Rule-Based Gillespie Simulation of Chemical Systems

[2509.01504] Rule-Based Gillespie Simulation of Chemical Systems Skip to main content Search Submit Donate Log in Quantitative Biology > Molecular Networks arXiv:2509.01504 (q-bio) [Submitted on 1 Sep 2025 ( v1 ), last revised 25 Aug 2026 (this version, v3)] Title: Rule-Based Gillespie Simulation of Chemical Systems Authors: Erika M. Herrera Machado , Jakob L. Andersen , Rolf Fagerberg , Christoph Flamm , Daniel Merkle , Peter F. Stadler View PDF HTML (experimental) Abstract: The MØD computational framework implements rule-based generative chemistries as explicit transformations of graphs representing chemical structural formulae. Here, we expand MØD by a stochastic simulation module that simulates the time evolution of species concentrations using Gillespie's well-known stochastic simulation algorithm (SSA). This module distinguishes itself among competing implementations of rule-based stochastic simulation engines by its flexible network expansion mechanism and its functionality for defining custom reaction rate functions. It enables direct sampling from actual reactions instead of rules. We present methodology and implementation details followed by examples which demonstrate the capabilities of the stochastic simulation engine. Comments: 20 pages, 7 figures Subjects: Molecular Networks (q-bio.MN) ; Chemical Physics (physics.chem-ph) Cite as: arXiv:2509.01504 [q-bio.MN] (or arXiv:2509.01504v3 [q-bio.MN] for this version) https://doi.org/10.48550/arXiv.2509.01504 Focus to learn more arXiv-issued DOI via DataCite Submission history From: Erika Magdalena Herrera Machado [ view email ] [v1] Mon, 1 Sep 2025 14:23:59 UTC (751 KB) [v2] Mon, 29 Sep 2025 12:42:03 UTC (733 KB) [v3] Tue, 25 Aug 2026 08:56:46 UTC (1,239 KB) Full-text links: Access Paper: View PDF HTML (experimental) TeX Source view license Current browse context: q-bio.MN < prev | next > new | recent | 2025-09 Change to browse by: physics physics.chem-ph q-bio References & Citations NASA ADS Google Scholar Semantic Scholar export BibTeX citation Bookmark Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer ( What is the Explorer? ) Connected Papers Toggle Connected Papers ( What is Connected Papers? ) Litmaps Toggle Litmaps ( What is Litmaps? ) scite.ai Toggle scite Smart Citations ( What are Smart Citations? ) Code, Data, Media Code, Data and Media Associated with this Article alphaXiv Toggle alphaXiv ( What is alphaXiv? ) Links to Code Toggle CatalyzeX Code Finder for Papers ( What is CatalyzeX? ) DagsHub Toggle DagsHub ( What is DagsHub? ) GotitPub Toggle Gotit.pub ( What is GotitPub? ) Huggingface Toggle Hugging Face ( What is Huggingface? ) ScienceCast Toggle ScienceCast ( What is ScienceCast? ) Demos Demos Replicate Toggle Replicate ( What is Replicate? ) Spaces Toggle Hugging Face Spaces ( What is Spaces? ) Spaces Toggle TXYZ.AI ( What is TXYZ.AI? ) Related Papers Recommenders and Search Tools Link to Influence Flower Influence Flower ( What are Influence Flowers? ) Core recommender toggle CORE Recommender ( What is CORE? ) Author Venue Institution Topic About arXivLabs arXivLabs: experimental projects with community collaborators arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs . Which authors of this paper are endorsers? | Disable MathJax ( What is MathJax? ) We gratefully acknowledge support from our major funders , member institutions , and all contributors. About · Help · Contact · Subscribe · Copyright · Privacy · Accessibility · Operational Status (opens in new tab) Major funding support from

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