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Illustrative Molecular Visualization

Physiological processes are of the temporal and spatial multi-scale and ranges from molecular level to the whole organism. Many of the processes have their begining in the molecular scale. Important processes such as polymerization, diffusion, reactions are all happening in the crowded environment full of different molecules. Also those processes have vast temporal range from nanoseconds (diffusion) to seconds (polymerization). Our first focus is therefore on the illustrative visualization of physiological processes in the molecular scale to provide intuitive visual representation, which the user can observe and interact with.

Illustrating Polymerization using Three-level Model Fusion


Feel free to download the unity prototype of our current research project. It contains Unity project, which can be opened by the Unity Editor. In the prototype project hierarchy there are models and materials used to create scenes and simulation, 7 scenes which covers the demonstration bundle of project and the scripts.

The demonstration bundle consist of 7 unity scenes. Three of the scenes: parp, cellulose and tubulin, are biological examples of our prototype described in the paper. For additional demonstration of approach there are examples: starpolymer, copolymer and showcase. StarPolymer scene demonstrates the creation of star polymer with our approach, copolymer on the other hand presents the creation of block linear copolymer. Showcase demonstration is described in more detail in the paper. The last scene demonstrates more advanced visualization of our system mentioned in the Discussion section of the paper.

Every scene have predefined GameObjects for important parts pf the system: LSystem and Agent system (see Fig. 1). Those objects contains their respective scripts, which handles the initialization and update of systems. For managing and setting the parameters of those system, there is provided Editor custom GUI in the Inspector panel.

LSystem GUI is divided to three parts. First is the part managing the alphabet of the L-System. Here are specified symbols, which are later used to define the rules and the axiom. The description and semantic meaning of those rules are detaily described in the paper. Second part manages the axiom, which is the starting point of the process. The axiom can only be a communication symbol, which tells by which subprocess it should start. Last section manages the rules. User can change/remove the existing rules or add the new ones.

Agent system is steered by the system of densities, which is another modeling layer described in more detail in System of Densities subsection in the paper. In thiswindow user can add or remove the type of molecule which is in environment. Every molecule has its own image preview and the density can be adjusted.

Simulation have two global parameters: time delta of the simulation, and the number of monomers of the resulting polymer. This variables are accesible from the editor window, which can be opened from LSystem or Agent system inspector.

 Last change: Ivan Kolesar, 2014-08-11