Kinder & Faulkner · manuscript draft, version 2.0, not submitted · source of record preprint/modeling_radioresistance_and_radiotropic_fitness.tex
The movement results and calibration gates below describe the original CPM. A separate synthetic survival, passive phase and nutrient-growth implementation is documented in diagnostics/fitness_phase. Its frozen production run completed from source 841d052 and its results are appended in PREDICTION.md; it supplies no biological calibration and does not implement the original fitness-field PSDE.
A mechanistic modelling framework for a seven-species biofilm community under ionising radiation, plus the calibration and transport machinery that decides what the framework is allowed to claim.
The consortium at the ensemble configuration, seed 42, MCS 0 to 100, two arms side by side.
A 40 × 40 × 40 lattice, six parcels per species; left, the full model; right, β_ion = 0 and
α_M = 0, so the acceptance rule keeps adhesion and volume only. Both arms start from the same
seeding frame. Colours name the seven species, in the order biofilms_potts.jl declares them.
The frames were written by diagnostics/melanin_ensemble/consortium_frames.jl (occupied sites
per MCS, gzipped, with a manifest naming the seed, configuration, arms, git commit, Julia version
and machine). A separate receipt records the clean renderer revision and input hashes for
tools/render_consortium.py with matplotlib and ffmpeg in the palette biofilms_potts.jl
declares. The manuscript's consortium figure is the MCS 0, 50 and 100 columns of the same frames.
Axes count lattice sites, not lengths. The pitch is D-PITCH, still awaiting_measurement, and
no physical time exists (seconds_per_mcs is NaN). Accumulated dose is zero in every frame. So
this shows the Cellular Potts model under its static radial field alone, with no transport
coupling. Figure 1 reports the 256-seed radial ensemble; these images show seed 42. Other diagnostics identify their own runs. Correction PRE-SEND-06 scopes this caption and records the separate clean render provenance.
Replaced 2026-09-24: the animation this replaces, assets/consortium_400mcs.gif, was N = 20
with two parcels per species and came from snapshots that recorded no seed, so it could not be
regenerated; it stays in assets/ and is embedded nowhere. The paragraph it carried, and its
2026-09-17 correction about cpm_seed, are in git history.
Four things run. A 3D Cellular Potts model (biofilms_potts.jl) evolves biomass parcels on a
cylindrical lattice under a four-term Metropolis acceptance functional — adhesion, volume, radiation
and melanin — with a static radial radiation field and a genuinely two-way melanin field. A
cylindrical radiodialysis transport model (biofilms_radiodialysis.R, and a second
implementation inside the CPM) solves a three-equation contaminant/sorbate/membrane system in which
membrane permeability is a dose-driven field rather than a fixed material constant — the most
interesting mechanism in the repository. An OpenMC photon-transport path (coupling/) builds
transport models from a lattice snapshot, tallies heating, converts it to absorbed dose and
attributes that dose to lineage labels. A calibration layer (calibration/) gates all three, and
currently refuses to emit a single physical unit.
julia --project=. biofilms_potts.jl --no-radiolysis # CPM only, N = 60, 200 MCS, seed 42The coupled entry point does not run. julia --project=. biofilms_potts.jl (no flag) calls
main_coupled(), which refuses on its first Monte Carlo step with RADIODIALYSIS: BLOCKED,
because the coupled loop marks its biomass basis as an occupancy mean and the gate refuses that
basis. That refusal is deliberate and is pinned by tests/radiodialysis_basis_gate.jl; it is not
a bug to be cleared by acknowledging the gate. See
Radiodialysis membrane transport.
The framework is uncalibrated. Its parameters are literature priors and declared model inputs. No lattice pitch, no seconds-per-Monte-Carlo-step and no material density has been selected, and no output has been compared to a measurement of a target system. Every simulation number below is reported in the dimensionless model units it was computed in.
On the manuscript's status: web searches on both 2026-08-15 and 2026-08-24 found no record of a
bioRxiv posting, and no DOI appears anywhere in the repository. Treat it as unposted — that is a
search result, not proof. (Its predecessor, the superseded modeling_radiotrophic_fitness.md, had
a closing "Notation Fixes Required Before Submission" section; the current, revised
.tex — the source of record — has no such section and no unresolved notation issues.)
Five phenomena travel under one loose word and they are not interchangeable. A survival curve cannot
calibrate a directional term. The full argument is in docs/calibration/integration_contract.md.
| Phenotype | What it means | Represented here? |
|---|---|---|
| radiotropic | directional redistribution toward or away from a source | yes — this is response.hamiltonian |
| radiotrophic | radiation measurably enhances growth or metabolism | no — requires growth, and there is none |
| radioresistant | elevated survival after exposure | no — requires death, and there is none |
| melanized_radioprotective | melanin measurably alters damage, survival or shielding | no — requires damage |
| radiation_responsive | molecular, morphological or material change after exposure | partly — response.melanin |
compute_delta_H adds β_ion[s]·I_γ when a parcel gains a site, so a negative β_ion lowers
the acceptance functional in high-dose sites and the parcel drifts up the gradient. That is a
tropism. It was previously labelled "metabolic energy gain", which conflates a Metropolis
acceptance functional in arbitrary units with an energy budget; the model creates no biomass for such
a gain to act on.
Radiotrophy and radioresistance are therefore structurally absent here, for the same reason
response.growth_survival is unsupported_by_current_model. They are not weakly supported. A model
with no birth and no death cannot express either, and no quantity of data changes that without a
model revision.
This has a consequence worth stating plainly: the published D10 evidence — which is strong, and is
what anchors the per-species β_ion magnitudes — is radioresistance evidence being spent on a
tropism coefficient. That substitution is legitimate as a declared modelling choice, and it is now
declared rather than left implicit in a sign convention. The constant is RADIOTROPIC in
biofilms_potts.jl@const RADIOTROPIC = Set([CN, CS]), renamed from RADIOTROPHIC; biofilms_3d.R's species flag likewise.
This is the most interesting single result in the repository, and it is a self-audit finding rather
than a simulation output. At the shipped constants I0 = 1.0 and T_cpm = 5.0:
| Term | ΔH | Metropolis acceptance bias |
|---|---|---|
ΔH_rad, radiotropic species (β = −5e−5) |
−5.0e−5 | 1.000010 |
ΔH_rad, most radiosensitive species (β = 7.5e−2) |
+7.5e−2 | 0.985 |
ΔH_mel over 256 seeds, M = 1.26 to 2.56 |
−0.630 to −1.281 | 1.134 to 1.292 |
β_ion is the one parameter Table 2 tabulates per species. It is also the one the entire sign
convention is written around.
It biases acceptance by one part in 10⁵ for one role of the two negatively signed species occupying a site. That figure is not the term's reach. Signed by role, the term extends to 7.505e-2.
The melanin term biases acceptance by 13.4% to 29.2% across seeds 42–297. That is larger by
about an order of magnitude, 8.39 to 17.06 in ΔH. The coefficient behind it is a 0.5 hard-coded
in compute_delta_H, appearing in no table and in no configuration file.
Corrected 2026-09-17. The two figures above read 15.5% and 9.6, both from seed 42 alone.
An independent Odin port ran seeds 42–297. There C. sphaerospermum's MCS-100 melanin runs from 1.2596 to 2.5613, and seed 42's 1.437157 is the 31st lowest of the 256.
The order-of-magnitude comparison survives. The two point values did not.
