Molecular dynamics simulation of reversibly self-assembling shells in solution using trapezoidal particles.

Area of Science:

• Computational physics
• Materials science
• Biophysics

Background:

• Viral capsids, like those of T=1 viruses, are polyhedral shells formed by protein subunits (capsomers).
• Understanding self-assembly processes is key to designing novel nanomaterials and synthetic viruses.

Purpose of the Study:

• To simulate and analyze the self-assembly of polyhedral shells from trapezoidal particles.
• To investigate the role of reversible bonding and intermediate structures in the assembly pathway.
• To compare the assembly process with previous studies using triangular particles.

Main Methods:

• Molecular dynamics simulations were employed.
• The simulations involved an atomistic solvent environment.
• Analysis focused on intermediate particle clusters, their structure, lifetime, and transitions.

Main Results:

• High yields of complete polyhedral shells (60 particles) were achieved under suitable conditions.
• Details on the structure and lifetime of intermediate clusters were elucidated.
• Reversible bonding was identified as critical for preventing incorrect assembly, similar to triangular particle systems.
• Maximal bonding preference was observed but became less pronounced during later stages of shell completion.

Conclusions:

• Trapezoidal particles can self-assemble into complete polyhedral shells, analogous to viral capsid formation.
• The assembly pathway involves transient intermediate clusters and is guided by reversible bonding.
• Particle shape and bond organization influence the assembly dynamics, offering insights into designing complex structures.