Dna 3d engine

<p align="center"> <img src="https://hsto.org/webt/r6/dp/ks/r6dpksrxkvmgumetfjvfjcwn4wy.png" alt="CubeCRN logo" width="400" /> </p> <h1 align="center">cube3d.dna</h1> <p align="center"> The most advanced and compact 3d engine ever implemented in DNA code. <br><br> <img alt="environment: in vitro" src="https://img.shields.io/badge/environment-in%20vitro-red"/> <img alt="platform: DNA | TMSD" src="https://img.shields.io/badge/platform-DNA%20%7C%20TMSD-white"/> <img alt="license: GPL-v.3.0+" src="https://img.shields.io/badge/license-GPL--v.3.0%2B-green.svg"/> <br> <img alt="lint status" src="https://github.com/pallada-92/dna-3d-engine/workflows/lint/badge.svg"/> <img alt="tests status" src="https://github.com/pallada-92/dna-3d-engine/workflows/tests/badge.svg"/> <img alt="coverage" src="https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/pallada-92/7b35716db8bedb6914c6cf2fab3a4dd0/raw/coverage_badge.json"/> <img alt="total lines" src="https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/pallada-92/7b35716db8bedb6914c6cf2fab3a4dd0/raw/loc_badge.json"/> <img alt="bundle size" src="https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/pallada-92/7b35716db8bedb6914c6cf2fab3a4dd0/raw/bundle_size_badge.json"/> <!-- <img alt="active installs: 0" src="https://img.shields.io/badge/active%20installs-0-yellow"/> --> </p> <br />

Getting started

• Getting started tutorial on ObservableHQ
• Try this in your browser on ObservableHQ

How to deploy

1. Synthesize the oligonucleotides from the cube3d.dna file.
2. Arrange the test tubes as shown in the diagram below.
3. Don't forget to provide the initial concentrations according to the table below.
4. Use a pipette to encode the position (row and column) of each tube to start the computation.

<details> <summary>Environment variables</summary>

q = 0.01
cxtm = 0.606
axp = 0.606
cytm = 0.898
ayp = 0.898
cztm = 1.243
azp = 1.243
mxyzm = 0.3
nx = 0.036 + 0.555 Col + 0.147 Row
ny = 0.853 + -0.517 Row
nz = 0.737 + -0.270 Col + 0.302 Row

</details> <p align="center"> <img src="https://habrastorage.org/webt/v8/hf/gw/v8hfgw7rpxrhw8owhwxewnalfle.png" width="600"/> </p>

Testing

1. Pick the <a href="https://en.wikipedia.org/wiki/Fluorophore">fluorophore</a> of your favorite color and attach it to the Strand R0, so that it activates when the R species are being produced.
2. Use a light source with a specific wavelength (depending on the fluorophore you've chosen) to render the result.

<p align="center"> <img src="https://hsto.org/webt/hv/q_/zy/hvq_zyw6uuwwfpg6umqthctq6tm.png" width="600"/> </p>

<i>Disclaimer: perhaps it would not be a good idea to try this experiment in a real lab, because it will cost you a lot of money and most likely won’t work as intended the first time.</i>

Ports to other languages

• SQLite version
• Excel version
• JavaScript version
• Russian (Русский)

