CellPyLib: A Python Library for working with Cellular Automata

Antunes, L.

doi:10.21105/joss.03608

Cited by 5 publications

(2 citation statements)

References 8 publications

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“…The membrane protein automata simulations were implemented as a custom written Python program, modified from the cellpylib package 69 . The simulations were analyzed using custom written MATLAB scripts, akin the experimental data analysis.…”

Section: Methodsmentioning

confidence: 99%

Membrane-mediated protein interactions drive membrane protein organization

et al. 2022

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The plasma membrane’s main constituents, i.e., phospholipids and membrane proteins, are known to be organized in lipid-protein functional domains and supercomplexes. No active membrane-intrinsic process is known to establish membrane organization. Thus, the interplay of thermal fluctuations and the biophysical determinants of membrane-mediated protein interactions must be considered to understand membrane protein organization. Here, we used high-speed atomic force microscopy and kinetic and membrane elastic theory to investigate the behavior of a model membrane protein in oligomerization and assembly in controlled lipid environments. We find that membrane hydrophobic mismatch modulates oligomerization and assembly energetics, and 2D organization. Our experimental and theoretical frameworks reveal how membrane organization can emerge from Brownian diffusion and a minimal set of physical properties of the membrane constituents.

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Section: Methodsmentioning

confidence: 99%

Membrane-mediated protein interactions drive membrane protein organization

et al. 2022

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“…However, these implementations typically focus on tuning an existing simulation form within a relatively narrow range of focus. For instance, CellPyLib (L. Antunes, 2023), netomaton (L. M. Antunes, 2019), and cellular_automaton (Feistenauer, 2021) are all libraries for simulating cellular automata, but they each are limited in the simulation geometry, the data type for the simulation state, the geometry of the neighborhood, or the strategy for applying the update rule. Similarly, lattice_mc (Morgan, 2017) is an excellent Monte Carlo program that focuses solely on diffusion in ionic solids.…”

Section: Statement Of Needmentioning

confidence: 99%

pylattica: a package for prototyping lattice models in chemistry and materials science

Gallant,

Persson

2024

JOSS

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pylattica provides a simple and flexible framework for prototyping lattice-based simulations such as atomistic Monte Carlo simulations or cellular automata. It is differentiated from other lattice simulation packages by i) its agnosticism toward the form of the update rule, simulation structure, neighborhood structure, and simulation state and ii) its interoperability with the pymatgen package which allows modeling of arbitrary crystalline systems (i.e. not only two or three dimensional square grids), and makes it particularly well suited to applications in materials science and chemistry.

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