Vetturini Anthony J, Cagan Jonathan, Taylor Rebecca E
Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
Nucleic Acids Res. 2025 Jan 11;53(2). doi: 10.1093/nar/gkae1268.
Recent advances in computer-aided design tools have helped rapidly advance the development of wireframe DNA origami nanostructures. Specifically, automated tools now exist that can convert an input polyhedral mesh into a DNA origami nanostructure, greatly reducing the design difficulty for wireframe DNA origami nanostructures. However, one limitation of these automated tools is that they require a designer to fully conceptualize their intended nanostructure, which may be limited by their own preconceptions. Here, a generative design framework is introduced capable of generating many wireframe DNA origami nanostructures without the need for a predefined mesh. User-defined objectives that guide the generative process are input as either single- or multi-objective optimization problems. A graph grammar is used to both contextualize physical properties of the DNA nanostructure and control the types of generated design features. This framework allows a designer to explore upon and ideate among many generated nanostructures that comply with their own unique constraints. A web-based graphical user interface is provided, allowing users to compare various generated solutions side by side in an interactive environment. Overall, this work illustrates how a constrained generative design framework can be implemented as an assistive tool in exploring design-feature trade-offs of wireframe DNA nanostructures, resulting in novel wireframe nanostructures.
计算机辅助设计工具的最新进展有助于迅速推进线框DNA折纸纳米结构的开发。具体而言，现在已有自动化工具能够将输入的多面体网格转换为DNA折纸纳米结构，极大地降低了线框DNA折纸纳米结构的设计难度。然而，这些自动化工具的一个局限性在于，它们要求设计者完全构思出其预期的纳米结构，而这可能会受到设计者自身先入之见的限制。在此，引入了一种生成式设计框架，该框架能够生成许多线框DNA折纸纳米结构，而无需预定义网格。作为单目标或多目标优化问题输入指导生成过程的用户定义目标。使用图文法来关联DNA纳米结构的物理特性并控制生成的设计特征的类型。该框架允许设计者在许多符合其独特约束条件的生成纳米结构中进行探索和构思。提供了一个基于网络的图形用户界面，允许用户在交互式环境中并排比较各种生成的解决方案。总体而言，这项工作说明了如何将约束生成式设计框架作为一种辅助工具来探索线框DNA纳米结构的设计特征权衡，从而产生新颖的线框纳米结构。