Radiation still reaches the dynamics. It reaches them indirectly, because melanin_drive is
copied from the radiation field:
radiation → production (α_M, tabulated) → M → ΔH_mel (0.5, untabulated) → tropism
Two consequences. A sensitivity analysis over β_ion would report the radiation response as
negligible — right about the coefficient, wrong about the mechanism. And only the product
α_M · k reaches the dynamics, so cpm.melanin_coupling and response.melanin are jointly
identifiable at best and never separately. The coefficient is now ledgered as cpm.melanin_coupling
in data/parameter_provenance.csv with status=blocked and sensitivity_rank=high. It is one of
five rows in that ledger not ranked unknown, and the only one outside the A0 transport sweep — the
other four (transport.mesh.base_dimension, transport.mesh.coarsening_factor, transport.batches,
transport.particles) were ranked by that sweep and carry sensitivity_domain = transport_numerical, which is a numerical-convergence rank and not a biological one. Every
biological-response row in the ledger is still unknown, because no sensitivity analysis has been
run over any of them; this one was measured by hand.
For scale: adhesion differences in the hand-specified J matrix are O(4–20) per neighbour pair, so
ΔH_adh remains the largest term and still sets the sorting structure. The ordering is
adhesion ≫ melanin ≫ radiation.
Each refusal below is enforced in code and pinned by a test. None of them is a caveat added in prose.
| Not claimable | Why | What would clear it | Where enforced |
|---|---|---|---|
| Any length in µm or cm | No lattice pitch is selected. A pitch is not identifiable from a cell volume alone: V_physical = V_sites · a³ constrains only a product. select_pitch() refuses without declared tolerances, refuses when any tolerance is unset, and refuses when no evaluation is marked held-out. An undeclared tolerance is never read as infinitely permissive. |
A calibrated 3-D stack of a target system with a genuine held-out acquisition, plus populated tolerances in config/cpm_spatial_acceptance_template.toml. |
docs/calibration/cpm_spatial_calibration.md, calibration/biofilm_calibration/spatial/pitch_selection.py |
| Any duration in seconds, or any dose in Gy | No seconds/MCS conversion exists. CPMParams.seconds_per_mcs ships NaN and accrue_dose! raises rather than run without it. The repository has two independent clocks — MCS count and radiodialysis seconds — with no declared conversion. |
The dynamic observable is already selected (biomass_autocorrelation_decay, status provisional). dt_MCS = a² · S_sim / S_exp still needs a pitch, so this is blocked on the other half. |
docs/calibration/time_observable_contract.md, data/calibration/spatial/time_observable.csv, biofilms_potts.jl |
Any mass, concentration, or g cm⁻³ |
No wet bulk density and no closed elemental composition. data/calibration/voxel_binding.csv carries both numeric fields blank; blank means NOT MEASURED and is never read as zero. wet_bulk_density() raises when a wet mass is divided by a cells_only volume. |
Replicate wet and dry mass with matched hydrated and dry blanks, a hydrated volume on a whole_biofilm_envelope basis, ash, and CHNS + ICP closing to 1 on a wet-bulk basis — on one specimen under one condition. |
docs/calibration/material_basis_contract.md, calibration/biofilm_calibration/materials/ |
| Growth, division, survival, or extinction | response.growth_survival is unfittable in principle, not merely unmeasured: the CPM has no growth dynamics and divide_cell! has no trigger. |
A model change. No quantity of data clears it. | docs/calibration/integration_contract.md, calibration/biofilm_calibration/schema.py |
| Anything per cell | One CPM cell ID is a computational biomass parcel, with literal_generation_claim_allowed = false for all seven species. Reading a parcel-volume distribution as a cell-size distribution, or comparing parcel counts to colony-forming units, is refused. |
A model in which one ID is one organism — again a model change, not data. | docs/calibration/cpm_entity_semantics.md, data/calibration/spatial/entity_semantics.csv |
| A per-organism spatial prediction for B. subtilis, C. sphaerospermum or A. niger | Three of the seven species have morphologies the model cannot hold at any pitch — rods and filaments need surface-area, elongation and connectivity terms compute_delta_H does not have. Verdict: MODEL_REVISION_REQUIRED. |
Those terms. | docs/calibration/cpm_spatial_calibration.md, calibration/biofilm_calibration/spatial/representability.py |
| A physical apparatus | Nothing here defines a physical system. The legacy R visualisation uses normalised R = 1, L = 2, so no value in it becomes centimetres by assigning a unit. The CPM additionally forces L = 2R — a topology fact, not a resolution one — so domain.semantics = "microvolume" is the only honest declaration available. |
A declared apparatus with an independent length scale, which would also relax L = 2R. |
docs/physical_reference_system.md |
| A coupled dose-driven remediation loop | STOP CONDITION RETAINED: no OpenMC dose enters the radiodialysis model until the constitutive choice is explicitly selected. In the current code m and P_eff are independent open-loop functions of time; neither reads the other. |
An explicit constitutive selection for how damage maps to permeability, then import_dose_field! on a real path. |
docs/online_coupling_design.md, docs/audit_biofilms_potts.md §6, §10 |
Two rules the whole repository runs on:
- Empty is not zero. A blank numeric cell means "not measured" and reads back as
None. Nothing here substitutes0.0for a missing measurement — the single most dangerous default in a calibration ledger. blockedis notunsupported_by_current_model. A blocked quantity awaits a measurement; an unsupported one awaits a model change, and no quantity of data will clear it.
The repository root also carries unsorted media and data artifacts — PDFs, MP4s, Tableau workbooks,
TSV exports, loose GIFs and PNGs — that are not part of the framework and are not listed here. One
of them is no longer unsorted: geolocator/ and the power-plant dataset beside it are a maintained
subsystem with its own provenance and tests, described under
Primary Fuel Source Geolocator. It is still
outside the framework, and it is documented so that sharing a repository is not mistaken for coupling.
.gitmodules declares an unrelated submodule (Lumped-Uncertainty-SLS-MPC) that is not checked out
and is referenced by nothing; git clone --recurse-submodules pulls an MPC repository you did not
ask for.
Biofilms/
├── biofilms_potts.jl # 3D Cellular Potts Model + radiodialysis coupling (authoritative)
├── biofilms_potts_jacc.jl # JACC/AMDGPU port (8-colour checkerboard)
├── biofilms_radiodialysis.R # Radiodialysis membrane PDE — Shiny app
├── biofilms_3d.R # Cylindrical bioreactor — Shiny app (legacy)
├── biofilms.R # Flat-domain particle Langevin SDE + k-means (legacy)
├── reactor_decision_tree.R # k-NN / logistic sketch over 4 fuel candidates (illustrative)
├── validate_serial.jl # Serial-vs-JACC statistical comparison
├── export_checkpoint.jl # HDF5 checkpoint / transport-snapshot export
├── scoby_3d.jl # empty (0 bytes)
├── Project.toml # Manifest.toml and LocalPreferences.toml exist locally
│ # but are gitignored — a clone resolves its own
│
├── calibration/ # biofilm-calibration (Python, numpy-only)
│ ├── biofilm_calibration/
│ │ ├── spatial/ # entity semantics, scale candidates, biomass-field
│ │ │ # coarse-graining, structure, occupancy, pitch selection,
│ │ │ # morphology, representability, time observable,
│ │ │ # ingest/readers, dataset screening
│ │ ├── materials/ # basis-tagged Quantity arithmetic, mixture/mass closure,
│ │ │ # seeded Monte-Carlo uncertainty, export gate
│ │ ├── integration.py # the voxel binding where the two branches join
│ │ ├── acquisition.py # acquisition contract, biosafety gate
│ │ ├── precision.py # derived replicate counts, detectability
│ │ └── schema.py # shared status / evidence vocabulary
│ ├── scripts/ # vcholerae_pilot (surrogate), detectability_pilot,
│ │ # emit_synthetic_reference_config, reference_d_status
│ └── tests/ # 20 modules, 429 tests collected
│
├── contract/ # biofilm-contract (Python; NO dependencies)
│ └── physical_contract/ # vocabulary, MaterialSpec, composition closure,
│ # source placement, git provenance, feedback
│ # gate verdicts. calibration/ may not import
│ # coupling/, so what both need lives here.
