Build Nanostructures for MD Simulations

Hard-soft complexes are commonly seen in many nanomaterials. Polymer-grafted nanoparticles widely used in nanomedicine, for example, PEO as a biocompatible polymer has been adopted to coat on nanoparticles to avoid protein adsorption. In this tutorial, examples are shown for build of nanomaterials for MD simulations.

Initial Nanostructure System Buildup

Various approaches can be applied to generate the initial system for MD simulations. Avogadro can be used to generate polymer molecules, as illustrated in previous tutorials. The only thing left is to build the initial system of the hard component, as shown above (nanoparticle, nanopore and nanorod). Here, atomsk is employed for the demonstration, which has been extensively utilized in metal plasticity analysis like edge/skew dislocation and polycrystals, etc. The basic steps to build the hybrid system can be split into:

  1. build the soft component, i.e., polymers
  2. build the hard component
  3. assemble them together

In this tutorial, only the generation of hard component (gold nanostructures) is demonstrated, with the left being covered in the upcoming tutorials.

atomsk for Nanostructure Generation

Here, generation of gold nanoparticle, nanopore and nanorod will be demonstrated. The general procedures for this task can be summarized as:

  • generate the cubic gold lattice (fcc with lattice constant of 4.08 Å)
  • generate supercell based on the cubic lattice
  • add or remove components from the super cell to finalize the nanostructure

The concrete code for this task is:

  
    # step-1: cubic lattice
    atomsk --create fcc 4.08 Au gold.xsf

    # step-2: gold nanocube
    atomsk gold.xsf -duplicate 10 10 10 GLD.cfg

    # step-3.1: gold nanoparticles with radius 2.0 nm
    atomsk GLD.cfg -select out sphere 0.5*box 0.5*box 0.5*box 20 -rmatom select GLD_sphere.cfg

    # step-3.2: gold nanopore with pore radius 1.5 nm
    atomsk GLD.cfg -select in cylinder Z 0.5*box 0.5*box 15 -rmatom select GLD_pore.cfg

    # step-3.3: gold nanorod with rod radius 1.0 nm
    atomsk GLD.cfg -select out cylinder Z 0.5*box 0.5*box 10 -rmatom select GLD_rod.cfg

The generated nanostructures are rendered below using vmd:

What’s the next

With the generated gold nanostructures, the next step is to incorporate polymers to assemble into the hybrid nanomaterials, such as PEO-grafted gold nanoparticle and nanopores. Stay tuned!