Model Description:

This app simulates coarse-grained ligand-receptor binding of ligand-decorated virus particles interacting with a cell wall. The viruses are modeled after P22 virus-like particles (VLPs) of diameter 60 nanometers, and ligands represent smaller nanoparticles of 6 nanometer diameter. Each virus is fully decorated with 60 ligands. Receptor are fixed on a lattice of tunable size.

Input parameters:

Lennard jones well depth (KbT) -- this parameter controls the ligand-receptor binding affinity and can be adjusted from 1 - 10 in increments of 0.1

[Ligand - Virus] concentration (nM) -- this parameter controls the concentration of the ligand-decorated virus and can be adjusted from 0.3 - 9 in increments of 0.1

Number of [Ligand - Virus] -- this parameter controls the number of ligand-decorated viruses in the simulation. This can be adjusted from 1 - 5000 in increments of 1. 

Receptor spacing (nm) -- this parameter controls the x & y spacing of the receptors. It can be tuned from 10 - 200 nm in 10 nm increments.

Simulation time (milliseconds) -- This controls the simulation run-time. It can be adjusted from 1 - 5000 in increments of 1.

Output:

There are several tabs on the right-panel. These contain simulation outputs.

Bound_receptors -- this will display the number of bound receptors out of the total available over the simulation run-time. It will display at the conclusion of the run.

Simulation Snapshot -- this displays real-time snapshots of the simulation. Wall-particles are shown in blue, ligands in green, and viruses in red. For visual clarity particles sizes are not to scale. The simulation snapshot data will not display when running in cluster mode.

Downloads -- all of the output files (bound receptor, movie file, energies, lammps log file) will be available to download on this tab at the conclusion of the simulation run. 

Representative Results -- this tab contains representative results for the default parameters for comparison purposes

Under the hood:

This  V.1 basic model uses hard-core lennard jones for interatomic forces and harmonic stretching for ligand-virus bonds. It is temperature controlled with Nose Hoover thermostat.

Simulations are performed using LAMMPS; pre- and postprocessing are done using C++ codes. The source code can be found on github.

Researchers should cite this work as follows:

• Nilsson, Lauren, JCS Kadupitiya, Vikram Jadhao (2020), "Polyvalent Nanoparticle Binding Simulator," https://nanohub.org/resources/nanobind. (DOI: 10.21981/FK34-3S64).

  BibTex | EndNote

1. Cell membrane
2. cell-receptor
3. Jupyter notebooks
4. LAMMPS
5. ligands
6. nano/bio
7. NanoBio Node at Indiana
8. nanoparticles
9. Site Binding
10. viruses