Multiscale Visibility Management in DNA Nanostructures



DNA has a great chemical stability and can fold into chemical reactive 3D structures. Due to its Watson-Crick base-pair complementarity, it is utilized as a building material to construct nanoscale objects. Arbitrary 2D and 3D nanostructures can be already created from DNA. For example, Andersen et al. [1] presented a DNA box with a controllable lid that can trap a cargo inside. The current in silico design [2, 3, 4] of nanoscale objects is a convoluted process.

In active collaboration with the Austrian Institute of Technology, we developed a software that allows scientists to analyze and modify DNA nanostructures on multiple semantic scales. However, for the analysis and design of objects of higher-order complexity, the visibility of these objects have to be managed. Schemes for efficient adjustment of visible elements are necessary in order to allow the user to inspect and interact with the relevant parts of the object.


The goal of this project is to come up with smart visibility management schemes (such as cutaway views [5]) for complex scenes such as DNA nanostructures, that consists of many different geometries (atoms, nucleotides, single strands etc.). The software should be implemented as an extension to the SAMSON Connect software [6].

Related Work

[1] E. S. Andersen, M. Dong, M. M. Nielsen, K. Jahn, R. Subramani,W. Mamdouh, M. M. Golas, B. Sander, H. Stark, C. L. P. Oliveira, J. S. Pedersen,V. Birkedal, F. Besenbacher, K. V. Gothelf, and J. Kjems. Self-assembly of a nanoscale DNA box with a controllable lid. Nature, 459(7243):73–76, May 2009.

[2] S. M. Douglas, A. H. Marblestone, S. Teerapittayanon, A. Vazquez, G. M. Church, and W. M. Shih. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Research, 37(15):5001–5006, Aug. 2009.

[3] E. Benson, A. Mohammed, J. Gardell, S. Masich, E. Czeizler, P. Orponen, and B. Hoegberg. DNA rendering of polyhedral meshes at the nanoscale. Nature, 523(7561):441–444, 2015. [4] R. Veneziano, S. Ratanalert, K. Zhang, F. Zhang, H. Yan, W. Chiu, and M. Bathe. Designer nanoscale DNA assemblies programmed from the top down. Science, 352(6293):1534:1–1534:15, June 2016.

[4] R. Veneziano, S. Ratanalert, K. Zhang, F. Zhang, H. Yan, W. Chiu, and M. Bathe. Designer nanoscale DNA assemblies programmed from the top down. Science, 352(6293):1534:1–1534:15, June 2016. 

[5] BURNS M., FINKELSTEIN A.: Adaptive cutaways for comprehensible rendering of polygonal scenes. In SIGGRAPH Asia (Singapore, 2008), ACM, pp. 154:1–154:7

[6] NANO-D, Inria. SAMSON – Software for adaptive modeling and simulation of nanosystems. Website:



  • Knowledge of English language (source code comments and final report should be in English)
  • Knowledge of C++
  • Commitment to collaborate with scientists in nanotechnology


For more information please contact Haichao Miao (