We present the development of a new graphical user interface driven molecular modeling, editing and visualization tool called Tiamat. Tiamat addresses the challenge of how to efficiently model large and complex DNA nanostructures. We describe the three major components of our system. First, we discuss design guidelines and data structures that form the basis of flexible and large-scale editing. Second, we explain a semi-automatic sequence generator that combines user input with random sequence generation to efficiently label the molecules in the DNA structure. Third, we outline the visualization techniques including a simplification algorithm that are used to render large designs. The results demonstrate how Tiamat was used to generate large and complex designs.
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References in zbMATH (referenced in 6 articles )
Showing results 1 to 6 of 6.
- Jin, Xian-an; Ge, Jun; Cheng, Xiao-Sheng; Lin, Yu-qing: The number of circles of a maximum state of a plane graph with applications (2021)
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- Cheng, Xiao-Sheng; Zhang, Heping; Jin, Xian’an; Qiu, Wen-Yuan: Ear decomposition of 3-regular polyhedral links with applications (2014)
- Gévay, Gábor: Constructions for large spatial point-line (( n _k)) configurations (2014)
- Jin, Xian’an; Zhang, Fuji: The architecture and the Jones polynomial of polyhedral links (2011)
- Williams, Sean; Lund, Kyle; Lin, Chenxiang; Wonka, Peter; Lindsay, Stuart; Yan, Hao: Tiamat: a three-dimensional editing tool for complex DNA structures (2009) ioport