A 3D numerical simulation framework for electroporation in lipid membranes using a diffuse-interface (phase-field) approach coupled with electrostatics and thermal fluctuations.
Based on the method described in:
S. Seifi and D. Salac, "A Diffuse-Interface Method for Pore Dynamics in Lipid Membranes under Electric Fields," arXiv:1611.03902
MemPore3D models how nanoscale pores form and evolve in lipid membranes subjected to external electric fields. The code couples three physical components:
- Phase-field solver -- Stochastic Allen-Cahn equation for pore structure evolution (spectral/FFT-based)
- 3D Poisson solver -- Electrolyte potential via spectral FFT or PETSc/GAMG (MPI-parallel)
- 2D transmembrane potential solver -- Implicit scheme coupling bulk ionic current with membrane properties
Thermal fluctuations enable spontaneous pore nucleation without artificial initial conditions.
conda env create -f environment.yml
conda activate mempore3dKey dependencies: NumPy, SciPy, Numba, PETSc (petsc4py), mpi4py, Matplotlib.
Run a simulation case:
python runs/electroporations/case_1.pyOr use one of the test entry points:
python run_electroporation_test.py # Full coupled simulation
python run_single_pore_test.py # Phase-field only
python run_electrostatic_test.py # Electrostatics onlyResults are saved as .npz snapshots in the corresponding case_*/ directories.
mempore3d/
core.py # Main simulation driver
parameters.py # Configuration dataclasses
plotting.py # Visualization utilities
solvers/
poisson_solver.py # 3D electrostatic solvers (Spectral & PETSc)
phase_field_solver.py # Stochastic Allen-Cahn solver
leaky_dielectric_solver.py # 2D Vm solver
runs/electroporations/ # Simulation case configurations (case_1 -- case_12)
plotting/ # Post-processing scripts and notebooks
utils/ # Data extraction utilities
Research code. Please cite the paper above if you use this work.