Paper Citation Record · LEDGER

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows

As of 19 August 2026, this Paper Citation Record lists 48 of 48 outbound references and 0 inbound Pith citation observations for arXiv:2608.02642.

A citation records a reference. It does not transfer a finding from one paper to another.

pith.paper-citation-record.v1
2608.02642 v1

Coverage vector

measured 48 of 48 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-15T15:25:23.863323Z

measured 48 of 48 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-18T06:34:40.430872+00:00

measured 0 of 0 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links

measured 0 of 1 external citation measurements

A source-named dated measurement, never combined with another source.

Source: cited_works

Reference resolution

48 of 48 outbound references displayed

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External citation measurements

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Outbound references

Observation aef25bd3-e942-4b97-9f27-224cbe55408f · outbound

This paper cites , title =.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows , title =

Reference 1

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Observation 45b2b995-8429-4dbf-8a91-d30de51d9b16 · outbound

This paper cites doi:10.5281/zenodo.20953922 , url =.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows doi:10.5281/zenodo.20953922 , url =

Reference 2

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Observation 5c0051c8-753f-4dea-9dda-76da300ef757 · outbound

This paper cites Qwen3 Technical Report.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Qwen3 Technical Report

Reference 3

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Observation caa7a204-63a2-40e3-8e6f-842fff5f03a1 · outbound

This paper cites Computer Physics Communications , volume=.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Computer Physics Communications , volume=

Reference 4

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Observation ae0f7150-0278-4bbc-b9de-3c3043cfdede · outbound

This paper cites Journal of Computational Chemistry , volume=.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Journal of Computational Chemistry , volume=

Reference 5

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Observation 44908388-6a22-4c6b-ac0c-ac2a98b85c0a · outbound

This paper cites Gemini: A Family of Highly Capable Multimodal Models.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Gemini: A Family of Highly Capable Multimodal Models

Reference 6

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows 0] , author=

Reference 7

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Observation d2854b4a-36fe-4962-879e-e88cfed4e1af · outbound

This paper cites BMC Research Notes , volume=.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows BMC Research Notes , volume=

Reference 8

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This paper cites 0: the sage small molecule force field , author=.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows 0: the sage small molecule force field , author=

Reference 9

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Observation c050d89f-d95d-490d-b399-d84fd1077adb · outbound

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Release , volume=

Reference 10

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Observation 536238e9-c9ad-4b23-8a2e-a0d1ff19adad · outbound

This paper cites Journal of Cheminformatics , volume=.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Journal of Cheminformatics , volume=

Reference 11

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Observation 463702f8-1794-4852-91b2-6cd408022dc5 · outbound

This paper cites International Conference on Machine Learning , pages=.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows International Conference on Machine Learning , pages=

Reference 12

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Observation dd019d9a-49c3-497b-aa59-99e02092549e · outbound

This paper cites Journal of Open Source Software , volume=.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Journal of Open Source Software , volume=

Reference 13

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Observation 54e553ac-d67d-4fc1-a044-8a67774268ca · outbound

This paper cites Computer Physics Communications , volume=.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Computer Physics Communications , volume=

Reference 14

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Observation 75e8b60c-4580-414a-9318-a809e1da6362 · outbound

This paper cites The Journal of Chemical Physics , volume=.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows The Journal of Chemical Physics , volume=

Reference 15

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Observation a04ed5ca-e8bb-4320-8f45-675708215a70 · outbound

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows PLOS ONE , volume=

Reference 16

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Journal of Open Source Software , volume=

Reference 17

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Observation 3981b578-6231-4973-ae78-123aac53cd30 · outbound

This paper cites Journal of Chemical Information and Modeling , volume=.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Journal of Chemical Information and Modeling , volume=

Reference 18

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Observation 4a36cc05-5b70-4882-8bb9-fac922e4aa9b · outbound

This paper cites DeepSeek-V3 Technical Report.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows DeepSeek-V3 Technical Report

Reference 19

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Observation d83a2e00-97bc-4876-89b3-7a0375d4931a · outbound

