Spatial water chemistry
O₂, CO₂, nitrogen compounds, algae, bacteria, and detritus are represented on an 18 × 10 chemistry grid. Continuous sandbox glass can block diffusion between neighboring chemistry zones, allowing separate water compartments to develop different chemistry. Very small enclosures inside one chemistry cell will not be chemically independent. Surface gas exchange and depth-dependent light remain simplified processes.

Tank Focus quotations
Quotations appear for about 8 seconds with a 20-second gap. Additional selections and author attributions follow Bucket List Journey’s nature quote collection.

Plants, growth & bubbles
The Plant removal tool harvests whole plants without adding detritus. Undo restores harvested plants while preserving current chemistry and growth of remaining plants. Plant biomass affects photosynthesis and respiration. Plants now change biomass gradually with modeled light and nutrient availability. Grass and ribbon forms can spread clonally when resources and space permit. Growth and spread rates are instructional parameters rather than calibrated species-specific rates. Visible bubbles remain qualitative indicators of active photosynthesis.

Plant rooting, cavities & substrate
Plant roots remain associated with the open-water cavity in which they were placed. A plant clicked beneath an overhang therefore roots on the lower substrate instead of relocating to the upper landscape. Sand, gravel, rock crevices, and the tank floor can support roots; bare glass cannot. Cave height can physically limit plant height.

Habitat shade & local light
Local photosynthetic light combines day/night cycle, the Light control, turbidity, water depth, and simplified habitat occlusion. Rock, sand, and gravel block direct light; glass transmits most light. Side openings provide partial indirect illumination, so shallow overhangs are shaded rather than automatically black. Deep enclosed caves can become very dim. This is a teaching approximation of light geometry, not optical ray tracing.

Substrate & oxygen
Sand, gravel, rock, and glass are not oxygen consumers by themselves. Their oxygen effect is indirect: they can shade producers, support rooted plants, create refuge, and trap sinking detritus. Organic matter trapped at substrate surfaces supports bacterial decomposition and nitrification, which can create localized oxygen demand. Anaerobic porewater inside deep sediment is not modeled.

Oxygen recovery
Photosynthesis, respiration, decomposition, nitrification, and gas exchange all contribute to dissolved oxygen. A die-off can depress O₂ for days while detritus is decomposed, but a well-lit producer-rich tank can recover as that organic load is consumed. Barrier-aware diffusion represents mixing between neighboring water zones; direct atmospheric exchange occurs only at the modeled water surface. Photosynthesis is also limited when dissolved CO₂ becomes scarce.

Animal behavior
Animals respond to food, predators, oxygen, habitat structure, depth, and boundaries using simplified steering rules. Minnows can select sheltered cruise targets and navigate into sufficiently wide cave-like spaces; solid structure still limits passage. Fish cruising, cave exploration, and schooling are behavioral approximations, not tracking data from a particular minnow species.

Predator-prey refuge
Vegetation, rock piles, and gravel create a modeled refuge score. Daphnia and scuds may move toward cover when fish are nearby, and prey in stronger cover are harder for minnows to capture.

Population dynamics
Energy, age, food, crowding, maturity, and stochastic reproduction influence populations. Lifespans and rate constants are tuned for instructional stability and are not experimentally calibrated predictions of exact real-world timing.

Scuds
Scuds are modeled as lower-water-column amphipod grazers/shredders that use detritus, algae/periphyton, and small amounts of soft plant tissue. Minnows can prey on them.

Modeled food & energy pathways
Every animal has an explicit food/energy pathway in the model. Daphnia graze suspended algae; snails graze algae/periphyton and detritus; scuds use detritus, algae, and limited soft plant tissue; minnows consume Daphnia and scuds and also graze algae and detritus. Bacteria process detritus and carcasses. Producers require light, inorganic nitrogen, and CO₂. These pathways are intentionally visible enough for students to infer a food web from observations rather than being presented as a complete real-community web.

Bacterial persistence
Existing bacteria grow through modeled decomposition and nitrification. Maintenance loss is proportional to biomass, so small populations can persist and respond when resources return. No minimum bacterial population is imposed. The single bacterial pool combines multiple microbial functions and uses instructional rate constants.

Oxygen budget & water chemistry condition
The optional oxygen budget accounts for the last simulated step, including photosynthesis, respiration, decomposition, nitrification, surface exchange, mixing, and numerical bounds. Water chemistry condition is an instructional 0–100 score based on selected chemistry, pH, and temperature. It does not measure population persistence, biodiversity, or future ecosystem stability.

Systems check 3.14.1
Chemical diffusion conserves dissolved material between equal-volume zones. Plant chemistry, added food patches, consumer resources, and spawning use the connected glass compartment. Fish cannot consume the same prey twice. Photosynthesis requires available CO₂; algae require an existing population. These are consistency checks of an educational model, not calibration against field data.

Glass compartments
Continuous glass blocks animal movement and chemistry diffusion. Only water compartments connected to the modeled surface receive direct atmospheric gas exchange. A fully submerged sealed compartment can therefore develop its own O₂, CO₂, and nitrogen chemistry. Animals search for food, predators, and higher-O₂ water only within their connected compartment.

