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oai:figshare.com:article/33972085 2026-09-23T08:41:58Z category_24220 category_24184 category_24208 category_24391 category_24379 category_24394 item_type_3 month_year_09_2026

Rising CO₂ closes the temperature window on the C3-to-C4 transition — model, data and verification Emre Yazar (25095388) Bülent Akgün (25095407) Ecological physiology Bioinformatic methods development Bioinformatics and computational biology not elsewhere classified Plant physiology Plant biochemistry Plant biology not elsewhere classified C2 photosynthesis C3–C4 intermediate CAM elevated CO₂ nitrogen allocation photorespiration Rubisco kinetics stomatal optimality This deposit contains everything behind the manuscript of the same name: theleaf model, the seven simulation batches that produced every number, the scriptthat draws every figure, and `verify.py`, which recomputes each quantitativeclaim in the paper from the deposited data and reports a pass or failure againstit. No new experimental data were generated. All validation is against publishedliterature. --- ## Quick start ```bashpip install numpy scipy pandas matplotlibpython scripts/verify.py # 150 checks; prints ALL PASSpython scripts/figures.py # redraws every figure into figures/``` Both run from any working directory and find the data relative to themselves.Set `PATHWAYS_DEPOSIT` to point them at a copy of this tree somewhere else. Reproducing a batch from scratch takes longer. Each script is resumable — itskips any row already present in its output CSV — so it can be stopped andrestarted freely: ```bashpython scripts/final.py --workers 16 # ~2301 leaf-dayspython scripts/vogan_axis.py --workers 16 # ~274 leaf-days, about 12 min``` Delete (or move aside) the corresponding `results_*/` directory first if youwant a genuinely fresh run rather than a resume. --- ## What is here ```pathways/ the model packagescripts/ the seven batch scripts, verify.py, figures.pyresults_final/ the production batch the paper reportsresults_barrier/ the matched-barrier and fixed-mean sweepsresults_controls/ hydraulic, drought and CAM controlsresults_light/ photon flux, leaf nitrogen, and the λ endpointsresults_vogan/ the continuous sweep along the ¹⁴C-fixation axisresults_topt_convention/ the thermal validation under the mean temperature conventionresults_superseded/ three earlier batches, deposited unchangedfigures/ output of scripts/figures.py, under its internal namesfigures_as_published/ the same figures under the numbers used in the paper``` ### The model `pathways/` implements one leaf in two compartments, mesophyll and bundlesheath, coupled by diffusion through the bundle-sheath conductance *g*bs. Thecarboxylation core is Farquhar–von Caemmerer–Berry in each compartment; the C4cycle follows von Caemmerer (2021). Six pathway configurations — C3, C2, twoC3–C4 intermediate states, C4 and CAM — are points in one continuousconfiguration space, not separate models, and they share a leaf-nitrogen budget,a soil–plant hydraulic system and a single marginal water cost λ. | file | what it holds ||---|---|| `leaf.py` | the two-compartment leaf and its steady state || `ledger.py` | the shared ATP/NADPH budget, c₁₄ ATP-synthase stoichiometry || `nitrogen.py` | the leaf-nitrogen budget and how capacity is bought from it || `kinetics_v2.py` | pathway-specific Rubisco kinetics and their temperature response || `optimal_stomata.py` | the Cowan–Farquhar optimality solution for *g*s || `soil.py` | the soil column and the plant hydraulic path || `cam.py` | the CAM configuration and the diurnal forcing || `config.py` | the configuration vector θ | Modules not imported by the seven batch scripts (`stomata.py`, `photo3.py`,`compete.py`, `kinetics.py`, `optimal_cam.py`) are earlier or alternativeimplementations, kept so that the superseded batches can be re-derived. ### The batches One leaf-day is one 24-step diurnal integration of one configuration under oneforcing. 6487 leaf-days in the current batches, plus 6850 superseded. | script | output | leaf-days | what it supports in the paper ||---|---|---|---|| `final.py` | `results_final/` | 2301 | the ladder, the acclimated grid, the respiration control, the Rubisco swap, the λ sweep, the thermal optima || `barrier.py` | `results_barrier/` | 810 | the second step at a matched barrier; the amplitude envelope at fixed reported mean || `controls.py` | `results_controls/` | 756 | evaporative demand × drought; the hydraulic null; CAM priced in the same water || `light.py` | `results_light/` | 2250 | photon flux 200–1600; leaf nitrogen 1.0–3.0 g m⁻²; the Way *et al.