The complexity of today's visualization applications demands specific visualization systems tailored for the development of these applications. Frequently, such systems utilize levels of abstraction to improve the application development process, for instance by providing a data flow network editor. Unfortunately, these abstractions result in several issues, which need to be circumvented through an abstraction-centered system design. Often, a high level of abstraction hides low level details, which makes it difficult to directly access the underlying computing platform, which would be important to achieve an optimal performance. Therefore, we propose a layer structure developed for modern and sustainable visualization systems allowing developers to interact with all contained abstraction levels. We refer to this interaction capabilities as usage abstraction levels, since we target application developers with various levels of experience. We formulate the requirements for such a system, derive the desired architecture, and present how the concepts have been exemplary realized within the Inviwo visualization system. Furthermore, we address several specific challenges that arise during the realization of such a layered architecture, such as communication between different computing platforms, performance centered encapsulation, as well as layer-independent development by supporting cross layer documentation and debugging capabilities.

Merge trees, a type of topological descriptors, serve to identify and summarize the topological characteristics associated with scalar fields. They present a great potential for the analysis and visualization of time-varying data. First, they give compressed and topology-preserving representations of data instances. Second, their comparisons provide a basis for studying the relations among data instances, such as their distributions, clusters, outliers, and periodicities. A number of comparative measures have been developed for merge trees. However, these measures are often computationally expensive since they implicitly consider all possible correspondences between critical points of the merge trees. In this paper, we perform geometry aware comparisons of merge trees. The main idea is to decouple the computation of a comparative measure into two steps: a labeling step that generates a correspondence between the critical points of two merge trees, and a comparision step that computes distances between a pair of labeled merge trees by encoding them as matrices. We show that our approach is general, computationally efficient, and practically useful. Our general framework makes it possible to integrate geometric information of the data domain in the labeling process. At the same time, it reduces the computational complexity since not all possible correspondences have to be considered. We demonstrate via experiments that such geometry aware merge tree comparisons help to detect transitions, clusters, and periodicities of a time-varying dataset, as well as to diagnose and highlight the topological changes between adjacent data instances.

A very stable binding site for the interaction between a pentameric oligothiophene and an amyloid-β(1–42) fibril has been identified by means of non-biased molecular dynamics simulations. In this site, the probe is locked in an all-trans conformation with a Coulombic binding energy of 1200 kJ mol⁻¹ due to the interactions between the anionic carboxyl groups of the probe and the cationic ε-amino groups in the lysine side chain. Upon binding, the conformationally restricted probes show a pronounced increase in molecular planarity. This is in line with the observed changes in luminescence properties that serve as the foundation for their use as biomarkers.