Illustrative Molecular Visualization with Continuous Abstraction

Zwan, Matthew van der; Lueks, Wouter; Bekker, Henk; Isenberg, Tobias

doi:10.1111/j.1467-8659.2011.01917.x

Cited by 45 publications

(51 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, we order the semantic abstractions and allow the experts to seamlessly transition between them (see Fig. 1)-inspired by the continuous transition between primary and secondary structures for proteins from van der Zwan et al [51]. In our approach, however, we not only explore a much higher number of abstraction stages and connect the molecular data to abstract, higher-level geometric structures (e. g., wireframe representations) but also designed a number of interaction techniques that can be applied in a scale-adaptive fashion.…”

Section: Overall Approachmentioning

confidence: 99%

“…Guo et al [21] transitioned between LOD representations based on view distance. Van der Zwan et al [33,51] seamlessly transformed the visualization of a molecule along three independent abstraction axes: the structural abstraction level, the visual stylization, and the support of spatial perception. Krone et al [27] proposed a molecular surface extraction approach that can also be used for LoD renderings.…”

Section: Related Workmentioning

confidence: 99%

See 1 more Smart Citation

Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures

Miao

Llano

Sorger

et al. 2018

IEEE Trans. Visual. Comput. Graphics

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Overall Approachmentioning

confidence: 99%

Section: Related Workmentioning

confidence: 99%

Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures

Miao

Llano

Sorger

et al. 2018

IEEE Trans. Visual. Comput. Graphics

Self Cite

View full text Add to dashboard Cite

show abstract

“…Zwan et al concentrate on the continuous transition between different visualization motifs for molecules, e.g. from space filling to ribbon rendering [46]. Lawonn et al add feature lines, and hatching to emphasize features like cavities, channels, and pockets [29].…”

Section: Related Workmentioning

confidence: 99%

Real-Time Molecular Visualization Supporting Diffuse Interreflections and Ambient Occlusion

Skånberg

Vázquez

Guallar

et al. 2016

IEEE Trans. Visual. Comput. Graphics

View full text Add to dashboard Cite

(a) Time step 1 (b) Time step 2 (c) Time step 3 Fig. 1. By deriving analytic expressions, we can enhance molecular visualizations and realize interreflections in real-time. The images (a-c) show three time steps of a molecular simulation investigating the interaction between a magenta-colored ligand and a receptor molecule, which receives exaggerated diffuse interreflections. Due to these interreflections it can be seen how the ligand enters the active site.Abstract-Today molecular simulations produce complex data sets capturing the interactions of molecules in detail. Due to the complexity of this time-varying data, advanced visualization techniques are required to support its visual analysis. Current molecular visualization techniques utilize ambient occlusion as a global illumination approximation to improve spatial comprehension. Besides these shadow-like effects, interreflections are also known to improve the spatial comprehension of complex geometric structures. Unfortunately, the inherent computational complexity of interreflections would forbid interactive exploration, which is mandatory in many scenarios dealing with static and time-varying data. In this paper, we introduce a novel analytic approach for capturing interreflections of molecular structures in real-time. By exploiting the knowledge of the underlying space filling representations, we are able to reduce the required parameters and can thus apply symbolic regression to obtain an analytic expression for interreflections. We show how to obtain the data required for the symbolic regression analysis, and how to exploit our analytic solution to enhance interactive molecular visualizations.

show abstract

“…By allowing the user to control the seamless transition between different molecule representations, these can be viewed in a combined manner and thus reveal information at different degrees of structural abstraction. The abstractions which are combined, are based on previous work presented by van der Zwan et al [van der Zwan et al 2011]. The authors classify molecular representations based on their illustrativeness, structural abstraction and spatial perception.…”

Section: Related Workmentioning

confidence: 99%

“…An open question remains how to provide a binding-site relevant visualization to the molecular biology domain so that analysts can obtain interactive frame-rates of molecular dynamics simulations on their desktop workstations without any visualization based precomputation. In the search for the appropriate solution we turn to the visual crafts for inspiration, which have been already successfully applied on molecular visualization [van der Zwan et al 2011]. …”

Section: Introductionmentioning

confidence: 99%

Seamless Visual Abstraction of Molecular Surfaces

Parulek

Ropinski

Viola

2013

Proceedings of the 29th Spring Conference on Computer Graphics

View full text Add to dashboard Cite

Three molecular examples demonstrating utilization of our seamless visual abstraction. We employ three different geometric representations (solvent-excluded surface, Gaussian kernels and van der Waals spheres) and their corresponding shading abstractions (diffuse shading and contours, constant shading with contours, constant shading without contours). The application of individual levels is based on the distance to the camera; i.e., the closest surface is based on highest geometrical and shading levels while the farthest are displayed via the lowest ones. In the presented examples we achieved 5 × −10× speed-up as compared to the SES representation only. a) Tubulin: RB3 stathmin-like domain complex. b) The phospholipase bound the lipid membrane. c) Immunoglobulin. AbstractMolecular visualization is often challenged with rendering of large sequences of molecular simulations in real time. We introduce a novel approach that enables us to show even large protein complexes over time in real-time. Our method is based on the level-ofdetail concept, where we exploit three different molecular surface models, solvent excluded surface (SES), Gaussian kernels and van der Waals spheres combined in one visualization. We introduce three shading levels that correspond to their geometric counterparts and a method for creating seamless transition between these representations. The SES representation with full shading and added contours stands in focus while on the other side a sphere representation with constant shading and without contours provide the context. Moreover, we introduce a methodology to render the entire molecule directly using the A-buffer technique, which further improves the performance. The rendering performance is evaluated on series of molecules of varying atom counts.

show abstract

Illustrative Molecular Visualization with Continuous Abstraction

Cited by 45 publications

References 30 publications

Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures

Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures

Real-Time Molecular Visualization Supporting Diffuse Interreflections and Ambient Occlusion

Seamless Visual Abstraction of Molecular Surfaces

Contact Info

Product

Resources

About