Biomolecule-directed assembly of nanoscale building blocks studied via lattice Monte Carlo simulation

Abstract

We perform lattice Monte Carlo simulations to study the self-assembly of functionalized inorganic nanoscale building blocks using recognitive biomolecule linkers. We develop a minimal coarse-grained lattice model for the nanoscale building block (NBB) and the recognitive linkers. Using this model, we explore the influence of the size ratio of linker length to NBB diameter on the assembly process and the structural properties of the resulting aggregates, including the spatial distribution of NBBs and aggregate topology. We find the constant-kernel Smoluchowski theory of diffusion-limited cluster-cluster aggregation describes the aggregation kinetics for certain size ratios.

Fabrication, Assembly, and Application of Patchy Particles

“…Many other models have been developed to describe patchy particle interactions and the main approaches are reviewed in the following section. There are four different categories of models to distinguish based on how the patchy interactions are incorporated in the simulations: i) patchy particle models, involving a pair potential function that depends on the distance and orientation of particles, [108][109][110][111][112][113][114][115][116][117] ii) particle models with distinguishable ''atoms'' belonging to the patch and the core particle, [36,41,42,[118][119][120][121][122] iii) models for interactions between proteins, [123][124][125][126][127][128][129][130] and, iv) a density functional theory (DFT) approach incorporating anisotropic interactions between particles. [38,40] Note that the various theoretical studies involving patchy interactions reviewed in the following are categorized based on the approach and the model involved to address the patchy interactions between particles rather than the type of method used in the simulations.…”

“…Particles with linear patches (Figure 1h and i) form 5-or 6-membered ring structures depending on the spacing between the patches, whereas double rings (Figure 1j-l) yield icosahedra, square pyramids, and tetrahedra. In a follow-up work, Chen, et al [118] used Monte-Carlo simulations to investigate the biomolecule-directed self-assembly of nanoscale building blocks. Glotzer's group also showed i) that a diamond-like structure of interest to photonics can be formed by a system of hard spheres with sticky patches in tetrahedral positions, [42] ii) that single tethers can be used to encode simple design rules into nanospheres for the subsequent assembly of unique structures, [36] and, more recently, iii) the formation of four unprecedented and highly-ordered structures from amphiphilically ditethered nanospheres.…”

Numerical study of DNA-functionalized microparticles and nanoparticles: Explicit pair potentials and their implications for phase behavior

“…b) Electronic mail: df246@cam.ac.uk. understanding of the interactions and the resulting phase behavior 14,25,27,28,[31][32][33][34][35][36][37][38][39][40] is still largely lacking. We therefore present here a numerical simulation method that allows us to generate the free energy profiles for a common class of systems, namely solid surfaces functionalized with relatively short and stiff DNA constructs, as used in for instance Refs.…”

Simulation Studies of the Self-Assembly of Cone-Shaped Particles

“…In addition, multiple independent runs at certain cone angles are performed with different initial configurations and along different cooling paths to investigate the path dependence of the structures. The cluster size distribution information is collected by using a previously developed analysis code [16].…”