# Difference between revisions of "Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Origami Layouts"

## Origami Layout For Various Experiments

### Regular Rectangular Origami

White dots: where we can extend the probes to attach other strands

Light-blue dots: marker to distingusich the orientation of the origami for AFM images

### Discussion about Arrangements of Tracks

##### Diagonal arrangement of tracks VS. Vertical arrangement of tracks

An important to consider is the particular arrangement of substrate strands for the walker. The particular random walker that we are using moves via strand displacement between two types of substrate (substrates A and B), with each walker-substrate pair having an equal number of conjugated bases. This walker performs a random walk via random, energetically neutral strand displacement4. We prefer this model of walker because it allows track substrate to be reused, unlike many burnt-bridges models of walkers that sacrifice track that has already been walked on in order to achieve directional motion5, and is easier to both design and work with. Because this walker can only move from one type of substrate to the other, it needs a path that alternates between substrate types for it to move between any two points. There are two ways of laying out substrate that we have considered: alternating diagonal bands , and alternating vertical bands . Vertical bands allow near-straight-line movement in the horizontal direction, whereas alternating bands allow straight-line movement in the vertical direction, along the short axis of the origami. As movement along the short axis is toward one of the goals, the diagonal arrangement in Figure 1 is thus preferable, as it minimizes the number of steps a walker has to take to get cargo from its planted location to its associated goal.

### Playground design for overall cargo reorganizing behavior

White dots: regular rectangle

Light-blue dots: marker to distingusich the orientation of the origami for AFM images

Blue dots: track 1

Red dots: track 2

Organge dots: cargo 1

Green dots: cargo goal 1

### Playground design for linear random walking

White dots: regular rectangle

Light-blue dots: marker to distingusich the orientation of the origami for AFM images

Blue dots: track 1

Red dots: track 2

Green star: walker goal

### Playground design for linear random walking with differenct lenghts of tracks

White dots: regular rectangle

Light-blue dots: marker to distingusich the orientation of the origami for AFM images

Blue dots: track 1

Red dots: track 2

Yellow star: walker goal