Soft Matter Modelling Lab's Software
In keeping with the spirit of open science and reproducibility of results, here we provide links to the repositories containing software packages developed by the group.
NPCoronaPredict - UnitedAtom & CoronaKMC
The NPCoronaPredict package contains all the software necessary for simulating the formation of the nanoparticle corona on spherical and cylindrical multi-component NPs, primarily the UnitedAtom and CoronaKMC software tools. The source code can be downloaded from (opens in a new window)the repository and contains the following components:
- UnitedAtom
- C++ implementation of the UnitedAtom methodology for computing protein - NP adsorption energy.
- Also contains Hamaker constants and PMFs for a range of metallic, inorganic and carbonaceous materials
- CoronaKMC
- Python 3 scripts for converting UA output to rate constants and running a kinetic Monte Carlo simulation of the formation of the corona
- Additional scripts for pre- and post-processing
- NPDesigner
- Graphical interface for designing multicomponent nanoparticles for use with UnitedAtom
- UAQuickRun
- Graphical interface for running UnitedAtom and interactive visualisation of results.
PMFPredictor
(opens in a new window)This repository contains all the scripts required to generate input for the prediction of PMFs, run the trained model ensemble for the generation of PMFs, and post-process the results to produce the PMFs and Hamaker constants required for UnitedAtom, available either as command line scripts or via the PMFPredictor-toolkit graphical interface.. We also provide the required Python script to train new versions of the model on a user's own dataset.
Datasets
The list below summarises datasets produced by the group and publicly released
- (opens in a new window)PMFPredictor Inputs and Outputs, trained models, code release - Zenodo dataset, November 2022