│
├── coupling/ # biofilm-openmc (Python; numpy, h5py)
│ ├── biofilm_openmc/ # config, model, materials, mesh, dose, lineage,
│ │ # snapshot, results, fingerprint, convergence, drivers,
│ │ # feedback_uq, feedback_gate
│ ├── scripts/ # a0_sweep, synthetic_e2e, import_dose_field.jl
│ ├── requirements.txt
│ └── tests/ # 22 unit modules + tests/integration/ (5, OpenMC-gated);
│ # 340 collected (6 modules skip without OpenMC)
│
├── config/
│ ├── coupling_template.toml # 21 REQUIRED-but-unset keys
│ ├── cpm_spatial_acceptance_template.toml # every threshold unset
│ ├── biofilm_material_acceptance_template.toml # every threshold unset
│ ├── reference_a0_water_phantom.toml # the first populated configuration
│ ├── reference_synthetic_biofilm_e2e.toml # synthetic; calibrates nothing
│ ├── reference_d_spatial_acceptance.toml # FROZEN declarations
│ ├── reference_d_material_acceptance.toml # FROZEN declarations
│ └── feedback_effect_policy_template.toml # threshold UNSET on purpose
│
├── data/
│ ├── parameter_provenance.csv # 44 rows × 21 columns, per-parameter provenance ledger
│ ├── sources.csv # 12 sources pinned by version / accessed_date / sha256
│ ├── a0_transport_convergence.csv # 100 data rows: the whole A0 sweep, 5×4×5
│ ├── calibration/
│ │ ├── spatial/ # entity semantics, structure, morphology, time observable,
│ │ │ # dataset_candidates.csv (+ .sha256),
│ │ │ # pilot_vcholerae.csv / .metadata.json / .preflight.json
│ │ ├── materials/ # blanks, bulk, components, elemental, metal loading (header-only)
│ │ ├── voxel_binding.csv # the join; both numeric fields blank
│ │ └── baseline_condition.csv # ships UNSET
│ └── research/ # radiotrophic compatibility audit ledgers
│ ├── radiation_response_candidates.csv # 64 data rows (116 preamble lines)
│ ├── radiotrophic_dataset_candidates.csv # 64 data rows
│ └── radiotrophic_materialization_candidates.csv # 26 data rows
│
├── docs/
│ ├── audit_biofilms_potts.md # the contract the coupling work was built against
│ ├── physical_reference_system.md, openmc_stack.md, exchange_schema.md
│ ├── online_coupling_design.md, jacc_coupling_port.md, adder_applicability.md
│ ├── a0_transport_resolution_decision.md, branch_report.md
│ ├── calibration/ # 8 contracts: entity semantics, spatial, time observable,
│ │ # material basis, material calibration, biomass field,
│ │ # integration, acquisition
│ └── research/ # radiotrophic compatibility audit, calibration map,
│ # lab gap, pilot recommendations
│
├── tests/ # runtests.jl, contract_csv.jl, deterministic_radiation.jl,
│ # genealogy_tests.jl, checkpoint_io_tests.jl, fixtures/
├── preprint/ # .tex (source of record; no .md derivative exists in the
│ # tree — the superseded .md is git history only),
│ # figures/ (4 × PDF + PNG). The built .pdf was REMOVED:
│ # it was a pre-revision build carrying withdrawn claims
├── assets/ # preview_bioreactor_3d.png, preview_radiodialysis.png,
│ # consortium_400mcs.gif (embedded at the top)
├── kmeans_species_trajectory (1).gif, biofilm_dynamics_7_species.gif # embedded below
├── Citations.md # predates data/sources.csv, unmaintained
└── .github/workflows/ # coupling-tests.yml (4 jobs)
The equations in this section are the paper's target formalism. They are stated because they define the model being aimed at; what each program actually integrates is stated in Simulations and differs.
The fitness of each species
No program in this repository integrates this equation. No file defines a field biofilms.R and biofilms_3d.R integrate particle positions, not a field; the CPM is a Metropolis
Markov chain. Three of the nine terms are dimensionally checkable as written; the remainder contain a
symbol with no declared unit (
The multi-species Hamiltonian:
density_g_cm3 in data/calibration/voxel_binding.csv, currently blank and blocked on the material
gate. There is no velocity or momentum state anywhere in the repository, so the kinetic term has no
counterpart in any implementation, and the equation closes dimensionally only if every term is
re-declared as an energy density. This is an open defect, carried forward from the April draft's own
notation list.
Mutualistic pairwise interaction potential:
In the CPM this is a reporting statistic, not a force: total_pairwise_energy is called once per
snapshot and γ_mutual / σ_mutual appear nowhere in compute_delta_H. The two R models each use a
different ad-hoc attraction law.
Radiation field (Beer–Lambert, cylindrical source), as implemented in the CPM:
tests/deterministic_radiation.jl. No attenuation length in cm exists. biofilms_3d.R uses
Melanin reaction–diffusion:
Implemented in form. In the code
The most carefully derived component in the repository, implemented twice —
biofilms_radiodialysis.R (method of lines + deSolve::lsoda) and biofilms_potts.jl (method of
lines + forward Euler with an automatic stability substep) — with the two implementations in
agreement. It postdates the April manuscript and appears in no version of it.
Mobile contaminant (cylindrical reaction–diffusion):
Immobile phase (biosorption + bioreduction):
Membrane damage and dose-driven permeability:
Robin boundary condition at the membrane wall
Permeability as an evolving field driven by cumulative dose, rather than a fixed material property,
is the interesting mechanism here and it survives intact. What does not survive is the units in the
Julia coupling, where every physically-labelled slot receives a non-physical value: params.N/2 — 20 lattice units — fed into a cm² s⁻¹ operator; g cm⁻³ slots and multiplied by rates in cm³ g⁻¹ s⁻¹;
mean() before it
reaches the solver, so the uptake sink is spatially uniform.
The material gate records this as RADIODIALYSIS: BLOCKED — "blocked by a units error in the
model, not by missing data." The gate blocks the biomass basis fed into the Julia coupling, not
the PDE system or its discretisation, both of which are sound and cross-validated between the two
implementations.
Also:
Julia, stdlib only for the simulation core. Cylindrical lattice, Metropolis Monte Carlo, and a four-term effective energy in the acceptance path:
The pairwise mutualistic energy is computed once per snapshot as a diagnostic and does not influence
the dynamics. H_CPM is a Metropolis acceptance functional in arbitrary units, dissipated toward a
minimum — not a conserved thermodynamic energy, and there is no symplectic integration anywhere in
this repository.
Field coupling is partial: melanin is genuinely two-way (occupancy drives init_radiation! and nothing feeds back into
it; the nutrient field is written and never read by the dynamics.
julia --project=. biofilms_potts.jl # coupled — REFUSES at MCS 1, see below
julia --project=. biofilms_potts.jl --no-radiolysis # CPM onlyRun provenance, both branches: the coupled default is N = 40, 6 parcels per species, 100 MCS,
seed 42. --no-radiolysis runs main(), which is N = 60, 8 parcels per species, 200 MCS,
seed 42. All reported numbers below come from the coupled N = 40 run.