* λ endpoints || `vogan_axis.py` | `results_vogan/` | 274 | the water step on Vogan's own ¹⁴C axis, swept continuously || `topt_convention.py` | `results_topt_convention/` | 96 | the thermal validation re-run under the mean temperature convention || `production.py` | `results_superseded/results_production/` | 2292 | superseded; see below | `results_vogan/vogan_axis.csv` carries 302 rows for 274 configurations. Ten"rung" jobs are written out with their actual *f*R,BS while the job spec leavesit blank, so the original resume key never matched them and they were recomputedon each restart. The duplicates agree to 2×10⁻¹⁰, `verify.py` de-duplicatesbefore using the file, and the key has been fixed in the deposited`vogan_axis.py` — re-running it against this CSV now reports "0 to run" ratherthan repeating those ten. The CSV is deposited as it was produced. ### Superseded batches Three earlier batches are deposited unchanged so that numbers quoted in earlierversions of this work can be re-derived. **They are not the batches the paperreports**, and where a superseded file and its replacement both exist the paperuses the replacement: - `results_production/` — run before day respiration was charged against the whole nitrogen budget. Its `gbs_band.csv` measures the second step without matching the bundle-sheath barrier, which `results_barrier/matched_barrier.csv` replaces.- `results_revision/` — run on a leaf-nitrogen allocation that gave *J*max/*V*cmax outside the measured range.- `results_testbatch/`, `sweep.csv` — exploratory. ### Figures `scripts/figures.py` redraws all eleven figures and writes a `.json` sidecarbeside each one recording the input files and their SHA-256 hashes, so a figurecan always be traced to the data it was drawn from. The script uses its owninternal names; the paper renumbers them: | in the paper | in `figures/` ||---|---|| Fig. 1 | `Fig1_crossover` || Fig. 2 | `Fig2_c2_advantage` || Fig. 3 | `Fig4_three_currencies` || Fig. 4 | `Fig6_undetermined_step` || Fig. 5 | `Fig7_rubisco_kinetics` || Fig. 6 | `Fig5_validation` || Fig. 7 | `Fig8_cam` || Fig. S1 | `Fig3_design_space` || Fig. S2 | `Fig9_water_robustness` || Fig. S3 | `Fig10_light` || Fig. S4 | `Fig11_nitrogen` | `figures_as_published/` holds the same files under the paper's numbering. `figures.py` refuses to run without `results_controls/`, because two of itspanels must not be built from the superseded nitrogen arm. --- ## verify.py The point of this deposit. `verify.py` transcribes each claim in the paper as aliteral, recomputes the same quantity from the deposited CSVs, and prints a passor failure. It does not import the manuscript, so a transcription error in thepaper fails here rather than being reproduced. ```$ python scripts/verify.py...==============================================================================ALL PASS``` 150 checks. Among them: the crossover temperatures and the window closing atboth ends; the C2 carbon and water results across every sensitivity axis; thematched-barrier second step; the Rubisco swap at equal nitrogen and at equal*V*cmax; the thermal optima under both temperature conventions; and the waterstep on the ¹⁴C axis, including the two failures the paper reports. Three checks in an earlier version failed once the `vogan_axis` batch wascomplete, and the claims were corrected rather than the checks relaxed. Thechecker is written so that this is the normal way a wrong number is caught. --- ## Two failures the paper reports rather than hides Both are checked here, so a reader can confirm them. **The thermal optimum.** On the quantity a cuvette *A*–temperature responseactually measures, the modelled C3 optimum is 6–10 °C too warm and reproduces42% of the measured shift with growth CO₂ (34% under the mean temperatureconvention). The C4 optimum moves −1.7 °C against a measured +2.5 — identicallyunder both conventions, so it is not an artefact of which temperature is calledthe growth temperature. **The water step.** Across the 50–65% ¹⁴C-fixation interval Vogan (2010)measured, the model gives 0.97–1.22× at 380 µmol mol⁻¹ and 1.06–1.35× at 180,against a measured 2–2.5×. Over the *whole* axis it gives 2.31× and 2.11× — thesize that was measured. The defect is where the water gain sits along the axis,not its total. --- ## Requirements Python 3.9 or later with `numpy`, `scipy`, `pandas` and `matplotlib`. Nocompiled extensions, no configuration, no network access. See`requirements.txt`. ## Depositing this elsewhere Nothing here is tied to a particular archive. `DEPOSIT-METADATA.txt` holds thetitle, authors, ORCIDs, description, keywords and licence in plain text, readyto paste into any repository's upload form; `zenodo.json` is the machine-readableform for Zenodo and other InvenioRDM sites, and `CITATION.cff` is read by GitHub,Dataverse and most citation tooling. Whichever archive is used, the DOI it issuesgoes into the manuscript's Data availability statement in place of"[DOI on acceptance]". ## Licence Code is MIT (`LICENSE`). Data files in `results_*/` and the figures areCC BY 4.0. Cite the manuscript and this deposit if you use either. 2026-09-23T08:41:58Z Dataset Dataset 10.6084/m9.figshare.33972085.v1 https://figshare.com/articles/dataset/Rising_CO_closes_the_temperature_window_on_the_C3-to-C4_transition_model_data_and_verification/33972085 MIT