This paper cites Automating MD simulations for Proteins using Large language Models: NAMD-Agent.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Automating MD simulations for Proteins using Large language Models: NAMD-Agent

Reference 20

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows and Tanikanti, Aditya and Ke

Reference 21

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Observation 0424b76d-0cc6-439a-b96e-21091fbb98f6 · outbound

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows 2025 , eprint =

Reference 22

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Observation 7ab55fa8-94df-45b0-a448-5bb172486d27 · outbound

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows 2026 , eprint =

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Observation 7fed8692-c34c-4dc3-b0c5-da3d9e775426 · outbound

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

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows PolyJarvis: An LLM-Orchestrated Agent for Automated All-Atom Molecular Dynamics of Amorphous Homopolymers

Reference 24

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Observation 7b798736-b641-4e39-a7ec-4c7cc575923a · outbound

This paper cites MDAgent: A Multi-Agent Framework for End-to-End Molecular Dynamics Research.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows MDAgent: A Multi-Agent Framework for End-to-End Molecular Dynamics Research

Reference 25

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Observation ec7c2bc7-2533-4933-ad89-e3e63545f04f · outbound

This paper cites MDGYM: Benchmarking AI Agents on Molecular Simulations.

MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows MDGYM: Benchmarking AI Agents on Molecular Simulations

Reference 26

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Observation e9ebdf69-1055-458a-955b-7925b6e957df · outbound

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows and Coveney, Peter V

Reference 27

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Observation 40ef5574-4358-4960-a7c9-bf33409209fc · outbound

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Journal of Chemical Theory and Computation , volume=

Reference 28

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Journal of Chemical Theory and Computation , volume=

Reference 29

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Observation 9e2c92a0-502a-484e-9ef6-bb5ea0037950 · outbound

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Wiley Interdisciplinary Reviews: Computational Molecular Science , volume=

Reference 30

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Observation eb3dbc9c-277e-45a6-8b15-7e334533e50a · outbound

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows A Survey of Large Language Models

Reference 31

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows ACM Transactions on Software Engineering and Methodology , year=

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows 2023 , doi =

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Observation 6b02981f-cf72-4364-9ba8-cff2a714f3fa · outbound

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows SoftwareX , volume=

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows The Journal of Physical Chemistry B , volume=

Reference 35

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Observation 0c934d55-68e5-4d1e-a08e-30c702485c95 · outbound

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Nature , volume=

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Journal of Computational Chemistry , volume=

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Observation e7e4dddf-03ff-4a42-ac1e-20f3b1dd8384 · outbound

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Neuron , volume=

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Observation b80b6a9c-acfa-4fa4-80bf-08f6d496f0f7 · outbound

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Reference 40

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Observation c8127b96-c2bb-4f4a-a9d5-f26fb6fa567b · outbound

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Nature Reviews Methods Primers , volume =

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows and Wettig, Alexander and Lieret, Kilian and Yao, Shunyu and Narasimhan, Karthik R

Reference 42

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Observation 5625be1b-aa18-4e32-8297-a0187b3da7b0 · outbound

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Reference 43

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Observation d6f2a173-58df-40b3-b29b-5594bf5d4efe · outbound

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Meta-Harness: End-to-End Optimization of Model Harnesses

Reference 44

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Observation 69997316-9ad3-45b0-9ab3-88f792b76b22 · outbound

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Harness Updating Is Not Harness Benefit: Disentangling Evolution Capabilities in Self-Evolving LLM Agents

Reference 45

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Observation d3f684dd-0b84-49c8-a56c-4a7ab00f35a3 · outbound

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Agentic Harness Engineering: Observability-Driven Automatic Evolution of Coding-Agent Harnesses

Reference 46

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Journal of Computer-Aided Molecular Design , volume=

Reference 47

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T15:25:24.605376Z

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Observation 6c9c3981-17b6-4dd4-88db-0ee5c4436353 · outbound

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MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows Nature Communications , volume=

Reference 48

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Pith citing papers

No inbound Pith citation observations are available.