Reversible formation of von-Willebrand-factor-platelet aggregates in microvascular blood flow

This repository contains the code and input files used in simulations for the manuscript “Reversible formation of von-Willebrand-factor–platelet aggregates in microvascular blood flow”. The code is based on LAMMPS (https://www.lammps.org) with a number of modified files to extend its functionality to simulations of blood flow at the cellular scale. The modifications include: (i) elastic membrane models for red blood cells and platelets, (ii) force-activated unfolding and adhesion dynamics of von Willebrand factor (VWF), (iii) smoothed dissipative particle dynamics (SDPD) method for modeling hydrodynamic flow, and (iv) reversible bond formation and dissociation between platelets and VWF in flow. 

Instructions for the code:
1) Download 19Nov2024 version of the LAMMPS code from the official website https://www.lammps.org. Other versions may not work with our modified files.
2) Copy all files from the archive file modified_LAMMPS_files_19Nov2024.tar to the source directory src/ of LAMMPS.
3) Compile LAMMPS as appropriate for your machine. There is enough information on the LAMMPS website.   

All input files are included in the archive file sampleFiles.tar. The core directory contains input files that include initial configuration (data.cell) of the simulation and input scripts (in.start and plane_init.dat) for initial relaxation. All folders correspond to different cases with various bond types and include input scripts (in.run and plane.dat).