That coupled run can no longer be executed as documented. run_simulation_coupled sets
basis_from_occupancy on its first installer tick, and main_coupled() builds its
RadiolysisParams without basis_gate_ack, so step_radiolysis! raises RADIODIALYSIS: BLOCKED
at MCS 1 and neither the membrane report nor the figure export is reached. The numbers below
therefore come from a run that predates the gate, and re-running them is blocked on measuring the
biomass basis (D-XRED), not on a code change. The acknowledgement is reserved for
validate_serial.jl, which records no radiodialysis quantity; acking main_coupled would print a
membrane report computed on the basis the gate refuses.
tests/radiodialysis_basis_gate.jl pins the refusal, and the ack census in the same file fails if
an acknowledgement is added here. julia --project=. biofilms_potts_jacc.jl [seeds] refuses the
same way and for the same reason: run_coupled defaults to RadiolysisParams().
Fixed: the two stale stdout banners (main() at biofilms_potts.jl@Hamiltonian: H = H_adh + H_vol + H_rad + H_mel,
main_coupled() at biofilms_potts.jl@println(" H = H_adh + H_vol + H_rad + H_mel) used to print H = H_adh + H_vol + H_rad + H_pair + H_mel — five
terms, where the acceptance path has four and H_pair is a diagnostic — and biofilms_potts.jl@Ḋ(R)=%.1f (placeholder, no seconds_per_mcs conversion — not Gy/s) used to print
Ḋ(R)=%.1f Gy/s for a quantity that is a dimensionless placeholder and for which
seconds_per_mcs is NaN. Both now state the true four-term acceptance path and label the
Ḋ(R) value as a placeholder rather than a physical rate. Nothing enforces agreement between the
banners and the code beyond the fix itself, so re-check them if the Hamiltonian terms or the
dose-rate handling change again.
Fig 1 — the radial ensemble: small mean-radius contrasts at the shipped constants (N = 40,
6 parcels/species, read at MCS 100, seeds 42 to 297, four arms of the acceptance rule on the same
seeds, paired within seed; diagnostics/melanin_ensemble/radial_sweep.jl, tests declared before
the run in PREDICTION_radial_n40_p6.md, ledger row RAD-ENS-01). The observable is the mean
parcel distance from the cylinder axis divided by R. Zeroing β_ion, zeroing α_M (so the melanin
field stays 0), or both, leaves every species' mean r/R within 0.002 of the full model's over 256
seeds; the pre-registered prediction that the melanin path moves the two radiotropic fungi inward
was wrong (full minus melanin-production-off paired shifts +0.0001 and −0.0004 r/R, p = 0.95 and 0.75). The inward drift every arm
shares, from 0.53 to about 0.51 r/R, is present with both terms off and is adhesion-and-volume
relaxation. The radiation field is maximal on the axis, so the high-radiation region is the
core, not the wall; β_ion is negative for the two radiotropic fungi and positive for
B. subtilis. Produced on x86_64 Linux under Julia 1.12.7, as the CSV header records; the full
arm's melanin printed identically to the Mac-generated melanin sweep for all 112 shared rows.
The single-seed figure this replaces (seed 42, C. neoformans 0.15 R outside B. subtilis) was one draw: the ensemble mean separation ranges from −0.0057 to −0.0048 r/R across arms, with a per-seed standard deviation of about 0.11.
Spatial sorting is dominated by the hand-specified adhesion matrix J. Within the radiation-derived
pathway, melanin exceeds β_ion by about an order of magnitude — 8.39 to 17.06 in ΔH across
seeds 42–297 — not by four (see
the melanin finding above).
tests/deterministic_radiation.jl demonstrates the inertness directly: it must deliberately amplify
Fig 2 — mean melanin field value over occupied sites, per producing species, to MCS 100. C. sphaerospermum reaches 1.44 at seed 42, and 1.26 to 2.56 across seeds 42–297.
The ordering among the three producers was corrected in 2026-09-17: it fails in 19 of those 256
seeds, so the input α_M (0.14 versus 0.10 and 0.065) does not fix it. The field equation has no
saturation, decay or substrate-limitation term (ledger row RM-G11-01).
Corrected 2026-09-22. This paragraph asserted more about the shape of the rise than the equation gives. Ledger row RM-G11-01 holds the withdrawn wording. The figure's increments fall: C. sphaerospermum gains about 0.53 over MCS 0 to 20 and about 0.14 over 80 to 100. Melanin diffuses, its source follows occupancy, and the mean is taken over occupied sites that move.
What is not set anywhere in the parameters is the spatial distribution and magnitude of
That is a genuine emergent quantity. It then feeds back into acceptance at 13.4–29.2% bias.
biofilms_potts_jacc.jl is a JACC/AMDGPU port using 8-colour checkerboard updates. Its contract is
statistical, not pathwise, and docs/jacc_coupling_port.md records that it is never the first
causal comparison vehicle. The literal comment # 13. Figure export in biofilms_potts.jl is a
load-bearing split marker: tests/runtests.jl@src = split(src, "# 13. Figure export")[1], validate_serial.jl@src = split(src, "# 13. Figure export")[1] and
biofilms_potts_jacc.jl@src = split(src, "# 13. Figure export")[1] all load the serial monolith by splitting the source on that exact
string and evaluating the first half in a sandbox module whose imports are hard-coded to
LinearAlgebra, Statistics, Random, Printf. The two rules are: never edit that line, and add nothing
above it that needs a non-stdlib package.
Withdrawn from the manuscript at version 2.0 and carried in preprint/radiodialysis_model.tex,
the model section of a companion experimental paper. Nothing below is a result of the
computational paper.
Shiny app. Method-of-lines finite-volume solver for the three-equation system, LSODA adaptive stiff
integration (deSolve), Robin condition at the wall and L'Hôpital treatment at
Rscript biofilms_radiodialysis.R # serves on 127.0.0.1:${SHINY_PORT:-7799}, no browser launchRscript is not present on the machine this README was verified against, so both Rscript commands
here are untested as written. The R app's units are declared but unvalidated. The Julia coupling's
units are wrong by construction (above).
Fig 3 — membrane integrity state.radiation, dt_rd = 0.5 carries the source
comment "tune to match CPM time scale", and seconds_per_mcs is NaN, so no conversion to grays
exists. The permeability ratio is exactly
Fig 4 — radial contaminant profile
Stale figure and label notice. Figures 3 and 4 predate the 2026-08-14 correction that
neutralised the reversed biological zone labels and removed the hard-coded dose annotation, so they
differ from current export_figures output; they are no longer in the manuscript, which withdrew
the radial transport model to preprint/radiodialysis_model.tex at version 2.0, and they are
shown here under that model's own heading. Figure 1 was replaced on 2026-09-24 by the ensemble
figure, rendered from the committed CSV by diagnostics/melanin_ensemble/radial_figure.py;
preprint/figures/fig1_radial_stratification.* stays on disk because ledger rows name it.
Figure 2 was rebuilt on 2026-09-22 by
regenerate_fig2.jl, which refuses to copy unless every plotted point matches the committed
ensemble, so it is current. In addition, the embedded Fig 4 prints
(1.0 − c_mean) * 100 under the label "% depleted" — the figure says depleted where the model
supports only non-penetrated. The preview image above assets/preview_bioreactor_3d.png likewise
predates the 2026-08-14 radiation sign fix.
Both are declared legacy and non-authoritative. The Julia seven-species registry is authoritative.
biofilms_3d.R — cylindrical bioreactor, Shiny app. Overdamped dynamics in a cylinder of radius
Rscript biofilms_3d.R # auto-prints the shinyApp object, which starts the server (untested here)This file carries Pseudoalteromonas, which appears nowhere else in the repository, and omits
O. intermedium. Its species ordering differs from both other registries, so any positional
cross-file mapping is silently mismatched. Two open defects: heat and nutrient contributions are
scalars added identically to the
biofilms.R — flat-domain particle Langevin SDE. Seven entities (one an unnamed placeholder;
O. intermedium absent) on a dimensionless gamma_intensity is a scalar constant added identically to both velocity components, producing a
uniform drift along the diagonal. Results are qualitative only and support no gradient or
niche-partitioning claim.
