Hierarchical self-assembly is one of the most promising tools in nanotechnology. In biological systems, such processes have been already perfected during evolution, and involve successive formation of building blocks from smaller units, which in turn self-assemble into larger structures in a hierarchical fashion (e.g. virus capsid proteins, keratin filaments, amyloid fibrils etc.). Presently, computational modelling of assembly processes on the nanoscale is possible only with coarse-grained methods, chosen appropriately for the size of the system and the particular problem. However, hierarchical self-assembly often happens across multiple scales, and each layer of the process has to be modelled differently: molecular mechanics force fields for protein folding, united atom force fields for oligomerization, shape-based coarse-grained models (e.g. bead models) for successive assembly of protein oligomers. To this date, no framework exists supporting modelling such processes across length scales.
The aim of the project is to use the experience of the PI with modelling anisotropic building blocks using the rigid body framework, and extend the method to bridge the gap between the different length scales. The method will involve a hierarchical calculation of building block parameters, obtained from extensively studying the energy landscape of their components. This approach will be scale-independent, and will allow bottom-up design of novel complex structures on the nanoscale.
During the project, we will created new methods and algorithms for determining coarse-grained parameters representing the shape of a building block modelled with atomistic potentials. Another priority was to determine the necessary conditions for selected building block shapes that determine their hierarchical self-assembling properties. We have created minimal physical models enabling hierarchical self-assembly into exotic structures such as Goldberg polyhedra, stacked rings, dodecahedral cages etc.
Summary of scientific activities between 01.10.2015 – 01.12.2016:
– development of hierarchical coarse-graining methods
– studying the aggregation of CCMV capsid proteins
– devising new design principles for hierarchical self-assembly by using macroions
A detailed version of the progress report can be downloaded from here.
Summary of scientific activities between 01.12.2016-30.09.2017:
– adaptation of the developed hierarchical coarse-graining methods for capsid proteins
– studying the dynamics of CCMV protein dimers, microsecond MD simulations
– designing addressable building blocks capable of hierarchical self-assembly
– creating a minimalistic model for hierarchical self-assembly of polyhedral shells of exotic symmetries
– coarse-grained modelling of spherical ‘Blackberry’ structures
Our computations are done on a small compute cluster by Supermicro, with three performant Nvidia Tesla K40M GPUs, and 44 CPU cores. Details of the architecture can be found here.
The project was implemented in the R&D department of Provitam Foundation. Address: 16 Muncitorilor street, Sfantu Gheorghe, Romania.
This video illustrates how kinetically trapped structures form in a system capable of forming a Kagome lattice (triblock Janus particles). This is a constant energy MD run adapted for ellipsoidal rigid bodies. Videos about large-scale rearrangements of self-assembling coarse-grained systems can be found on my Youtube channel.