Generator

One strand, through every helix, once

A generator in the folding nobody designed library, called 57 times across 9 essays. Below: what it draws with nothing specified and with the settings the essays give it, what it checked while drawing, and everywhere it is used.

scaffold-route is one function. Everything below was drawn by it when the site was last published, at settings taken from the essays rather than invented for this page — so a figure here is the same figure a reader meets in an essay, and when the generator changes, this page changes with it.

With nothing specified

One strand, through every helix, onceEach circle is one helix seen end-on and each step is a crossover to a lattice neighbour. The route is found by a search that never looks at the colouring; the colour counts are computed separately, and a shape whose two colours differ by more than one is refused before any search is run.a route the search found123456121110987131415161718242322212019helices 24colours 12 : 12a route is not forbiddenscaffold used 21%48 staples of 3224 helices · 1536 bases · 48 staples · colours 12 : 12

view: "fooled", show: "corridors", lattice: "honeycomb", survivor: "piece", upTo: 16, through: "corridor"

The corridors of a 16-helix survivorThe 16-helix shape on the honeycomb lattice that every earlier cheap test let through, drawn with its corridors of two-neighbour helices each in a colour and its junctions numbered. Every junction of three has one compulsory mouth too many, and only one end of the route is free to absorb one, so the count refuses the shape.the honeycomb lattice's 16-helix survivor, read by its corridorsa junction is a helix with other than two neighbours; a corridor runs between junctions through helices with twoeach corridor in its own colour; numbered circles are the junctions with three neighbours or more123end16 helices, 4 corridors, 3 junctionsjunction 1: 3 compulsory mouths, 1 to absorbjunction 2: 3 compulsory mouths, 1 to absorbjunction 3: 3 compulsory mouths, 1 to absorb1 helix with one neighbour spends an end1 end left to lie inside a corridorneeds 3, has 1: refused

view: "fooled", show: "tally", lattice: "honeycomb", stage: "piece", upTo: 16, through: "corridor"

The corridor count on the honeycomb survivorsEvery placement of 16 helices on the honeycomb lattice that the colour count, the ends, the cuts, the forced steps, the end colours and the piece test let through and no route reaches, grouped by how many junctions of three it has, how many ends those junctions need and how many the route has free.the 6 placements of 16 helices on the honeycomb lattice that every earlier test lets througheach read by its junctions and the ends a route has to spareplacementsjunctions of three or moreends the junctions needends freethe corridor count6331refusedthe corridor count refuses 6 of the 6 and lets 0 through

view: "fooled", show: "census", lattice: "honeycomb", upTo: 16, through: "corridor"

Every shape to 16 helices on the honeycomb latticeEvery connected shape of four to 16 helices on the honeycomb lattice, how many pass the colour count, the count of ends and the cut conditions, how many of those have no route, and how many of those also pass the forcing test and the colour of the forced ends.every connected shape on the honeycomb lattice, size by sizethe last three columns are shapes no route reaches that the tests named so far let throughhelicesshapespass the countsno route, of thoseand forcing passesand end colours passand the piece test passesand the corridor count passes4141200000536240000069443000007250840000086751620000091,83831200000105,053579000001114,0161,110000001239,1692,11118000013110,1944,142156000014311,7517,734282000015886,16015,1921,05612000162,529,26028,2211,7226660a shape counted in a later column passes every test named before it, and the search finds no route through it

What it checked while it drew

Collected while it drew, not written by hand. The count is how many separate times that claim was put to the test.

Where it is called

Every figure listed here is drawn by the same rule, so a mistake in the rule would be in all of them at once, and so would a correction.

A corridor has two mouths

Every cheap test for whether a strand can be routed through a bundle of helices had been built on knowing where the route ends, and the honeycomb's sixteen-helix survivor is a shape where the ends are mostly unknown. A test that needs no ends at all reads the shape by its corridors — chains of helices with two neighbours — and its junctions. A route passes a junction once, so a junction with three corridors leaves one of them to be entered only from its far mouth, which needs an end of the route inside it. The survivor has three such junctions and one free end. The count refuses all six of its placements, leaves the honeycomb with no survivor to sixteen helices, and on the square lattice refuses one of the two twelve-helix shapes and not the other.

A domain too short to be unique

A staple holds the scaffold by pairing with a stretch of it, and two arguments decide how long that stretch has to be. One is combinatorics — a stretch of seven bases has about four hundred other places in a 7,249-base strand it would also match. The other is thermodynamics, and it is the one that binds: a duplex that is unique at eleven base pairs still comes apart at the temperature the design is held at, and staying paired takes seventeen. Rounded up to the crossover period, that is three periods on both lattices, and the lattice the helix prefers is the one whose three-period domain leaves some of its staples unattached.

A row the route cannot leave

Every rectangular block of helices up to ten by eight routes on the square lattice. On the honeycomb, the lattice a double helix's pitch prefers, twenty of the eighty do not — and every block odd in both directions fails for a reason visible along one row: every second helix on the top row has no neighbour off it, the two corners have one neighbour each, and a route forced through them runs the length of the row and ends. The colour count passes all of them, and a degree count along a single row refuses them.

A sheet that routes itself

DNA origami folds one long strand into a shape by holding it against itself with a few hundred short ones. There is no sheet and no crease — what has to be designed is a route — and the first thing that can go wrong is a counting argument crease patterns already know under another name.

A test that only knows one lattice

The cheapest argument that refuses the smallest shape no cheap test could refuse was read off that shape: cut at one helix, find the piece with no end in it, and count the colours of the stretch the route is then forced to cross. Added to the census it refuses every one of the square lattice's thirty-two eleven-helix survivors and pushes the smallest survivor to twelve, where twelve placements of two shapes survive out of half a million. On the honeycomb it refuses none of the six at sixteen. A test inherits the lattice of the witness it was read off, and the staircase is two staircases.

Every cheap test misses a shape

A strand routed through a bundle of helices has to visit each once, and whether a shape allows that is hard to decide — so the cheap tests that refuse shapes are necessary and never sufficient, and for every set of them there is a smallest shape they pass and no route reaches. Listing every connected shape and searching the ones the tests let through finds it: nine helices on the square lattice for the colour count, the ends and the cuts, eleven once the steps a route's ends force are added, and still eleven once the ends' colours are checked. On the honeycomb the same three stages give twelve, fifteen and sixteen. Each test pushes the smallest unroutable shape out or leaves it where it is; none removes it.

The helix chooses the lattice

A strand can cross to the next helix only where its backbone faces that helix, and a double helix turns about 34.3° a base. Three neighbours a third of a turn apart are faced exactly every seven bases. Four neighbours a quarter of a turn apart are never faced exactly by any whole number of bases — the nearest miss by 4.3°, and the misses do not average out, they add: 17° over thirty-two bases, 137° over two hundred and fifty-six. The lattice a design is drawn on is decided by the molecule before any shape is chosen.

Two ceilings

A DNA origami is limited by the length of one viral strand and by whether its helices can be visited once each in a single pass. Grown one step at a time, a square block runs into the first at a hundred helices and a plus runs into the second at five — so which limit a shape meets is decided by the shape and not by the chemistry.

Two things called folding

A protein folds and a sheet folds, and the word is the same word by accident. Both have exponentially many states and that is not the difference. The difference is that one of them can be filtered by four conditions checked at a single point, and the other cannot be filtered by anything local at all.

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