New perspectives have been developed to understand the processes of modeling heterogeneous membranes. These are crucial steps prior to applying advanced techniques like molecular dynamic simulations of whole membrane systems. Lipid, protein, and membrane packing problems are addressed based on biochemical properties in combination with computational optimization techniques. The CELLmicrocosmos 2.2 MembraneEditor (CmME) is introduced as an appropriate framework to handle such problems by offering diverse algorithmic approaches. Its algorithm plug-in-interface enables modelers to generate problem-specific algorithms. Good solutions concerning runtime and lipid density are realized by focusing on the outer shapes of the PDB-based molecules. Application cases are presented like the publication-based modeling of inner and outer mitochondrial membrane-fragments, semiautomatic incorporation of proteins, and the assembly of rafts. Concerning geometrical aspects of the lipids, the achieved results are consistent with experimental observations related to lipid densities and distributions. Finally, two membranes simulated with GROMACS are analyzed and compared: the first is generated with conventional scripting techniques, the second with the CmME Distributor algorithm. The examples prove that CmME is a valuable and versatile tool for a broad set of applications in analysis and visualization of biomembranes.

Cell visualization is an important area of scientific and educational visualization. There is already a number of astonishing animations illustrating the structural and functional properties of biological cells available in the Internet. However, these visualizations usually do not take advantage of three-dimensional (3-D) stereoscopic techniques. The stereoscopic visualization of the microcosmos cell-invisible to the human eye-bears high potential for educational as well as scientific approaches. Using open source tools it will be shown that it is possible to generate statically rendered as well as interactive stereoscopic cell visualizations. First, the 3-D modeling software Blender in conjunction with Schneider's stereoscopic camera plug-in will be used to generate a stereoscopic cell animation. While static renderings have an advantage in that the stereoscopic effect can be optimized for spectators, interactive stereoscopic visualizations always have to adjust and optimize the stereoscopic effect for users who can freely navigate through space. Cell visualization is paradigmatic for this problem because the scale differences from the mesoscopic to the molecular level account for a factor of 100,000. Therefore, two stereoscopic approaches of the CELLmicrocosmos project will be introduced, which address the stereoscopic scaling problem. The stereoscopic quality was positively evaluated by 20 students. Downloaded From: http://electronicimaging.spiedigitallibrary.org/ on 05/15/2015 Terms of Use: http://spiedl.org/terms

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