The library

WaterSim

Liquid water, and what follows from hydrogen bonds.

• temperature
• phase change
• ice floating
• salt dissolving

molecules · bulk

Membrane

A bilayer, its proteins, and what crosses.

• diffusion
• osmosis
• selectivity
• pumps and ATP
• resting potential
• chemiosmosis

membrane · bulk

ElectronTransport

Respiration's chain pumping protons out, and the turbine they turn coming back.

• complexes I–IV
• NADH and FADH₂
• no oxygen, uncouplers
• the ATP getting out

membrane · bulk

LightReactions

Light lifts electrons out of water, and the thylakoid turns that into ATP and NADPH.

• PSII, b6f, PSI
• water split, O₂ off
• NADP⁺ to NADPH
• one flash at a time

membrane · bulk

Molecule

One molecule in 3D, any in the library by name.

• an atom lit up
• hydrogens on or off
• beside its diagram

molecules · single

Condense

Two molecules joining, and the water that leaves.

• glycosidic · ester · peptide
• α against β
• hydrolysis, run backwards

molecules · single

RespirationReaction

One step of respiration, on two molecules.

• glycolysis · Krebs · fermentation · the chain
• click the bond
• a carrier turning over

molecules · single

Proteinbox

Any protein in the library, from deposited coordinates.

• primary to quaternary
• ribbon · surface · fold
• two side by side

macromolecule · single

HbCrowd

A crowd of hemoglobins, and the moment HbS starts a fibre.

• HbA against HbS
• a fibre starting

macromolecule · bulk

BloodCell

One red blood cell, cut open.

• tonicity
• lysis and crenation
• sickling

cell · single

AnimalCell

An animal cell cut open, with its organelles.

• naming the parts
• animal against plant
• vesicle traffic

cell · single

Mitochondrion

One organelle cut open, membrane by membrane.

• two membranes
• cristae as sacs
• the chain, and the protons

organelle · single

Chloroplast

One chloroplast cut open, membrane by membrane.

• grana and lamellae
• the light reactions, placed
• protons, and the oxygen

organelle · single

PlantCell

A plant cell cut open, and what water does to it.

• turgor and wilting
• plasmolysis
• cyclosis

cell · single

Leaf

A leaf in cross-section, tissue by tissue.

• gas exchange
• transpiration
• stomata opening

tissue · bulk

BloodFlow

A vessel of red cells, narrowing.

• vaso-occlusion
• stiff against flexible

organ · bulk

Tree

A tree, the air around it, and where its mass came from.

• Van Helmont's willow
• day and night

organism · single

Diagram

One molecule, drawn flat, in the notation its chemistry wants.

• Haworth · Lewis · skeletal
• lone pairs
• an atom lit up

no rung · a notation is not in the world

Graph

A chart of measurements, or a live trace off a running sim.

• scatter · line · bar
• fit and error bars
• live trace

no rung · a chart is not in the world