Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures

Abstract

Abstract-We present an approach to represent DNA nanostructures in varying forms of semantic abstraction, describe ways to smoothly transition between them, and thus create a continuous multiscale visualization and interaction space for applications in DNA nanotechnology. This new way of observing, interacting with, and creating DNA nanostructures enables domain experts to approach their work in any of the semantic abstraction levels, supporting both low-level manipulations and high-level visualization and modifications. Our approach allows them to deal with the increasingly complex DNA objects that they are designing, to improve their features, and to add novel functions in a way that no existing single-scale approach offers today. For this purpose we collaborated with DNA nanotechnology experts to design a set of ten semantic scales. These scales take the DNA's chemical and structural behavior into account and depict it from atoms to the targeted architecture with increasing levels of abstraction. To create coherence between the discrete scales, we seamlessly transition between them in a well-defined manner. We use special encodings to allow experts to estimate the nanoscale object's stability. We also add scale-adaptive interactions that facilitate the intuitive modification of complex structures at multiple scales. We demonstrate the applicability of our approach on an experimental use case. Moreover, feedback from our collaborating domain experts confirmed an increased time efficiency and certainty for analysis and modification tasks on complex DNA structures. Our method thus offers exciting new opportunities with promising applications in medicine and biotechnology.

Scale Trotter: Illustrative Visual Travels Across Negative Scales

“…For instance, van der Zwan et al [57] carried out structural abstraction with seamless transitions for molecules by continuously adjusting the 3D geometry of the data. Miao et al [38] substantially extended this concept and applied it to DNA nanostructure visualization. They used ten semantic scales and defined smooth transitions between them.…”

“…Existing multi-scale visualizations of DNA [36,38,57] or other data [41] often use geometry manipulations to transition from one scale to the next. For the full genome, however, this approach would create too much detail to be useful and would require too many elements to be rendered.…”

“…They often provide intermediate representations that may not be entirely accurate, but show how one scale relates to another one, even in a still image. Viewers can appreciate the properties of both involved scale levels, such as in Miao et al's [38] transition between nucleotides and strands. Specifically, we take inspiration from traditional illustration where a related visual metaphor has been used before.…”

Multiscale Molecular Visualization

“…It supports complex modeling tasks through integrated analyses and recommendations. An important requirement in visual modelitics is that the visualizations consist of simple geometries, which, in turn, facilitate [44], the authors developed ten scales for examination and interaction purposes that enable the designer to apply targeted operations. An example of such a multiscale approach is shown in Fig.…”

Adenita: Interactive 3D modeling and visualization of DNA Nanostructures

“…Our visualization concept, depicts the DNA nanostructure in various forms of details, which we call scales. In our multiscale approach [29], the user can continuously transition between multiple scales and related atomic representation to high-level double stranded representation (Figure 2). This multiscale provides users with means to operate in any desired scale and expect the results to be represented in other scales.…”