These pages contains a summary of the work done in the PACE consortium to join experiments and simulations of the self-assembly of vesicles as units into larger structures. Following the reviewers proposition that ”the partners should emphasize the challenges of programming real protocells, so that they display preferential attachment spots on their surface and functional reactions”, different simulators were built with which simulated data and experiments can be compared. Within PACE, five different approaches towards the simulation of higher-order self-assembly have been pursued:
Dissipative particle dynamics (DPD)
Dissipative particle dynamics is a well-established method in soft matter simulations, especially with respect to amphiphilic systems. In its conventional form, its suitability for PACE-related investigations is limited; based on extension developed in BioMIP, major enhancements were achieved and a scale-up enabling fundamental vesicular processes, such as self-assembly or curvature induced fission, were investigated. DPD and its extensions are particle-based, momentum conserving methods including fluctuation-dissipation processes. In order to account for mesoscopic self-assembly, BioMIP kept the point-like nature of the particles but equipped them with additional structure, namely multipole moments.
Newtonian Spring Models
The AILab in Zurich avoids complications raised by extended and non-isotropic particles by utilizing beads connected via (possibly) multiple springs. In other words, non-isotropic building blocks are further resolved into pre-composed assemblies of springs and beads. The advantage of this approach is, besides numerical simplicity, that one can start with generically harmonic interactions (thereby establishing to a large number of theoretical results), and include anharmonic interactions as perturbations.
Simulation of self-assembly developed in connection to the experimental work on vesicles
During the last year a new software platform related to the experimental work in WP8 (specific self-assembly of vesicles) has been developed. This simulator is based on a modular robotics simulator, which has been extended for vesicular simulations.
Rigid Body Mechanics
Here, the particles are explicitly assumed to have spatial extensions. This allows very efficiently establishing contact between known structure data of building blocks and simulation entities. Spatial extension of building blocks, besides clear advantages, requires a sophisticated handling of distances, the intersection problem and, directly related to this latter problem, the time-steps one can use.
--> Rigid body mechanics simulation
Potts-based simulation of growing cell aggregates
In this simulation model, we have used a cellular automaton modelling technique that allows for the study of growth and division of cells into larger aggregates.
The Chalmers group has set up an according simulation framework. These four approaches reflect different possibilities to account for the fact that the building blocks involved in the self-assembly process are not just to be regarded as small spheres interacting isotropically. The approaches all have specific pros and cons. Pursuing different approaches may look costly on a first glance, but is justified by relevant benefits:
• Specific settings are tackled with the most appropriate means.
• Employing different approaches allows to differ readily between true phenomena
and method-related artifacts.
• Comparison of results uncovers mistakes.
The software for the last two simulation models with instructions, example files, and software model presentation is available in the Virtual lab.