Applications of LAMMPS in Biomedical Engineering: from Coronavirus and Red Blood Cells to Inertial Microfluidics

We applied LAMMPS to study several important biophysical problems at different scales. First, by using a one-particle-thick lipid bilayer model we developed for LAMMPS, we simulated the endocytosis of Covid-19 virus at the coarse-grained molecular dynamics scale. Second, we developed a multi scale model of red blood cells (RBCs) based on LAMMPS and simulated the splenic filtration of RBCs at the cellular level. Third, we studied the blood rheology from healthy and sickle cell patients using dissipative particle dynamics (DPD), and simulated how the viscosity changes with varying percentage of rigid sickle cells and compared with experiments at the blood/tissue level. Finally,  we applied smoothed particle hydrodynamics (SPH) in LAMMPS to simulate the inertial microfluidic separation of shaped particles, such as cells and bacteria, at the continuum level. These applications demonstrated the strong capability of LAMMPS as a versatile code for simulating science and engineering problems at various levels.