Multiscale simulations of self-assembly and chemical kinetic phenomena are necessary to reach the right space and timescales, inaccessible to molecular dynamics. Following experience with many coarse-grained simulation tools, including lattice and off-lattice models, from Lattice-Boltzmann to Ginzburg-Landau, in ECCell we shall initially concentrate on one core method, combining it with recent improvements in the efficiency of stochastic chemical kinetics beyond the Gillespie algorithm. As the central physical simulation method, we will employ dissipative particle dynamics (DPD), a coarse-grained particle based method that conserves momentum and is therefore especially suited for investigations of the dynamics of extended objects composed of large number of individual entities. DPD combines three types of forces: conservative interactions, determining the macroscopic dynamics of extend objects, and dissipative and random forces that integrate the effects of molecular motion on faster timescales in a thermodynamically consistent way. The BioMIP group has extended classical DPD by including chemical reactions and by enabling an efficient self-organized treatment of supramolecular structures via macroscopically parameterizable multipolar potentials . The motivation behind this extension is the idea that a DPD-particle’s dipole moment defines a local direction and can be understood as a surface or line element that can be used to build up extended curved lower-dimensional objects such as membranes and networks embedded in space. This extension is compatible with other recent extensions improving the efficiency of DPD. BioMIP has already connected this simulation with detailed microfluidic component geometry descriptions, enabling the development of a modular component simulation tool as required in this project.
In recent years, various methods based on dissipative particle dynamics have been applied to the study of block copolymer self-organization including transitions between micelles, laminar membranes, vesicles and gels. Most of these implement membranes as being composed of polymer chains constructed from conventional DPD-particles. In order to get chains that exhibit some stiffness, Shilcock and Lipowski introduced a bond-angle potential in their chains. The DPD technique has already been applied to phase transitions in block copolymers . We shall extend further the DPD framework to be useful for ionic block copolymer transitions (linking with polyelectrolyte theory), and link our development both with efficient parallel packages such as LAMMPs (which we have already extended to chemical DPD), and with modular component MEMS simulation tools (including COMSOL).
