Software

  1. Budding Yeast Jamming: 2D, cell-based simulation of growing budding yeast populations. The code generates cellular packings at and above the jamming point (J-point). To do that, a new “time-bisection” algorithm was developed. The repository also contains the code to calculate the shear modulus for the generated packings. The code is open-source under the BSD-3 license, and it is implemented in Fortran 95.
    https://github.com/pgniewko/jamming-growth
    Reference: https://arxiv.org/abs/1810.01999
  2. Elastic shells simulations: 3D Finite Element simulation software for elastic and pressurized shells. The code generates disordered and compacted packings of elastic shells. It implements FE with St. Venant-Kirchhoff energy functional with or without a bending term. The energy can be minimized with MD-type optimizers, and the code is optimized to be efficient up to 1M DOFs. The code is open-source under the BSD-3 license, and it is implemented in C/C++.
    https://github.com/pgniewko/elasticshells
    Reference: P. Gniewek, “Mechanics of Confined Microbial Populations”, UC Berkeley, PhD Thesis (2018)
  3. Permeability of porous material: Permeability and hydraulic tortuosity calculation of porous material with Lattice-Boltzmann simulation. The code is suitable for low Reynolds number flows, and the calculation can be performed with periodic and non-periodic boundary conditions using BGK or MRT relaxation models. The code is open-source under the BSD-3 license, and it is implemented in C++ as a wrapper to the Palabos CFD engine.
    https://github.com/pgniewko/porous-LB
    Reference: https://arxiv.org/abs/1807.00249