Modeling Self-Assembly Processes Driven by Nonbonded Interactions in Soft Materials

Abstract

This Centennial Feature Article provides an overview of research in the general area of self-assembly modeling, with particular emphasis on the self-assembly of molecules into soft nanoscale structures where the driving force for assembly is provided by nonbonded interactions (hydrogen bonds and electrostatics). The models have been developed at many different levels of theory, going all the way from simple analytical models of packing effects to atomistic descriptions using molecular dynamics methods. In between these limits are mean-field and coarse-grained models, including models for DNA, peptides, and lipids that can be used to describe the assembly of hybrid (amphiphilic) materials. Several recent applications to specific systems are discussed, including the description of peptide amphiphile assembly to make cylindrical micelles, the assembly and melting of DNA hairpins, the use of DNA tethers to assemble nanoparticles into aggregates and crystalline structures, and the use of coarse-grained lipid models to make lamellar and high-curvature phases. These examples demonstrate the difficulties associated with brute force atomistic methods, and they also show the opportunities (but uncertainties and ambiguities) associated with simpler models such as coarse-grained models. The examples also demonstrate the usefulness of successful modeling methods in the design of new materials, including an understanding of the relationship between structure and function.

Exploring the sequence space for (tri-)peptide self-assembly to design and discover new hydrogels

“…A number of researchers have recently studied molecular selfassembly in a supramolecular materials context using computational approaches 27,28 . In previous work, we have shown that the propensity of dipeptides (two amino acids) to aggregate can be predicted using coarse-grain (CG) molecular dynamics (MD) 29 .…”

Water ordering controls the dynamic equilibrium of micelle–fibre formation in self-assembly of peptide amphiphiles

“…There have been a plethora of experimental as well as simulation studies based on atomistic, coarse-grained (CG), simple bead and packing models to study the structure and self-assembly of peptides1011 and PA fibres157121314151617. In general, these studies were focused on understanding and exploiting the role of molecular interactions and secondary structure in PA self-assembly process.…”

What Controls the Hybridization Thermodynamics of Spherical Nucleic Acids?

“…To probe this question, we developed a coarse-grained (CG) polyelectrolyte model of the SNA that provides the relationship between the radius of gyration ( R G ) of unhybridized anchored strands as a function of n (see Supporting Information for details). 14 Briefly, in this bead–spring CG model, we have explicitly included NaCl salt ions and a charged DNA backbone. The inclusion of ions has two main effects on the R G of strands—the presence of an ion profile of the SNA (Figure S7) as a function of n , and the exchange of ions between the bulk and SNA during hybridization—each of which has important effects on the Δ G of hybridization.…”