Accommodating space, time and randomness in network simulation

Modeling Three-Dimensional Spatial Regulation of Bacterial Cell Division (Dissertation)

“…In Chapter 1 we have looked at the prominent spatial modeling methods with a summary of their features listed in (Ridgway et al, 2006;Takahashi et al, 2005). Instead, we use a time-driven, lattice-based method to skip two costly operations -molecule search and distance calculation -required by off-lattice methods (Andrews and Bray, 2004;van Zon and ten Wolde, 2005b;Ridgway et al, 2008) to resolve collisions.…”

Modeling Three-Dimensional Spatial Regulation of Bacterial Cell Division (Dissertation)

“…Processes that are strongly dependent on the cell morphology, multicompartmental interaction and dynamic localization of molecules such as cell signaling Neves et al, 2008), bacterial cell division (Lutkenhaus, 2007;Adams and Errington, 2009) and chemotaxis (Greenfield et al, 2009;Rao and Ordal, 2009), require realistic models with spatial representation Ridgway et al, 2006;Morris and Jensen, 2008). The processes rely on intricately controlled reaction and diffusion of molecules in and between cytoplasm (or nucleoplasm) and membrane compartments to perform their functions.…”

The Realistic Modeling of Biological Systems: A Workshop Synopsis

“…In terms of space, the volumes of components that are relevant to life can range from less than 1 nm ) in the case of an oxygen molecule, to 1,000 nm 3 in the case of a ribosome, to 10 9 nm 3 for a simple cell. While off ering high-fi delity, agent-based models can be intensely computational and one has to question the feasibility of attempting to traverse such a broad range of scale with a single computational tool [29] .…”