From Virtual DNA to Simulation: Exporting Designs from Adenita

Designing DNA nanostructures virtually is an exciting and increasingly common task among molecular modelers, bioengineers, and synthetic biologists. But the practical challenge often arises at a critical moment: how do you take your virtual design and prepare it for simulation? If your designs live exclusively inside CAD-like tools with no seamless way to export valid simulation-ready files, you’re facing a serious productivity bottleneck.

If you’re using Adenita, the powerful SAMSON Extension for DNA nanostructure modeling, you’re in luck. Let’s walk through how you can efficiently export your work for downstream simulation workflows—in formats like CSV and oxDNA.

Why export matters 🧬

Design without export is like building without a door. Simulations help validate structural stability, binding behavior, and general functionality of your DNA nanostructure before you ever step into the lab. Formats like oxDNA are essential for coarse-grained simulations that let you see DNA dynamics under various conditions.

Exporting from Adenita in SAMSON

Once your build is complete in Adenita, exporting is straightforward and offers flexibility depending on your downstream needs:

  • List of sequences: Export as a CSV file to get the linear representation of nucleotide sequences per strand. This is useful for synthesis ordering or archiving your parts library.
  • oxDNA format: Select this to prepare your nanostructure for coarse-grained modeling in oxDNA. It will include the topology and sequence in the format expected by oxDNA tools.

To access export options:

  1. Open Adenita inside SAMSON (you’ll find it under Home > Apps or by searching via Find everything…).
  2. Click the export icon Export on the interface toolbar.
  3. Choose between exporting as CSV or oxDNA format, depending on your simulation goals.

What gets exported?

Only structures made and managed by Adenita will be included. This ensures the exported data is clean and appropriate for subsequent modeling or simulation tools. If you’ve loaded non-DNA entities (like protein structures), they will not be part of the DNA-focused export.

Practical workflows with oxDNA

Once exported, your oxDNA files can be input directly into the oxDNA simulation engine, where you can study behaviors such as:

  • Folding dynamics under thermal fluctuations
  • Mechanical responses to external forces
  • Thermodynamic stability of designed motifs

If you need to convert atomistic-level representations to coarse-grained models, make sure all sequences are defined and scaffold positions are clarified using Adenita’s scaffold tools before export.

Export Tip: Partial Design?

If you want to simulate a subcomponent only, use the Save selection tool Save selection. Exporting only parts can greatly reduce simulation time and allow targeted investigations.

Conclusion

Exporting designs for simulation directly from Adenita removes a major friction point in the DNA nanostructure design workflow. With just a few clicks, you transition from virtual modeling to practical testing—streamlining your research process.

You can explore other export tools and settings in the full Adenita documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.

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