Simplified representation of vector fields
VIS '99 Proceedings of the conference on Visualization '99: celebrating ten years
Visualizing dynamic molecular conformations
Proceedings of the conference on Visualization '02
Computing Smooth Molecular Surfaces
IEEE Computer Graphics and Applications
TexMol: Interactive Visual Exploration of Large Flexible Multi-Component Molecular Complexes
VIS '04 Proceedings of the conference on Visualization '04
Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization
IEEE Transactions on Visualization and Computer Graphics
Two-Level Approach to Efficient Visualization of Protein Dynamics
IEEE Transactions on Visualization and Computer Graphics
BioBrowser: a framework for fast protein visualization
EUROVIS'05 Proceedings of the Seventh Joint Eurographics / IEEE VGTC conference on Visualization
Visualization of the Molecular Dynamics of Polymers and Carbon Nanotubes
ISVC '09 Proceedings of the 5th International Symposium on Advances in Visual Computing: Part II
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Water is known to play a crucial role in protein structure, flexibility and activity. The use of molecular dynamics simulations allows detailed studies of complex protein-solvent interactions. Cluster analysis and densitybased approaches have been successfully used for the identification and analysis of conserved water molecules and hydration patterns of proteins. However, appropriate tools for analysing long-time molecular dynamics simulations with respect to tracking and visualising the paths of solvent molecules are lacking. Our method focuses on visualising the solvent paths entering and leaving cavities of the protein and allows to study the route and dynamics of the exchange of tightly bound internal water molecules with the bulk solvent. The proposed visualisation also represents dynamic properties such as direction and velocity in the solvent. Especially, by clustering similar pathlines with respect to designated properties the visualisation can be abstracted to represent the principal paths of solvent molecules through the cavities. Its application in the analysis of long-time scale molecular dynamics simulations not only confirmed conjectures based on previous manual observations made by chance, but also led to novel insights into the dynamical and structural role of water molecules and its interplay with protein structure.