.gif)
Neither subsystem appeared in the April documents. Together they are now the largest part of the repository and they govern what the rest may claim.
An installable Python package, deliberately numpy-only, which must not import the coupling package. Two branches meeting at one contract:
- spatial — entity semantics, scale-candidate enumeration, biomass-field coarse-graining, structural observables, occupancy mapping, pitch selection, morphology and representability diagnostics, synthetic validation fields, the dynamic-observable contract, format-agnostic ingest with optional microscopy readers, and a public-dataset screening ledger.
- materials — basis-tagged
Quantityarithmetic, mixture and mass-closure checks, seeded Monte-Carlo uncertainty, and an export gate. - integration — the voxel binding that joins them, and the only place where a whole class of
error becomes visible.
docs/calibration/integration_contract.mdnames six rejected combinations whose individual clauses each pass their own branch's gate — the canonical one being a literal cell fragment, whose density comes from bulk wet biofilm, whose lineage is claimed as a biological cell lineage. Neither branch can see the contradiction alone. Only the join does. - campaign — the acquisition contract, derived replicate counts and detectability.
It selects no pitch, exports no material and emits no config, because no measured dataset of a target system exists.
The gates refuse, and the refusal is the tested behaviour. emit_transport_config() prints
REFUSING to emit a biofilm transport config with the full reason list. apply_occupancy() refuses
while the mapping is unset, and mass_preserving refuses without a declared seed — an unseeded
lattice cannot be reproduced or reviewed. precision.detectability() refuses and names the right
remedy: more biomass per coupon, or a substrate with a lighter, more reproducible blank — not more
replicates. The material export gate blocks proxy, derived_proxy, synthetic, declared and
unresolved evidence, because shipping it would launder it into a measurement.
The dataset ledger records rejections as first-class results.
data/calibration/spatial/dataset_candidates.csv holds 12 screened candidates: 1 use_first,
3 inspect_first, 2 diagnostic_only, 6 rejected. The informative half is what was turned down —
a search that only records what it accepted is not a provenance trail. Two none_found rows are
recorded as findings: no volumetric dataset covers the seven-species community, and no public record
pairs a calibrated 3-D volume with wet mass, dry mass and matched blanks for one system. That is a
search result, not proof of non-existence — but it is enough to conclude that the target campaign
should be designed rather than waited for. The most instructive rejection is an excellent
exact-species S. oneidensis single-cell tracking dataset, rejected on representational grounds
because it answers the wrong question — independent confirmation that single_cell_msd was correctly
rejected as a seconds/MCS observable.
Biosafety follows strains, not species. Several components are commonly BSL-1 while
C. neoformans strains are commonly BSL-2, and collection material under one species name can carry
different assigned levels, so a species list cannot determine a facility class. The enforced chain is
exact strain IDs → institutional review → containment decision → approved procedures, and the gate
blocks on a missing institutional_approval_id. Nothing in this repository describes a
field-deployable system.
calibration/scripts/vcholerae_pilot.py ran against Dryad doi:10.5061/dryad.zcrjdfnph (CC0), with
reference_system_id = public_vcholerae_surrogate and target_calibration = false written into its
own output so the distinction survives being copied out of context. V. cholerae is not one of the
seven modelled species. A successful run licenses exactly one claim — that the spatial calibration
machinery was exercised against a named public 3-D biofilm reference system — and never that a
biological pitch was calibrated.
Preflight found no file in the Dryad set that is both 3-D and time-resolved. The spatial pass
therefore ran on Dataset_3_Fig3c_VPS-Bap1.nd2, a static Z = 94 × 3-channel × 1024² stack with
voxel size (0.065, 0.065, 0.13) µm read from the file rather than typed, has_time_axis: false,
time_metadata_source: "absent". The temporal observable stayed blocked — not deferred, blocked,
because the file has no time axis to observe.
Two rows in data/calibration/spatial/pilot_vcholerae.csv:
| coarsening | pitch µm | passed | biovolume frac | porosity | interface area | corr. length | thickness | comp. size q50 |
|---|---|---|---|---|---|---|---|---|
| 1 | 0.065 | true | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
| 2 | 0.130 | false | 0.0 | 0.0 | 0.463 | 0.260 | 0.235 | 15.0 |
Row 1 passes by construction — it is the field compared against itself, so every error is identically zero and it is not evidence of anything. Row 2 is the result: one factor-of-two coarsening destroys every structural observable, worst of all the median connected-component volume at a relative error of 15.0, while the two intensive volume-fraction observables — biovolume fraction 0.047702 and porosity 0.952298 — hold exactly. Volume fraction is preserved by block averaging; geometry is not. That is the loss curve, and it is steep.
Both rows carry segmentation_basis = unresolved (the channels are fluorescent reporters, and a
microscope records what a channel detected, not what it is intended to represent) and
holdout_kind = none, since no frame of one file is an independent held-out stack — so select_pitch
refuses these rows regardless of the numbers.
The dataset download was declined rather than defeated on the first attempt: the host's
proof-of-work is a deliberate control against exactly the kind of client this is. Four SHA-256
digests are recorded so a manual copy verifies byte-for-byte, and the input digest is recorded as
sha256_verified: true in the run metadata.
A defect was found and fixed by this pilot. nd2.ND2File.voxel_size() returns (1.0, 1.0, 1.0)
for a file that carries no calibration, and the reader's old v > 0 guard passed that straight
through as a calibrated 1 µm voxel. The guard now consults axesCalibrated
(calibration/biofilm_calibration/spatial/readers.py). This is the pilot's most durable output.
An installable Python package (deps exactly numpy, h5py) that builds OpenMC photon-transport
models from a CPM lattice snapshot, tallies heating, converts it to absorbed dose, attributes dose to
lineage labels, and evaluates a two-way-feedback gate offline. One console script,
biofilm-dose-scan. The online (two-way) driver is NOT IMPLEMENTED; its design and its gates are
recorded instead.
Real transport has run against a pinned stack: conda-forge openmc 0.15.3, Python 3.13, HDF5 1.14.6,
official ENDF/B-VIII.0 photoatomic data with recorded SHA-256.
The OpenMC result is a feasibility benchmark, not a physical calibration.
config/reference_a0_water_phantom.toml says it of itself: "This is a numerical-validation geometry,
NOT an apparatus. Every value below is either evaluated nuclear data or a DECLARED modeling choice —
none of it is measured, and none of it describes a real reactor." All dose values are voxel-averaged
absorbed dose under OpenMC's charged-particle local-deposition approximation, not single-cell
microdosimetry.
What it demonstrated:
- Energy balance closes to a relative error of 5.2 × 10⁻⁹ (1 000 000.0 eV deposited per 1 MeV source photon in a reflective water box), and uncollided transmission through 1, 2 and 3 cm of water is exponential within 15%.
- The feasibility run reported its own bad news: 75% of occupied voxels scored no heating at the 10 µm demo tally pitch, median relative error ≈ 1. Recorded, not hidden. The 10 µm feasibility mesh is a tally pitch and never a biological pitch.
- The A0 sweep (100 runs + 1 reference: 5 coarsening factors × 4 history counts × 5 seeds, plus a
48³ / 6.4 × 10⁷-history reference at an unswept seed) sets the A0 mesh and history count and
establishes a hard ceiling of
coarsening_factor ≤ 4. Sparsity is a scale problem, not a method problem, and the A0 geometry does not have it. Two metrics are reported because one of them cannot see discretization:field_diff_vs_referencehas zero discretization error by construction on nested meshes,resolution_lossdoes not — conflating them would have made every mesh look convergent.
