CMInject: Python framework for the numerical simulation of nanoparticle injection pipelines

Abstract

CMInject simulates nanoparticle injection experiments of particles with diameters in the micrometer to nanometer-regime, e.g., for single-particle-imaging experiments. Particle-particle interactions and particle-induced changes in the surrounding fields are disregarded, due to low nanoparticle concentration in these experiments. CMInject's focus lies on the correct modeling of different forces on such particles, such as fluid-dynamics or light-induced interactions, to allow for simulations that further the scientific development of nanoparticle injection pipelines. To provide a usable basis for this framework and allow for a variety of experiments to be simulated, we implemented first specific force models: fluid drag forces, Brownian motion, and photophoretic forces. For verification, we benchmarked a drag-force-based simulation against a nanoparticle focusing experiment. We envision its use and further development by experimentalists, theorists, and software developers. Program summaryProgram Title: CMInjectCPC Library link to program files:https://doi.org/10.17632/rbpgn4fk3z.1Developer's repository link:https://github.com/cfel-cmi/cminjectCode Ocean capsule:https://codeocean.com/capsule/5146104Licensing provisions: GPLv3Programming language: Python 3Supplementary material: Code to reproduce and analyze simulation results, example input and output data, video files of trajectory moviesNature of problem: Well-defined, reproducible, and interchangeable simulation setups of experimental injection pipelines for biological and artificial nanoparticles, in particular such pipelines that aim to advance the field of single-particle imaging.Solution method: The definition and implementation of an extensible Python 3 framework to model and execute such simulation setups based on object-oriented software design, making use of parallelization facilities and modern numerical integration routines.Additional comments including restrictions and unusual features: Supplementary executable scripts for quantitative and visual analyses of result data are also part of the framework.