{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/an-open-source-pipeline-for-solving","title":"An open-source pipeline for solving continuous reaction-diffusion models in image-based geometries of porous media","arxiv_id":"2304.11165","date":"2023-04-17","proceeding":null,"authors":["Justina Stark","Ivo F. Sbalzarini"],"abstract":"We present a versatile open-source pipeline for simulating inhomogeneous reaction-diffusion processes in highly resolved, image-based geometries of porous media with reactive boundaries. Resolving realistic pore-scale geometries in numerical models is challenging and computationally demanding, as the scale differences between the sizes of the interstitia and the whole system can lead to prohibitive memory requirements. The present pipeline combines a level-set method with geometry-adapted sparse block grids on GPUs to efficiently simulate reaction-diffusion processes in image-based geometries. We showcase the method by applying it to fertilizer diffusion in soil, heat transfer in porous ceramics, and determining effective diffusion coefficients and tortuosity. The present approach enables solving reaction-diffusion partial differential equations in real-world geometries applicable to porous media across fields such as engineering, environmental science, and biology.","url_abs":"https://arxiv.org/abs/2304.11165v2","url_pdf":"https://arxiv.org/pdf/2304.11165v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"links_only","authors_date_abstract":"arXiv metadata, CC0 1.0 (https://info.arxiv.org/help/license), from the Kaggle arXiv metadata snapshot of 2026-09-12"},"code_links":[{"paper_slug":"an-open-source-pipeline-for-solving","repo_url":"https://git.mpi-cbg.de/mosaic/software/image-based-modeling/reactiondiffusion_imagebased_porousmedia","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}