Gallery

<table> <tr> <td align="center" valign="center" width="50%"> <img src="https://habrastorage.org/getpro/habr/post_images/9e2/fc9/d46/9e2fc9d4605a01c82ae317775fad1e10.gif" width="100%" /><br> Ray marching common implementation<br> <img src="https://habrastorage.org/webt/gl/b_/e8/glb_e8-jvkdoyhuri8gctsnysy4.png" width="200" /> </td> <td align="center" valign="center" width="50%"> <img src="https://habrastorage.org/webt/8n/r_/6o/8nr_6oqof2xrvhf8mbt0r4lmtmu.gif" width="100%" /><br> Ray marching differential form used here<br> <img src="https://habrastorage.org/webt/ao/ze/qh/aozeqh4htzkzvbh_po67dmh_zho.png" width="200" /> </td> </tr> <tr></tr> <tr> <td align="center" valign="center"> <img src="https://habrastorage.org/webt/gw/zb/v1/gwzbv1w5humyabeelkyx_c3gq7k.gif" width="100%" /><br> Simplified animation of the toehold mediated strand displacement technique (based on supplementary materials from [2]) </td> <td align="center" valign="center"> <img src="https://habrastorage.org/webt/ph/iv/ax/phivaxoqftqzm2h7qvbbj41dwiq.png" width="100%" /><br><br> The types of oligonucleotides required for a single reaction (based on supplementary materials from [2]) </td> </tr> <tr></tr> <tr> <td align="center" valign="center"> <img src="https://habrastorage.org/webt/ww/9k/xd/ww9kxd64xtigxtbpc5mm3tvsswg.png" width="100%" /><br> Data flow graph of the JS implementation. </td> <td align="center" valign="center"> <img src="https://habrastorage.org/webt/uj/_l/2_/uj_l2_q26onfetzrpq_0wfetxic.png" width="100%" /><br> Species interaction graph of this implementation. </td> </tr> <tr></tr> <tr> <td align="center" valign="center"> <img src="https://habrastorage.org/webt/-j/ak/5i/-jak5iv5d7pkkosrhl_g4r3oo34.png" width="100%" /><br><br> Unminified source code of this implementation which just comprises plain reactions with a few macros. The minifier was written in Wolfram Language specially for this project. </td> <td align="center" valign="center"> <br> <img src="https://habrastorage.org/webt/qn/-j/bu/qn-jbugqz0opyuxhvm6j09wv5te.png" width="100%" /><br><br> CRN++ source code for comparison (<a href="https://github.com/marko-vasic/crnPlusPlus">CRN++</a> is not used in this implementation). </td> </tr> <tr></tr> <tr> <td align="center" valign="center"> <img src="https://habrastorage.org/webt/lv/ah/vs/lvahvszdgpw5vbvottwja7gwtjw.png" width="100%" /><br><br> 10 reactions after the minification used in this project. Since the piperine compiler doesn't support more than 2 products on the right-hand side, the reactions were split. </td> <td align="center" valign="center"> <br> <img src="https://habrastorage.org/webt/lh/hx/j8/lhhxj842nxuxdocbz1zsyazvfok.png" width="100%" /><br><br> CRN++ 70 reactions output for comparison (<a href="https://github.com/marko-vasic/crnPlusPlus">CRN++</a> is not used in this implementation). </td> </tr> </table>

Building from source

1. Install the <a href="https://github.com/DNA-and-Natural-Algorithms-Group/piperine">piperine compiler</a> by the DNA and Natural Algorithms Group.
2. Run the following command

piperine-design cube3d.crn --maxspurious 0.765

3. Wait 2-3 hours for the compilation results.

References

1. David Soloveichik, Georg Seelig and Erik Winfree<br>
   <a href="https://www.pnas.org/content/107/12/5393">DNA as a universal substrate for chemical kinetics</a><br>
   Proceedings of the National Academy of Sciences Mar 2010, 107 (12) 5393-5398; DOI: 10.1073/pnas.0909380107<br><br>

2. Niranjan Srinivas, James Parkin, Georg Seelig, Erik Winfree and David Soloveichik<br>
   <a href="https://science.sciencemag.org/content/358/6369/eaal2052.full">Enzyme-free nucleic acid dynamical systems</a><br>
   Science 358, eaal2052 (2017).<br>
   Some images were taken from <a href="https://science.sciencemag.org/content/suppl/2017/12/13/358.6369.eaal2052.DC1">supplementary materials</a><br><br>

3. Chalk, Cameron, Niels Kornerup, Wyatt Reeves, and David Soloveichik.<br>
   <a href="https://arxiv.org/abs/1907.00053">Composable rate-independent computation in continuous chemical reaction networks.</a><br>
   International Conference on Computational Methods in Systems Biology, pp. 256-273. Springer, Cham, 2018.<br><br>

4. Chen, Ho-Lin, David Doty, and David Soloveichik.<br>
   <a href="https://dl.acm.org/doi/abs/10.1145/2554797.2554827">Rate-independent computation in continuous chemical reaction networks.</a><br>
   Proceedings of the 5th conference on Innovations in theoretical computer science. 2014.<br><br>

5. Marko Vasic, David Soloveichik and Sarfraz Khurshid<br>
   <a href="https://arxiv.org/abs/1809.07430">CRN++: Molecular Programming Language</a><br>
   Natural Computing (2020) 19:391–407 DOI: 10.1007/s11047-019-09775-1<br>
   <a href="https://github.com/marko-vasic/crnPlusPlus">CRN++ on GitHub</a><br><br>

6. Inigo Quilez<br>
   https://www.iquilezles.org/www/index.htm<br>
   Introduction to Raymarching Signed Distance Functions