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H. Miao,  T. Klein,  D. Kouřil,  P. Mindek,  R. Schatz,  E. Gröller,  B. Kozlikova,  T. Isenberg,  I. Viola (2019)

Multiscale Molecular Visualization

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Journal of Molecular Biology

Abstract

We provide a high-level survey of multiscale molecular visualization techniques, with a focus on application-domain questions, challenges, and tasks. We provide a general introduction to molecular visualization basicsand describe a number of domain-specific tasks that drive this work. These tasks, in turn, serve as the generalstructure of the following survey. First, we discuss methods that support the visual analysis of moleculardynamics simulations. We discuss, in particular, visual abstraction and temporal aggregation. In the secondpart, we survey multiscale approaches that support the design, analysis, and manipulation of DNAnanostructures and related concepts for abstraction, scale transition, scale-dependent modeling, andnavigation of the resulting abstraction spaces. In the third part of the survey, we showcase approaches thatsupport interactive exploration within large structural biology assemblies up to the size of bacterial cells.We describe fundamental rendering techniques as well as approaches for element instantiation, visibilitymanagement, visual guidance, camera control, and support of depth perception. We close the survey with abrief listing of important tools that implement many of the discussed approaches and a conclusion thatprovides some research challenges in the field.

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