HemoCell#
HemoCell (HighpErformance MicrOscopic CELlular Library) is a parallel computing framework for the simulation of dense deformable capsule suspensions, with special emphasis on blood flows and blood-related vesicles (cells). The library implements validated mechanical models for Red Blood Cells (RBCs) and is capable of reproducing emergent transport characteristics of such complex cellular systems [1]. HemoCell handles large simulation domains and high shear-rate flows, providing a virtual environment to evaluate a wide palette of microfluidic scenarios [2, 3, 4].
For the simulation of dense flows, HemoCell employs the Immersed Boundary Method (IBM) to couple immersed vesicles — e.g. RBCs, platelets (PLTs), leukocytes, or custom cell types — to the fluid (e.g. plasma). The cells are tracked with a Lagrangian discrete-element approach, while the flow field is solved with the lattice Boltzmann method (LBM), built on the Palabos library. HemoCell manages all required data structures — materials and cell models, their interactions within the flow field, load balancing, and inter-processor communication — so that the parallelism is largely hidden from the user. See Concepts for the ideas behind the framework.
High-level structure of HemoCell.#
Where to start#
Install and build HemoCell, then run and post-process your first simulation.
Worked example cases, from a single shearing cell to full pipe flow with a pre-inlet.
The IBM–LBM coupling, units and scaling, the cell model, and how simulations are parallelised.
Task-oriented recipes: custom cells, pure-flow runs, repulsion, visualisation, and the helper tools.
Configuration tags, the HemoCell C++ API, output fields, mechanical models, and the full Doxygen API.
Internals, coding conventions, extending HemoCell, and known limitations.
FAQ, common mistakes, downloads, how to contribute, and how to cite HemoCell.
What you can simulate#
Single-cell mechanics. Quick simulations (seconds to minutes, often on a single processor) used to investigate or validate mechanical models for immersed cells, such as shearing, stretching, or “parachuting” of a single cell, or the interaction between colliding cells.
Bulk flows. Large domains with many immersed particles, typically derived from straight-channel flow. These range from quick runs on a workstation to long simulations on HPC clusters with thousands of cores. See Pipe flow and Pipe flow with periodic inflow.
Citing HemoCell
When using HemoCell, please cite the corresponding HemoCell paper(s). See Citing HemoCell for details.