A model of spatio-temporal regulation within biomaterials using DNA reaction–diffusion waveguides

In multi-cellular organisms, cells and tissues coordinate biochemical signal propagation across length scales spanning micrometres to metres. Designing synthetic materials with similar capacities for coordinated signal propagation could allow these systems to adaptively regulate themselves across space and over time. Here, we combine ideas from cell signalling and electronic circuitry to propose a biochemical waveguide that transmits information in the form of a concentration of a DNA species on a directed path. The waveguide could be seamlessly integrated into a soft material because there is virtually no difference between the chemical or physical properties of the waveguide and the material it is embedded within. We propose the design of DNA strand displacement reactions to construct the system and, using reaction-diffusion models, identify kinetic and diffusive parameters that enable super-diffusive transport of DNA species via autocatalysis. Finally, to support experimental wavegui..., The data was collected from fluorescence measurements of qPCR experiments and raw outputs from spatial simulations obtained from reaction-diffusion models. The resulting data from experiments and simulations were processed in Matlab., , # Data Repository for: A model of spatiotemporal regulation within biomaterials using DNA reaction-diffusion waveguides

[https://doi.org/10.5061/dryad.rxwdbrvb3](https://doi.org/10.5061/dryad.rxwdbrvb3)

## Description of the data and file structure

The following document outlines the structure of the data package which encompasses all spatial simulations of the reaction-diffusion waveguide & well-mixed experimental analyses of the strand displacement reaction network. Datasets for each result are placed into a corresponding folder which contains MATLAB code used to analyze the data. In the next section, the structure of the repository is listed.

### 1. Spatial Models:

* Idealized Waveguide: contains simulations of the abstract waveguide with and without patterned Sink, .csv, and .txt data output files for each model, and MATLAB scripts for analyzing waveguide dynamics. Each MATLAB file describes the analysis it conducts as well as the dataset it pulls from within the folder.
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