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Driven by rapid advancements of Large Language Models (LLMs), agents are empowered to combine intrinsic knowledge with dynamic tool use, greatly enhancing their capacity to address real-world tasks. In line with such an evolution,…

Automatic differentiation (AD) enables powerful metasurface inverse design but requires extensive theoretical and programming expertise. We present a Model Context Protocol (MCP) assisted framework that allows researchers to conduct inverse…

Computational Physics · Physics 2026-04-13 Yi Huang , Bowen Zheng , Yunxi Dong , Hong Tang , Huan Zhao , S. M. Rakibul Hasan Shawon , Sensong An , Hualiang Zhang

Large Language Models (LLMs) have evolved into AI agents that interact with external tools and environments to perform complex tasks. The Model Context Protocol (MCP) has become the de facto standard for connecting agents with such…

Cryptography and Security · Computer Science 2026-04-27 Christoph Bühler , Matteo Biagiola , Luca Di Grazia , Guido Salvaneschi

Ad hoc dataset search requires matching underspecified natural-language queries against sparse, heterogeneous metadata records, a task where typical lexical or dense retrieval alone falls short. We reposition dataset search as a…

Information Retrieval · Computer Science 2026-04-21 Riccardo Terrenzi , Phongsakon Mark Konrad , Tim Lukas Adam , Serkan Ayvaz

The Model Context Protocol (MCP) has emerged as a de facto standard for integrating Large Language Models with external tools, yet no formal security analysis of the protocol specification exists. We present the first rigorous security…

Cryptography and Security · Computer Science 2026-01-27 Narek Maloyan , Dmitry Namiot

The integration of large language models (LLMs) into scientific research is accelerating the realization of autonomous ``AI Scientists.'' While recent advancements have empowered AI to formulate hypotheses and design experiments, a critical…

Quantum Physics · Physics 2026-05-27 Masaki Shiraishi , Ikko Hamamura , Tatsuya Ishigaki , Tadashi Kadowaki

The Model Context Protocol (MCP) enables large language models to invoke external tools through natural-language descriptions, forming the foundation of many AI agent applications. However, MCP does not enforce consistency between…

Cryptography and Security · Computer Science 2026-02-04 Zhihao Li , Boyang Ma , Xuelong Dai , Minghui Xu , Yue Zhang , Biwei Yan , Kun Li

Modern process simulators enable detailed process design, simulation, and optimization; however, constructing and interpreting simulations is time-consuming and requires expert knowledge. This limits early exploration by inexperienced…

Chemical Physics · Physics 2026-05-22 Jingkang Liang , Niklas Groll , Gürkan Sin

The increased adoption of the Model Context Protocol (MCP) for AI Agents necessitates robust security for Enterprise integrations. This paper introduces the MCP Gateway to simplify self-hosted MCP server integration. The proposed…

Cryptography and Security · Computer Science 2025-04-29 Ivo Brett

Bioinformatics tools are essential for complex computational biology tasks, yet their integration with emerging AI-agent frameworks is hindered by incompatible interfaces, heterogeneous input-output formats, and inconsistent parameter…

Quantitative Methods · Quantitative Biology 2025-10-03 Florensia Widjaja , Zhangtianyi Chen , Juexiao Zhou

The Model Context Protocol (MCP) standardizes tool use for LLM-based agents and enable third-party servers. This openness introduces a security misalignment: agents implicitly trust tools exposed by potentially untrusted MCP servers.…

Cryptography and Security · Computer Science 2026-02-25 Zhenhong Zhou , Yuanhe Zhang , Hongwei Cai , Moayad Aloqaily , Ouns Bouachir , Linsey Pang , Prakhar Mehrotra , Kun Wang , Qingsong Wen

The Model Context Protocol (MCP) has rapidly become a de facto standard for connecting LLM-based agents with external tools via reusable MCP servers. In practice, however, server selection and onboarding rely heavily on free-text tool…

Software Engineering · Computer Science 2026-02-24 Peiran Wang , Ying Li , Yuqiang Sun , Chengwei Liu , Yang Liu , Yuan Tian

Model Context Protocol (MCP) has recently gained increased attention within the AI community for providing a standardized way for large language models (LLMs) to interact with external tools and services, significantly enhancing their…

Distributed, Parallel, and Cluster Computing · Computer Science 2025-11-12 Zihao Ding , Mufeng Zhu , Yao Liu

The MCP Solver bridges Large Language Models (LLMs) with symbolic solvers through the Model Context Protocol (MCP), an open-source standard for AI system integration. Providing LLMs access to formal solving and reasoning capabilities…

Artificial Intelligence · Computer Science 2025-04-08 Stefan Szeider

Agentic frameworks powered by Large Language Models (LLMs) can be useful tools in scientific workflows by enabling human-AI co-creation. A key challenge is recommending the next steps during workflow creation without relying solely on LLMs,…

Multi-agent systems represent a significant advancement in artificial intelligence, enabling complex problem-solving through coordinated specialized agents. However, these systems face fundamental challenges in context management,…

Multiagent Systems · Computer Science 2025-05-01 Naveen Krishnan

Large Language Model (LLM) agents face security vulnerabilities spanning AI-specific and traditional software domains, yet current research addresses these separately. This study bridges this gap through comparative evaluation of Function…

Cryptography and Security · Computer Science 2025-07-10 Tarek Gasmi , Ramzi Guesmi , Ines Belhadj , Jihene Bennaceur

Large language models (LLMs) have recently demonstrated remarkable capabilities to comprehend human intentions, engage in reasoning, and design planning-like behavior. To further unleash the power of LLMs to accomplish complex tasks, there…

While powerful and well-established, tools like ParaView present a steep learning curve that discourages many potential users. This work introduces ParaView-MCP, an autonomous agent that integrates modern multimodal large language models…

Human-Computer Interaction · Computer Science 2025-05-13 Shusen Liu , Haichao Miao , Peer-Timo Bremer

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…

Artificial Intelligence · Computer Science 2026-01-27 Peter Pak , Achuth Chandrasekhar , Amir Barati Farimani