Software

The software that I develop and use for my research is (when possible) shared in public github repositories; these will be summarised on this page. Software that is not yet publicly shared (but of which the output is used in my publications) is usually available on request.

AggresomeIPBM

AggresomeIPBM simulates the collective dynamics of protein using a kinetic Monte Carlo algorithm. In X. Jin et al., Science Adv. 7, 43 (2021) this software was used to simulate the LLPS of proteins, as well as the fluorescence recovery after photobleaching (FRAP), in living bacteria.

Bombyx

Bombyx uses a brute-force algorithm to fit the sticky-reptation model to the measured linear-viscoelastic response of silk feedstock, produced by the Bombyx mori silkworm. The code is written in C, and its output is peer reviewed in the scientific publication Schaefer et., Macromolecules 2020. I aim to improve the algorithm further, and implement it into RepTate (see below).

MorusMD

MorusMD simulates the coarse-grained molecular dynamics of sticky polymers in flow in 1D. The simulation output is peer reviewed in the scientific publication Schaefer & McLeish, Phys. Rev. Lett (2021).

RepTate (contribution)

RepTate is a software package that enables to analyse experimental (typically rheological) data using state-of-the-art polymer-physics models. The package was developed by the polymer-physics community of the United Kingdom. While my contribution of implementing the sticky reptation model is modest, I find new future contributions very likely.

ZiltoidLIB

ZiltoidLIB is my personal, but publicly shared, C/C++ library.