A predictive description of the synthetic processes leading to complex macromolecules requires consideration of the spatial models. Hierarchical, structural and dynamic complexities of such systems require new methodological developments. The presented work provides effective tools for the modelling of the complex synthetic processes in the 3D space under controlled conditions. We propose constructing a parallel computing system which realizes the 3D architecture and the cooperative dynamics based on the dynamic lattice liquid (DLL) model. This can create new standards in the spatial resolution of the models allowing simulations of the systems comparable in sizes and complexity with the biological cells in the future.