Every physical value ships REQUIRED-but-unset in config/coupling_template.toml (14 keys, staged
transport → dosimetry → cpm_feedback → membrane_feedback), and the loaders enumerate every missing
key in one error and refuse. biofilm-dose-scan exits 2 with the complete missing-key list rather
than evaluating.
Block sum versus block mean, in two packages, pinned by tests in both. Deposited energy is
extensive, so coupling/.../mesh.py:coarsen_field block-sums; a biomass volume fraction is
intensive, so calibration/.../spatial/field.py:coarse_grain block-averages. Same concept,
opposite operation, and using the wrong one is off by factor³. The two packages deliberately do not
import each other, so the distinction is restated where it can be seen. (The V. cholerae pilot is
the same fact from the other side: block averaging preserved volume fraction exactly and destroyed
every geometric observable.)
The array boundary is not an interface, and an edge-truncated chord is not a chord. The first
version of specific_interface_area did count the boundary, and a test caught it: the metric changed
when the same slab was cropped.
docs/research/radiotrophic_compatibility_audit.md (2026-08-15) is an evidence audit across eleven
data repositories and the sequence archives, run as seven parallel retrieval tracks each re-verified
by a second pass, with the ledgers in data/research/. It populates no parameter. Nine access
controls were encountered and none was circumvented.
| Question | Verdict |
|---|---|
| Exact radiotrophic data for the modelled species | TARGETED_LAB_EXPERIMENT_REQUIRED |
| CPM calibration from public data | PUBLIC_DATA_CAN_VALIDATE_PIPELINE_ONLY |
| Materialization (density, composition) | TARGET_WET_BULK_MEASUREMENT_REQUIRED |
| Integrated (one system, all components) | PUBLIC_COMPONENTS_FOUND_BUT_NOT_PAIRED |
The headline: radiotrophy is not established for any of the seven species. The claim rests on one 2007 paper whose exposure was characterised by analogy rather than by a stated dosimeter, whose growth effects are single-digit percentages, and whose integrated cell dose is not stated. Against it stand a same-species independent report of no substantial melanin protection under gamma, a same-species negative melanin-pathway result at 1 and 3 kGy, a same-genus null under a TLD-anchored ¹³⁷Cs field, an isogenic null in A. niger across three ionizing modalities, and a formal energy-budget critique. Peer review struck the word from the flagship ISS title. No author contact resolves this, because the discriminating experiment has not been run by anyone.
Radioresistance, by contrast, is well evidenced — and it is the evidence that anchors the
per-species β_ion magnitudes, which is exactly why the phenotype table above matters.
Radiotropism has its own candidate and it is blocked twice. Zhdanova 2004 reports directed hyphal growth toward a source; whether its dose gradient was measured or calculated is unverified, and directed hyphal elongation has no CPM representation, because a parcel is isotropic and there is no elongation or connectivity term. One blocker awaits a measurement, the other awaits a model change.
Public exact-species volumetric imaging exists for exactly one of the seven (B. subtilis), and for none of the four with radiation data. Two of the seven have no ionizing-radiation record in the audit at all. O. intermedium AM7 has a total public footprint of 1086 base pairs and one paywalled abstract, and has never been irradiated in any public experiment.
From the coupled CPM + radiodialysis run in biofilms_potts.jl: N = 40, 6 parcels per species,
100 MCS, seed 42, single realisation, no replicates. Not from the preprint — none of these numbers
appears in it. Every value below is dimensionless; nothing in this table is in grays, seconds,
centimetres or grams, because no conversion to any of those exists.
| Result | Value | Status |
|---|---|---|
| C. sphaerospermum melanin, MCS 100 | 1.26 to 2.56 over 256 seeds |
Dimensionless field units. Mean of a dimensionless field over occupied sites. Seed 42 gives 1.437157, the 31st lowest of the 256. CORRECTED 2026-09-17: the row read 1.44, one seed's value. The ordering among the three producers fails in 19 of the 256, so α_M does not fix it; magnitude and spatial distribution are emergent. |
| Melanin unclipped Metropolis factor over that range | 1.134 to 1.292 (13.4% to 29.2%) |
Dimensionless. Computed from the shipped 0.5 coefficient and T_cpm = 5.0, so the bias equals exp(0.1 × M); about an order of magnitude above the β_ion bias AT THE TERM'S REACH, 1.0151. Not above 1.000010, which is one ROLE of one pair of species occupying a site -- comparing against it is the withdrawn comparison. CORRECTED 2026-09-17: the row read 1.155 (15.5%) and a 10.2x ratio of excesses, all from seed 42 alone. The dominant radiation-derived term, and undeclared until 2026-08-15. |
| Membrane integrity after 100 MCS | m = 0.779 |
Dimensionless. No physical dose exists: Ḋ = 1.0 is a placeholder, dt_rd = 0.5 is an uncalibrated MCS→second knob, seconds_per_mcs is NaN, and accrue_dose! raises rather than run without it. There is no value of Gy this corresponds to. |
| Permeability ratio | P_eff / P₀ = e ≈ 2.72 |
Dimensionless, and exact by construction. A closed-form function of four hand-set constants (P₀ rescaled by that factor, and a literature prior is not a calibration. |
| Interior contaminant, unweighted node mean | c / c_ext = 0.024 |
Dimensionless ratio. Measures non-penetration, not depletion: c(t=0) ≡ 0 everywhere, so the interior never held contaminant to remove. The mean is unweighted over radial nodes, not volume-weighted. The embedded figure labels this "% depleted"; the figure is wrong and the model supports only non-penetration. |
| Radial position of parcels | C. neoformans mean r/R = 0.65; B. subtilis mean r/R = 0.50 |
Dimensionless, and one seed's draw. REPLICATED 2026-09-24 (RAD-ENS-01): over 256 seeds the full-arm means are 0.507 and 0.512 r/R; across the four arms the C. neoformans − B. subtilis mean separation ranges from −0.0057 to −0.0048 r/R, with per-seed sd about 0.11. The earlier 0.15 gap is one draw from that spread. The melanin prediction fails its stated criterion, and each direct-term paired mean-radius contrast meets the ±0.05 r/R equivalence bound; smaller effects remain possible. CORRECTED 2026-09-29 (PRE-SEND-01, PRE-SEND-02). The original reading stands as written: Both terms are lattice units, so the ratio is legitimate. But the figures come from main_coupled() at N = 40, six parcels, 100 MCS, so R = 20 and parcel centres are rejection-sampled uniformly over radial_dist < R − 4 = 16 = 0.8R, giving a centres-only null of E[r/R] = ⅔(0.8) ≈ 0.53 — the B. subtilis value sits 0.43 SE from it, indistinguishable from the initial condition; n = 6 parcels on one seed gives SE ≈ 0.077 against a 0.15 gap, ≈ 1.4 SE of the difference; and the direction is opposite to the implemented physics, since a negative β_ion biases C. neoformans toward the high-radiation axis. Note that 0.58 is itself only an approximation: parcels occupy volume and grow toward V_target, so the mean over occupied sites is not the mean over seed centres, and the true null has to be simulated rather than derived. The paired four-arm ensemble now supplies the simulated comparison from shared initial placements. |
| Pairwise community energy | −34.4 → −41.5 |
Model units, diagnostic only. total_pairwise_energy never enters Metropolis acceptance, so nothing in the simulation minimises it. It records mutualistic-pair proximity under adhesion, not a selected-for outcome. |
| Parcel persistence | 42 / 42 seeded biomass parcels, where 42 = 7 species × 6 parcels is the ceiling as well as the floor |
A property of the model, not a survival result. There is no division (divide_cell! has no trigger) and the only death path is volume erosion under a volume constraint that opposes it. Parcels are not cells. response.growth_survival is unsupported_by_current_model. |
On the "self-regulating remediation loop." The intended design is: radiation damages the membrane
→ P_eff rises → more contaminant enters → metal-reducing S. oneidensis, co-located by CPM
dynamics, immobilises it. Every arrow in that chain is currently open. m and P_eff are
independent laws and neither reads the other; P_eff is a function of import_dose_field! exists to make a real link explicit, and no run
currently invokes it. Wiring the loop is gated on the retained m-versus-P_eff stop condition. It
is a design hypothesis; nothing in this repository tests it.
