Developing and maintaining open-source software is key to scientific discovery and collaboration, both computationally and experimentally. A major aspect of my work involves creating software that is used as a versatile computational tool to model a wide range of biological systems, or as digital twins of actual experiments in biology and material science. All of my code is hosted on GitHub. Below, I have linked some of my repositories. Please visit my GitHub profile (yue-sun) for more details.

A fully integrated lattice Boltzmann method for fluid–structure interaction
In this work, we develop a C++ implementation of the lattice Boltzmann reference map technique (LBRMT) for fully Eulerian fluid–structure interaction simulations. The repository includes the source code and several examples demonstrating the use of LBRMT to model multiple finite-strain deformable solids as they rotate, settle, and mix in fluids. To build locally, please refer to the README.md for compilation instructions. To customize simulations, please modify /sims/*.cfg files.

Three-dimensional simulation of sample vitrification in cryo-plunging
In this work, we develop a computational tool to simulate the plunging freezing step in cryo-EM sample preparation. The repository will be updated shortly, and will include the source code and several examples of benchmarking thermocouple experiments and actual plunging experiments at different plunging speeds. To build locally, please refer to the README.md for compilation instructions (need to have AMReX and AMReX-Hydro).