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This app simulates the self-assembly of charged nanoparticles (NPs) into aggregates mediated by smaller, oppositely-charged linkers under different ionic physiological conditions. Users can input control parameters such as NP charge, linker concentration, and ionic strength to predict formation of NP aggregates. This information may be useful in designing NP features to produce desired effects when NPs interface with biological entities. Outputs are structural information such as pair correlation functions (often denoted as g(r)) and simulation snapshots (with only NPs shown for clarity). The NPs are modeled after P22 virus-like particles (VLPs) of diameter 56 nanometers, and linkers represent smaller nanoparticles (dendrimers) of 6 nanometer diameter. Linker charge is fixed to about 35e Simulations are performed using LAMMPS; pre- and postprocessing are done using C++ codes. Simulation results are tested and validated using SAXS and dynamic light scattering measurements of the VLP aggregates; experiments also guide the model design. After you click Run, the application pre-processes the input parameters and loads the input script in the LAMMPS engine; this may take a couple of minutes after which the output log should appear in the Output text pane. As the output shows, the images will start to populate the "Simulation Snapshot" tab; the slider can be used to navigate through the images. At the end of simulation run, g(r) will be produced in the "Pair Correlation" tab.
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