The vocabulary is the code's.
spatial: READY_FOR_TIME_CALIBRATION | PROVISIONAL | MODEL_REVISION_REQUIRED | NOT_EVALUATED
material: READY_FOR_OPENMC_BIOFILM_TRANSPORT | READY_FOR_RADIODIALYSIS_MAPPING
| PROVISIONAL | BLOCKED | NOT_EVALUATED
feedback: PASSED | FAILED | NOT EVALUATED
row status: ready | provisional | blocked | unresolved | not_applicable
| unsupported_by_current_model
| Gate | Verdict |
|---|---|
| CPM spatial | PROVISIONAL — entity semantics are declared for all seven species; everything else is missing |
| Material, OpenMC path | OPENMC: PROVISIONAL |
| Material, radiodialysis path | RADIODIALYSIS: BLOCKED — blocked by a units error in the model, not by missing data |
| Voxel binding | coherent, incomplete · Emission: REFUSED — a coherent sentence with blanks in it is still a sentence with blanks |
| Offline feedback gate | NOT EVALUATED — by design |
| Online (two-way) coupling | NOT IMPLEMENTED |
| JACC coupling port | design only — no JACC coupling code exists on this branch, deliberately |
| Time observable | SELECTED: biomass_autocorrelation_decay, row status = provisional (runner-up interface_rearrangement_rate); seconds/MCS still blocked on the pitch half |
| Baseline condition | Ships UNSET — a protocol contract, not a claim about a specimen that exists |
| Reference D declarations | FROZEN — all twelve modelling decisions made, reference_d_acceptance_v1; three declared criteria carry enforcement = not_implemented and may not close a gate |
| Reference D campaign | CAMPAIGN_READY: no — blocked by exactly one thing, D-APPROVAL, which only a biosafety committee can issue |
| Offline feedback gate | NOT_EVALUATED — no effect threshold declared, and none may be defaulted |
| Online feedback | DISABLED, fail-closed — every prerequisite defaults to its refusing value |
Provenance ledger distribution (data/parameter_provenance.csv, 49 rows × 21 columns): status —
22 ready, 10 not_applicable, 9 blocked, 7 provisional, 1 unsupported_by_current_model.
model_compatibility — 34 direct, 10 requires_transform, 5 unsupported. A row whose status is
ready must carry a source_id; unresolved and blocked rows must not carry a value.
julia --project=. tests/runtests.jl # 146 passed, 0 failed (re-run 2026-08-24 at HEAD)
julia --project=. biofilms_potts_jacc.jl --selftest
pip install -e "coupling[dev]" && (cd coupling && pytest -rs tests) # 340 collected
pip install -e "calibration[dev]" && (cd calibration && pytest -rs tests) # 429 collectedThe Julia figure is 2 + 34 + 68 + 42 across the four suites, re-run on this tree rather than quoted
from docs/branch_report.md, which records the older 2026-08-13 branch-end figures and is stale on
the Python counts.
Run together in the coupling venv, the two Python suites collect 769 tests
(measured 2026-09-16 on this merge: coupling 340, calibration 429). In the worktree these were
measured in, 767 pass and two fail: coupling/tests/test_julia_interop.py requires HDF5, and
that worktree has no Manifest.toml. Where a Julia project with HDF5 is installed, those two
pass and the figure is 769 passed. The count is a property of the tree; the two failures are a
property of the machine, and the two are reported separately for that reason.
Six coupling modules skip on import openmc in a bare venv — the five in
coupling/tests/integration/ plus coupling/tests/test_model_build.py. Those six skip at import
and never reach collection, so 340 + 429 = 769 excludes them. No calibration module skips.
Four superseded figures have appeared in this paragraph. 259 passed with four skips, measured
2026-08-15 and left unrevised after two integration modules were added the same day. 534 (coupling
233, calibration 301) corrected that on master on 2026-09-16. 616 was re-run 2026-08-24 on an
earlier branch. 760 (coupling 340, calibration 420) was measured on #12's merge earlier on
2026-09-16, and this branch's one added calibration module superseded it nine tests later. Each
was correct for the tree it was measured on and wrong for the next one.
No calibration test skips: the pilot ND2 file is present on this machine, so test_pilot.py runs.
The OpenMC integration tier is manual opt-in: activate the openmc-biofilms
environment, set OPENMC_CROSS_SECTIONS, then run the coupling suite. CI is
.github/workflows/coupling-tests.yml — julia-tests, python-unit, calibration-unit, and
openmc-integration behind a workflow_dispatch input (API tier only; no nuclear data, so
the five tests/integration/ modules still skip there). Real-data-backed verification of the
golden-tally fixture (coupling/tests/fixtures/golden_tally_water_phantom.json) is a separate
workflow, .github/workflows/golden-tally-verification.yml, triggered by workflow_dispatch
by every pull_request touching a path that can change what the tally produces, and by a push
touching one of those paths on master, feat/**, ci/** or research/** — a push on any other
branch matches no trigger, which is why the pull_request half is the one that always applies.
Those paths are the transitive closure of the modules the regeneration script imports, plus the
two editable-install manifests, environment.yml, docs/openmc_stack.md, the fixture and the
workflow itself. coupling/tests/test_gate_composition.py
derives that closure from the script's own imports and fails when a path is missing from either
trigger. An earlier version of this sentence said the fixture "only change[s] when" the
OpenMC or nuclear-data version does, and named only workflow_dispatch and push; both halves
were wrong, and the first told a maintainer to dismiss a drift caused by a producer edit.
What the tests pin:
tests/contract_csv.jl— byte-identical CSV output against a golden fixture, pinning the serial RNG stream. The fixture is Julia-1.12-dependent.tests/deterministic_radiation.jl— field shape (maximum on the axis, monotone radial decay), the exact local ΔH sign per species, and multi-seed drift direction with a deliberately amplified β, because the production β is too small to be detectable. The local sign is a contract; the collective drift is a result.tests/genealogy_tests.jl— the lifecycle/dose contract, and that the windowed API is identical to the legacy loop.tests/checkpoint_io_tests.jl— snapshot orientation probes and bit-exact restart resume.coupling/tests/test_mesh.py— the nesting invariant and the coarsening trap: taking the dose denominator fromvoxel_pitch_cmafter coarsening understates every dose by exactlyfactor³.coupling/tests/test_fingerprint.py— thattransport_state_hashexcludessource.photons_per_secondwhiledose_state_hashincludes it.calibration/tests/test_spatial_schema.py—test_gate_is_provisional_not_ready,test_gate_returns_model_revision_required_for_a_literal_cell_claim,test_gate_is_not_evaluated_without_semantics.calibration/tests/test_material_basis.py— thatsite_occupancyis refused everywhere a concentration is required.calibration/tests/test_integration_binding.py— the six incoherent bindings.calibration/tests/test_precision.py— that extra imaging fields buy nothing when between-batch variance dominates.
preprint/modeling_radioresistance_and_radiotropic_fitness.tex is the source of record:
Does a Dose Gradient Move Biomass Parcels? A Seed Ensemble of a Multispecies Cellular-Potts
Biofilm with an Executed One-Way OpenMC Interface (version 2.0; versions 1.0 to 1.2.1 were titled
Modeling Radioresistance and Radiotropic Fitness in Multispecies Biofilms).
