Lambda-PFLOTRAN 1.0: a workflow for incorporating organic matter chemistry informed by ultra high resolution mass spectrometry into biogeochemical modeling
| Autor: | K. A. Muller, P. Jiang, G. Hammond, T. Ahmadullah, H.-S. Song, R. Kukkadapu, N. Ward, M. Bowe, R. K. Chu, Q. Zhao, V. A. Garayburu-Caruso, A. Roebuck, X. Chen |
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| Jazyk: | angličtina |
| Rok vydání: | 2024 |
| Předmět: | |
| Zdroj: | Geoscientific Model Development, Vol 17, Pp 8955-8968 (2024) |
| Druh dokumentu: | article |
| ISSN: | 8955-2024 1991-959X 1991-9603 |
| DOI: | 10.5194/gmd-17-8955-2024 |
| Popis: | Organic matter (OM) composition plays a central role in microbial respiration of dissolved organic matter and subsequent biogeochemical reactions. Here, a direct connection of organic matter chemistry and thermodynamics to reactive transport simulators has been achieved through the newly developed Lambda-PFLOTRAN workflow tool that succinctly incorporates carbon chemistry data generated from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) into reaction networks to simulate organic matter degradation and the resulting biogeochemistry. Lambda-PFLOTRAN is a Python-based workflow, executed through a Jupyter notebook interface, that digests raw FTICR-MS data, develops a representative reaction network based on substrate-explicit thermodynamic modeling (also termed lambda modeling due to its key thermodynamic parameter λ used therein), and completes a biogeochemical simulation with the open source, reactive flow and transport code PFLOTRAN. The workflow consists of the following five steps: configuration, thermodynamic (lambda) analysis, sensitivity analysis, parameter estimation, and simulation output and visualization. Two test cases are provided to demonstrate the functionality of the Lambda-PFLOTRAN workflow. The first test case uses laboratory incubation data of temporal oxygen depletion to fit lambda parameters (i.e., maximum utilization rate and microbial carrying capacity). A slightly more complex second test case fits multiple lambda formulation and soil organic matter release parameters to temporal greenhouse gas generation measured during a soil incubation. Overall, the Lambda-PFLOTRAN workflow facilitates upscaling by using molecular-scale characterization to inform biogeochemical processes occurring at larger scales. |
| Databáze: | Directory of Open Access Journals |
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