Overview

Our project aims for the biological implementation of cellular automata, so we had to find a way to create a regular grid of cells with a defined neighborhood as shown in the pictures below. On the left side a classical cellular automata is depicted, on the right side an outline of our biological version consisting of a grid-like polydimethylsiloxane (PDMS) chip filled with cell colonies encapsulated in alginate beads.

Classical grid from cellular automata theory (ON state=back, OFF state=white).

Outline of a PDMS-made grid loaded with cells confined in alginate beads for the biological implementation of cellular automata (ON state=sfGFP/green, OFF state=white).

In the following, we have investigated the combination of additive manufacturing (3D-printing) and PDMS chip fabrication for applications in synthetic biology. This rapid prototyping approach allowed us to update our chips continuously according to new insights from modeling or the wet lab and in particular to avoid more intricate photolitographic approaches, which generally require clean room access, relatively expensive raw materials, and in depth knowledge of etching techniques. As a result, we are convinced that the tinkering with 3D-printing for mold creation is more economical for our applications and perfectly in line with the do-it-yourself spirit of iGEM.

Mold Design

Our custom-made plates and molds were design using a common personal computer (MacBook Air, 13-inch, early 2014, 1.7 GHz Intel Core i7, 8 GB 1600 MHz) and a 3D computer aided design (CAD) software package that is freely available for Mac OS X 10.9.4 ([http://www.123dapp.com/design Autodesk123D Design]). The CAD models were exported as mesh files (.stl) to the 3D printer's software ([http://www.makerbot.com/support/makerware/troubleshooting/ MakerWare]). The dimensions of the device-structures were usually between 1 mm and 5 mm, falling in the range of millifluidics.

3D-Printing and Rapid Prototyping

The mold designs were printed with a commercial 3D-printer (2nd generation MakerBot with MakerWare software; MakerBotIndustries, Brooklyn, US; 5th generation US$ 2'899) with acrylonitrile butadiene styrene (ABS, about US$ 160 per kg). The maximum object size printable is [mm]: 225 x 145 x 150. The precision and minimum feature size are given as [mm]: 0.011 (XY-axis), 0.0025 (Z-axis); and 0.4 (XY-axis), 0.2 (Z-axis) respectively. The printing time varied with the size of the mold but was usually below 4 hours. All fabricated structures were ready to use after removing the support structures and did not require additional surface treatments like sonication, curing, painting or silanization. The molds were then directly used for PDMS chip production. In addition, custom made black 96-well plates (connected wells for diffusion assays, plate reader compatible) were printed but found to be leaky over time.

PDMS Chip Preparation

Time-Lapse Movies