It reports executed computational work, one ensemble answer about the model's own acceptance rule, and an implementation audit. It infers no target physical parameter, and its transport section reports that the one-way CPM–OpenMC path executed rather than reporting results from it — no gate verdict, no lever magnitude, no dose in physical units. The Ethics statement records that the work involved no culture, no recombinant or synthetic nucleic-acid experiment and no irradiation, so no institutional approval was required for it, and that any future campaign waits on prospective strain-, protocol-, facility- and source-specific approvals.
It cites the parent of the commit that adds it. A document cannot cite the commit that
contains it, which is the same structural limit the run artifacts record for their own provenance
— git_commit there names the parent and carries a -dirty marker for the same reason.
The repository has moved past that revision, and some of what it moved past was our own
published numbers. A false-positive control that could not fail, a squared difference reported
as a variance, an unprovenanced sensitivity table, and one synthetic-gate verdict withdrawn as not
resolution-converged. None of those numbers appears in the manuscript. The full record is
data/claims_ledger.csv and docs/calibration/.
The superseded sources are in git history, not in the tree. modeling_radiotrophic_fitness.{md,tex}
and the pre-revision PDF carried a fabricated Computational Methods section, a Th-232 comparison
against data that exists in no data/ file, organisms named in no file here, and a symplectic
integrator the Project.toml has never contained. Those claims are catalogued as 115 PP-* rows
in the claims ledger, 34 of them delete.
And the ledger is now enforced. calibration/tests/test_claims_ledger.py asserts that no
claim marked delete reappears in the document that carried it. Until it existed, nothing in
the repository checked the ledger at all — and until 2026-08-28 it read only the manuscript,
because it selected rows by claim_id prefix rather than by the document column each row
declares. The 25 delete verdicts on other documents were unguarded by a test that could not
have failed for them.
Its real coverage is 20 of the 34, and the other fourteen are named in the test output as still needing a human. An earlier version of this note said "30 of 34", which counted rows that yield a searchable phrase rather than rows the guard can actually find — many ledger entries are reconstructions across the two superseded sources rather than verbatim quotes from either. The guard is calibrated against the pre-revision manuscript recovered from git history: it must detect at least 18 of the deleted claims there, because a guard that cannot find known-bad input is not a guard, and the first version of it detected 12.
DOI archiving is an author action: preprint-v1.2.1 is the tag to archive (preprint-v1 marks version 1.0 at 5ccadac), and enabling Zenodo
requires the account owner.
Figures are generated by biofilms_potts.jl below its split marker. The .tex includes them
without an extension, so a pdflatex build resolves preprint/figures/*.pdf.
This supports no claim in this repository. The geolocator is a visualization and infrastructure-data subsystem that shares this repository. It is not coupled to the Cellular Potts model, the radiodialysis transport stack, the calibration harness, or the claims gates. No gate reads it, no figure depends on it, and nothing it renders is evidence for anything the framework asserts.
It is documented for the opposite reason to an unexplained artifact. A stray file invites a reader to infer a relationship that does not exist; a named, maintained subtree invites the same inference unless the boundary is stated. This is the statement.
geolocator/ serves a globe of the world's power plants over the WRI Global Power Plant Database
(v1.3.0, CC BY 4.0), vendored here as an immutable snapshot rather than fetched at run time, so a
given commit always means a given dataset. power_plant_database_global.provenance.json records the
publisher, version, licence, canonical source and the SHA-256 of the committed bytes. A test checks
that hash against the file, because a provenance declaration that can drift from what it describes
turns unknown into confidently wrong. The dataset is pinned -text, since under line-ending
normalisation a content hash is not reproducible across platforms and the declaration would be
unverifiable by construction.
The part worth borrowing is the freshness model, which refuses to let one signal stand for another. Reload detection and freshness authority are separate: a stat fingerprint decides when to reread a file, while a timestamp inside the data decides whether it is current. Touching a file rereads it and changes nothing else, because touching a file does not make the world newer. Sources declare what kind of thing they are — a reference dataset has a declared vintage and is never stale by clock, since a versioned snapshot does not drift toward wrong; a live source is measured against a clock; an authored source carries no semantic timestamp at all and reports that absence rather than letting a file modification time impersonate one. Absence of an authority is a state to publish, not a gap to paper over.
The stack is FastAPI and three.js with no build step; run it with
python3 -m uvicorn geolocator.api:app. Its own tests live in geolocator/tests/. An optional local
market adapter is not included in this repository, and its absence is reported explicitly rather than
rendering as an empty result — an uninstalled producer must not read as a producer that found
nothing.
The Tableau workbook and screen recording at the repository root are this subsystem's ancestor, retained for provenance. They plot the same dataset coloured by primary fuel. They are not the implementation, and neither they nor it bear on the biofilm work.
Julia 1.12 — the tested version; the CSV golden fixture pins the RNG stream to it.
Project.toml [deps] is AMDGPU, CairoMakie, HDF5, JACC. HDF5 is required by
export_checkpoint.jl; JACC (with AMDGPU) by biofilms_potts_jacc.jl; CairoMakie by the
figure-export path in biofilms_potts.jl (below the # 13. Figure export split marker — the
sandbox module the splitters build has hard-coded imports that never consult Project.toml, so
this declaration only fixes Pkg.instantiate(), not what the split marker's own sandbox imports).
Fixed: CairoMakie was previously undeclared, so the figure-export path failed at its
using CairoMakie line unless CairoMakie happened to already be present in the default
environment. It is now declared in Project.toml.
That fix does not make julia --project=. biofilms_potts.jl run. An earlier version of this
paragraph said it did, naming the dependency as "that command's previous open defect" — it was
one defect of two, and the command now stops earlier, at the RADIODIALYSIS: BLOCKED refusal on
MCS 1 described in Radiodialysis membrane transport. The
export path is reachable through --no-radiolysis, which is what the declaration unblocks.
That is a declaration, not a lock. Manifest.toml is gitignored (.gitignore:377), so a
clean checkout has no resolved dependency graph and Pkg.instantiate() resolves versions afresh
against whatever the registry offers that day. An earlier version of this line said CairoMakie
was "resolved in Manifest.toml" — true of the working tree it was written in, and false of
every clone, which is the same shape of error as an absence claim that names only the one place
someone looked.
R — deSolve, shiny, plotly, ggplot2, dplyr, MASS, class (the last two for
reactor_decision_tree.R).
install.packages(c("deSolve", "shiny", "plotly", "ggplot2", "dplyr", "MASS", "class"))No R version floor is enforced or evidenced in the code, and no R command in this README has been executed on the machine it was verified against.
Python ≥ 3.11 (both pyproject.toml files) — two independent packages, neither importing the
other. The pinned OpenMC stack is Python 3.13.
pip install -e "calibration[dev]" # numpy only
pip install -e "coupling[dev]" # numpy, h5pyOpenMC is optional and out-of-band: a pinned conda-forge stack (openmc 0.15.3, HDF5 1.14.6,
ENDF/B-VIII.0 photoatomic data with recorded SHA-256), documented in docs/openmc_stack.md. Until it
is installed, every OpenMC-dependent result is reported as blocked or skipped, never as passed.
The manuscript is unpublished and has no DOI. Cite the repository at a commit.
Kinder, H., Faulkner, B. (2026). Modeling Radioresistance and Radiotropic Fitness:
Spatiotemporal Dynamics of Microbial Communities Under Ionizing Radiation Stress.
Unpublished manuscript.
https://github.com/aurascoper/Biofilms, commit 5d1b777.
data/sources.csv is the working source registry, pinning each cited document by
document_version, accessed_date and sha256, and it records honest failures alongside successes —
two rows read NOT LOCATED and NOT VERIFIED against the primary report. Citations.md predates
that registry and is not maintained.
See LICENSE.txt.