From biochemical reaction networks to 3D dynamics in the cell: The ZigCell3D modeling, simulation and visualisation framework

Systems-oriented research accelerates our understanding of biological processes and helps in identifying novel drug candidates. However, development of good models and our intuition is hampered by the biological complexity. To be able to see how candidate models evolve in front of the user in an interactive virtual 3D cell at various zoom levels, therefore is a crucial aspect and a challenging problem. The motivation for creating the ZigCell3D software, is thus a holistic view ranging from being able to change model parameters, see how they affect 3D versions of the cell at molecular levels, while at the same time being able to verify the simulated model against a real experimental fluorescence microscopy image. ZigCell3D is a virtual 3D whiteboard approach to chemical reaction modelling. It aims to provide a realtime interactive environment, where complex biophysics research is turned into a creative and game-like 3D environment. The complete system entails modelling, simulation and visualisation as part of a unified framework. The core visualisation is based on a multi-core parallel C/C++ ray tracing engine, that builds a complete 3D iso-surface model of the cell, its organelles and molecules down to the atomic level using PDB files. The simulator itself is based on coarse-grained Brownian motion of the individual molecules, which is visualised in detail in a tightly coupled manner. Using a virtual fluorescence microscope the virtual simulation environment can be benchmarked against real life experimental data