PUCHIK (Python Utility for Characterizing Heterogeneous Interfaces and Kinetics) is a new open-source Python package for analyzing molecular dynamics simulations of nanoparticles. Accurately describing a nanoparticle's interface is crucial for understanding its internal structure, interfacial properties, and ultimately, its functionality. While current computational methods provide reasonable descriptions for spherical and quasi-spherical nanoparticles, there remains a need for effective models for aspherical structures such as capsules and rod-like systems. PUCHIK addresses this gap with an algorithm that works for both spherelike and aspherical particles.
With an accurate description of the location of the interface of the nanoparticle, this algorithm then allows for various other important quantities (e.g., densities of different atom/molecule types relative to the interface, volume of the nanoparticle, amount of solubilized molecules within the nanoparticle) to be calculated. In developing the software, the authors focused on providing good performance for computationally demanding projects, while ensuring that the methodological approach can be adapted as a protocol for other code implementations. Developed by Hrachya Ishkhanyan, Alejandro Santana-Bonilla, and Christian D. Lorenz, it was published in the Journal of Chemical Information and Modeling in February 2025.