Carcasses & decomposition
A dead minnow sinks until it contacts the actual modeled floor, sand, gravel, rock, or glass structure beneath it. Decomposition promotes local bacterial biomass, contributes detritus and ammonia, consumes dissolved oxygen, and releases carbon dioxide. Multiple carcasses have additive local effects. The model now includes a simplified high-CO₂ stress response, but its threshold is instructional rather than species-specific.

Conservation of matter (3.18)
Carbon, nitrogen and phosphorus are tracked through dissolved pools, algae, plants, animals, carcasses, detritus, bacteria and sediment. Every process moves atoms between pools; only CO₂ exchange with the air, runoff and your own actions add or remove them. Open Mass balance to see the totals. Oxygen is linked to carbon: photosynthesis releases, and respiration and decomposition use, one O₂ for each CO₂ (quotient 1). Nitrification uses 3.43 mg O₂ per mg N oxidized to nitrite and 1.14 to nitrate.

Light, nutrients & producers
Photosynthesis follows a Steele light curve: it rises with light, peaks near the optimum, and declines in very bright light (photoinhibition). Algae shade the water below them (Lambert–Beer), so blooms darken deeper water. Growth is limited by the scarcer of nitrogen and phosphorus (Monod kinetics with Liebig’s law of the minimum); the default tank is phosphorus-limited, as many fresh waters are. Growth rises about twofold per 10 °C (Q10).

Sediment phosphorus
Oxic sediment binds phosphate (iron-bound P); when bottom water loses oxygen, the sediment releases it. This internal loading can amplify eutrophication: a bloom decomposes, bottom water becomes hypoxic, phosphate is released, and the next bloom is fed. The model does not include denitrification, burial or a bicarbonate buffer; the pH slider sets pH directly.

Ammonia toxicity
Total ammonia (NH₃ + NH₄⁺) is shown as Ammonia-N. Only the un-ionized NH₃ fraction is toxic; it is computed from pH and temperature (Emerson et al. 1975). At pH 7.2 and 22 °C about 0.7% is NH₃; at pH 8.6 and 28 °C it is about 22%. Animal stress begins near 0.02 mg/L NH₃-N.

Food webs & reproduction
Minnows capture prey following a Holling type II functional response (intake = aN / (1 + ahN)), so feeding saturates when prey are plentiful. A few prey per compartment are protected in refuges. Minnows also graze algae and detritus. Grazers feed at a rate that saturates with food concentration. Eaten food is egested (30%), stored as body reserves, or respired. Offspring are built from stored reserves, so births depend on food; juveniles grow from reserves before they reach adult size. Hungry prey accept more predation risk to keep feeding. Starvation is a rising risk in poor condition rather than a sudden threshold, and minnows have a small background mortality.

Plant dynamics
Macrophytes photosynthesize by day, respire continuously, and shed about 1% of their tissue per day as detritus. They take N and P from the root zone. Shade, turbidity or heat above 30 °C can push a plant below its die-back threshold; after 4 days there it dies and all its tissue becomes detritus that bacteria must decompose. Healthy plants spread by runners (grass, ribbon) or rooting fragments (stem plants), with the daughter’s tissue coming from the parent.

Cycle view (3.19)
The 🔄 Cycle view draws every recorded transfer of carbon, nitrogen or phosphorus between pools while the model runs. Arrow width follows the flow rate and circle size the amount stored (log scale, because the dissolved pools are much larger). “Right now” averages roughly the last hour, so it shows day/night changes; “24-hour average” smooths them. The flows add up exactly to each pool’s change, so the picture is a complete account of where matter went.

Organic soil (3.35)
The ▤ Soil brush lays nutrient-rich organic soil (like pond mud or aquarium soil) on the bottom; chambers can have none, thin or deep soil. Each soil cell holds organic matter that bacteria decompose at about 1.2% a day at 20 °C (Q10 = 2; about a third as fast without oxygen). Decay takes O₂ from the water just above the soil and returns CO₂ there; its ammonium and phosphate go into the soil’s porewater. Rooted plants feel the porewater’s high concentration (nutrients in a small pore volume) and take from it first, so plants rooted in soil grow faster. Porewater not used by roots seeps into the water at about 7% a day, where algae can use it. Sand, gravel and rock remain chemically inert: they lift plants toward the light, shade, give scuds refuge and trap sinking detritus. Not modeled: soil layers that go fully anoxic at depth, denitrification, and methane.

Experimental chambers & grow lamp (3.34)
🧫 Experimental chambers (Quick-start list or View & data) divide the tank into 2, 3, 5, 6 or 9 equal glass chambers; with 5 the last 3 litres stay an open water bath. Each chamber can have a glass lid (no gas exchange), shade cloth (0% = a dark bottle), extra nutrients (+1 mg/L nitrate-N and +0.03 mg/L phosphate-P per dose) or CO₂ (+4 mg/L per dose), and its own algae (none, or a standard culture of 0.5 units at ½×, 1× or 2×), plants and Daphnia. Natural variation gives each chamber a slightly different starting algae so replicates differ. Chambers start with freshly mixed water (the tank’s average chemistry and bacteria in every zone). A magnetic stirrer option keeps a chamber mixed; without it, settling detritus and the busier bacteria near the bottom slowly build a top-to-bottom oxygen gradient. Temperature is shared, because the chambers sit in one water bath. A grow lamp can replace the sun: always on, or on a 16 h or 12 h timer; at 100% it equals the midday sun. Under a grow lamp the background becomes a still lab wall, with no moving sun or moon. The results table reports gross photosynthesis from the model’s oxygen ledger, the net O₂ change a probe would see, and the light-and-dark bottle estimate.

