Visualization Of Simulation Data Research Articles

The Structural Characteristics and Phase Transformation in Al2O3 Glass. A Molecular Dynamics Simulation

In this work, we have performed a simulation to study the structural characteristics and phase transformation in Al2O3 glass under compression. The structural characteristics of Al2O3 glass were examined via AlOx units, OAly linkages, the average bond distance distributions, order parameters, and visualization of simulation data. The result showed that the network structure of Al2O3 glass is built mainly by AlOx (x = 3, 4, 5, 6, 7) units that are linked to each other via common O atoms. We found that the distribution of AlOx units in network structure is not uniform but tends to form clusters contained AlOx units. In addition, during a moderately long time, the glass has a two-phase that consists of separate low-density (LD) and high-density (HD) phases. The size of these phases significantly depends on the compression.

The study of structure and dynamics of liquid Al2O3·2SiO2 at higher temperatures

ABSTRACTIn this paper, we investigated the structure and dynamics of liquid Al2O3·2SiO2 (AS2) by molecular dynamics simulation and visualization of simulation data. The local structural characteristics are considered through topology statistics of basic structural TOn and OTm units (T is Si or Al; n = 3, 4, 5; m = 1, 2, 3). The amount of distribution, as well as the spatial distribution of basic structural units at higher temperature, is also clarified. The intermediate-range order structure, the amount and spatial distribution of all types of OTm linkages are investigated in detail. The self-diffusion of Si, Al and O atoms is calculated through mean square displacement. The variation of diffusion coefficients is explained in relation to the structural characteristics. The structural and dynamical heterogeneities and micro-phase separation are also discussed in this paper.

MCMap-A Computational Tool for Mapping Energy Landscapes of Transient Protein-Protein Interactions.

MCMap is a tool particularly well-suited for analyzing energy landscapes of transient macromolecular complexes. The program applies a Monte Carlo strategy, where the ligand moves randomly in the electrostatic field of the receptor. By applying importance sampling, the major interaction sites are mapped, resulting in a global distribution of ligand–receptor complexes. This approach displays the dynamic character of transiently interacting protein complexes where not a single complex but an ensemble of complexes better describes the protein interactions. The software provides a broad range of analysis options which allow for relating the simulations to experimental data and for interpreting them on a structural level. The application of MCMap is exemplified by the electron-transfer complex of cytochrome c peroxidase and cytochrome c from baker’s yeast. The functionality of MCMap and the visualization of simulation data are in particular demonstrated by studying the dependence of the association on ionic strength and on the oxidation state of the binding partner. Furthermore, microscopically, a repulsion of a second ligand can be seen in the ternary complex upon the change of the oxidation state of the bound cytochrome c. The software is made available as open source software together with the example and can be downloaded free of charge from http://www.bisb.uni-bayreuth.de/index.php?page=downloads.

Dynamic Building Environment Dashboard: Spatial Simulation Data Visualization in Sustainable Design

When communicating the results of environmental building performance analysis, It Is Important to display resultant information in order (1) to be holistically understood and (2) to guide architectural design decisions. This article proposes a spatial dashboard of environmental performance data as a means to intuitively relate architectural form and performance and achieve the two goals above. The dashboard visualizes daylighting, natural ventilation, and thermal comfort information spatially localized throughout axonometric representations of buildings. Results can be customized by time of day, adding time as another analytical dimension in addition to space. Environmental data, normally hidden, is visually revealed in relation to architectural form. The dashboard enables intuitive design decisions to be made relative to performance measures across time and space.

Network structure of SiO2 and MgSiO3 in amorphous and liquid States

Network structure of SiO2 and MgSiO3 at 300 K and 3200 K is investigated by molecular dynamics simulation and visualization of simulation data. Structural organization of SiO2 and MgSiO3 is clarified via analysis the short range order (SRO) and intermediate range order (IRO). Network topology is determined via analyzing the bond between structural units, the cluster of structural units as well as spatial distribution of structural units. The polyamorphism as well as structural and dynamic heterogeneities are also discussed in this work.

Structural and compositional heterogeneities in liquid aluminosilicate: insight from a grain structure model

Network structure as well as structural and compositional heterogeneities in aluminosilicate (Al2O3-2SiO2) under compression is investigated by analysis and visualization of simulation data. Structural and compositional heterogeneities are clarified through analysis of topology structure and size distribution of TOx-clusters (T = Si, Al; x = 3, 4, 5, 6) as well as OTy-clusters (y = 2, 3, 4). The TOx-cluster can be considered as TOx-grains. It appears that the structure of aluminosilicate is the mixture of TOx-grains with a different short-range order structure and this is the origin of structural heterogeneity. Regarding their composition, the OSiy- and OAly-clusters can be considered as silica- and alumina-grains respectively, and the structure of aluminosilicate can thus be considered to be formed from silica- and alumina-grains. This results in compositional heterogeneity. Moreover, the degree of polymerization and polyamorphism as well as dynamic heterogeneity is also discussed in detail.

Managing Spatial Selections With Contextual Snapshots.

Spatial selections are a ubiquitous concept in visualization. By localizing particular features, they can be analysed and compared in different views. However, the semantics of such selections often depend on specific parameter settings and it can be difficult to reconstruct them without additional information. In this paper, we present the concept of contextual snapshots as an effective means for managing spatial selections in visualized data. The selections are automatically associated with the context in which they have been created. Contextual snapshots can also be used as the basis for interactive integrated and linked views, which enable in-place investigation and comparison of multiple visual representations of data. Our approach is implemented as a flexible toolkit with well-defined interfaces for integration into existing systems. We demonstrate the power and generality of our techniques by applying them to several distinct scenarios such as the visualization of simulation data, the analysis of historical documents and the display of anatomical data.