during code modifications and provides AI-generated suggestions for performance optimization and accurate refactoring. We evaluate CelloAI using real-world HEP applications from ATLAS, CMS, and DUNE experiments, comparing different embedding models for code retrieval effectiveness. Our results demonstrate the AI assistant's capability to enhance code understanding and support reliable code generation while maintaining the transparency and safety requirements essential for scientific computing environments.

Mohammad Atif, Vincent Garonne, Eric Lancon et al.

As the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory concludes 25 years of operation, preserving not only its vast data holdings ($\sim$1 ExaByte) but also the embedded scientific knowledge becomes a critical priority. The RHIC Data and Analysis Preservation Plan (DAPP) introduces an AI-powered assistant system that provides natural language access to documentation, workflows, and software, with the aim of supporting reproducibility, education, and future discovery. Built upon Large Language Models using Retrieval-Augmented Generation and the Model Context Protocol, this assistant indexes structured and unstructured content from RHIC experiments and enables domain-adapted interaction. We report on the deployment, computational performance, ongoing multi-experiment integration, and architectural features designed for a sustainable and explainable long-term AI access. Our experience illustrates how modern AI/ML tools can transform the usability and discoverability of scientific legacy data.