Dead bodies & the nitrogen cycle (3.33)
Dead Daphnia, snails and scuds now sink as visible bodies and decay over about 5 days at 20 °C (faster when warm, slower with little oxygen or few bacteria). Before 3.33 their tissue became detritus instantly where they died. Decay releases ammonium (yellow specks), CO₂ and phosphate where the body lies, and part of the body becomes detritus and bacteria. The ⚗️ Chemistry panel shows each nitrogen transformation as it happens, from the model’s own ledger: ammonification, nitrification step 1 (NH₄⁺ → NO₂⁻) and step 2 (NO₂⁻ → NO₃⁻), uptake of ammonium and nitrate, and excretion. Denitrification and nitrogen fixation are not modeled.

Oxygen realism (3.32)
The model’s animals are small in biomass so that a tank’s algae can feed the food web, which also means their food-based respiration uses far less oxygen than real animals (about 0.015 mg O₂ a day for a model minnow, against roughly 12 mg for a real 2 g minnow). Gentle keeps that forgiving scale. Realistic adds each animal’s routine respiration at real rates for its size (minnow 0.5, snail 0.02, scud 0.006, Daphnia 0.0008 mg O₂ per hour at 20 °C, Q10 = 2), drawn from the water around it, and the real oxygen demand of a decaying fish (about 400 mg O₂ for a 2 g minnow). Water mixes within hours, as in a real tank. Strict is still, warm water: slower mixing, half the surface gas exchange and a quarter more demand. Pond snails at the surface film breathe air. The extra oxygen use is O₂ only; carbon, nitrogen and phosphorus stay exactly conserved. Tested: a minnow sealed in a 4-litre glass box suffocates in about 1½ days at Realistic and survives indefinitely at Gentle.

Glass walls (3.32)
The glass tool draws straight walls 2 terrain squares thick by default (snapping level or upright onto the 1-litre chemistry grid, because water chemistry is uniform within each litre; Shift for freehand). Animals that touch glass slide along it and, if their target is out of reach, detour around it; animals caught inside newly drawn glass are moved to the nearest open water.

Snails (3.30)
Pond snails crawl; they do not swim. Each snail is always on a surface (the bottom, a rock, a plant, the tank glass or a glass wall, or the underside of the surface film) and climbs only where there is something to climb. Snails make regular grazing trips up plants and the glass to scrape periphyton (the algae film on surfaces), and graze algae and detritus on the bottom. A snail that lets go sinks back down. In low oxygen they crawl to the surface to breathe air, because pond snails such as Physa and Lymnaea are pulmonates with a lung. Click a snail with Inspect to see what it is doing.

Day and night (3.27–3.29)
The sun is above the horizon exactly when the model has daylight (06:00–18:00), following the same half-sine the model uses for photosynthesis. The “light” figure in the day/night badge above the tank is the sunlight reaching the water surface after the Light slider and turbidity. Dawn and dusk colours appear in the hour or so either side of sunrise and sunset, when the model’s light is zero or very low. The moon is decorative and does not light the model.

Cycle view investigations (3.26)
An Oxygen tab shows O₂ made by photosynthesis and used by respiration, decomposition and nitrification, plus exchange with the air; these add up exactly to the change in dissolved O₂. Predict hides the arrow sizes so students choose which flow a change will alter most, then compares the 24 h before with the 24 h after. Before / after does the same comparison for any change. Both use exact running totals of every flow, so the numbers are precise rather than smoothed. Tracer atom moves one atom between pools at random, with each pool’s stay drawn from an exponential distribution whose mean is the amount stored ÷ the outflow, and exits chosen in proportion to the flows (a simple Markov model of real isotope-tracer studies). The Energy pyramid converts the 24-h carbon flows to energy at ≈39 J per mg C and computes production as assimilation (70% of food eaten) minus respiration. Clicking a circle opens its balance sheet: inflows, outflows, net change and turnover time. None of these tools change the model.

Parameter table
Every tuned rate in the model, with units and the kind of evidence behind it. Values marked instructional are tuned for a stable classroom model rather than taken from one study. Run node tests/sensitivity.js to see how each parameter affects persistence.

What the * preset means
The hidden * configuration is a reference ecosystem that has been stability-tested within this model. It is not a claim that those exact organism numbers form an optimal real ecosystem. Scuds remain intentionally absent from that preset.

Interpretation
Use the model to investigate mechanisms, patterns, feedbacks, and evidence. Treat exact numerical outcomes as outputs of this educational model rather than measured ecological forecasts.