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@Biochemical-Networks

AMOLF Theory Groups

Theoretical research groups at the AMOLF research institute in the Netherlands.

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  1. egfrd egfrd Public

    Forked from gfrd/modern_egfrd

    A modern C++ implementation of eGFRD.

    C++

  2. PathWeightSampling.jl PathWeightSampling.jl Public

    Forked from manuel-rhdt/PathWeightSampling.jl

    Julia implementation of Path Weight Sampling (PWS) to compute information transmission rates

    Julia

  3. ActinRingsMC.jl ActinRingsMC.jl Public

    A Julia simulation package with functions for running adaptive umbrella sampling Monte Carlo simulations of crosslinked actin rings.

    Julia

  4. Cellcycle Cellcycle Public

    Forked from MareikeBerger/Cellcycle

    This code implements different mechanistic models of the regulation of replication initiation in E. coli.

    Jupyter Notebook

Repositories

Showing 10 of 15 repositories
  • ActinRingsMC.jl Public

    A Julia simulation package with functions for running adaptive umbrella sampling Monte Carlo simulations of crosslinked actin rings.

    Biochemical-Networks/ActinRingsMC.jl’s past year of commit activity
    Julia 0 MIT 0 0 0 Updated Feb 4, 2025
  • Chemotactic-Receptor-Array-MWC-Ising Public

    Jupyter notebooks for modelling E. coli's chemotactic receptors, including variations of both the MWC and the Ising model. Important: the final simulations are in the notebook chemotaxis.ipynb

    Biochemical-Networks/Chemotactic-Receptor-Array-MWC-Ising’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Jul 3, 2024
  • Tradeoffs-cellular-prediction Public

    Reproduce the figures of 'Trade-offs between cost and information in cellular prediction'

    Biochemical-Networks/Tradeoffs-cellular-prediction’s past year of commit activity
    Mathematica 0 0 0 0 Updated Oct 13, 2023
  • Synchronous-Replication-Initiation Public

    This code simulates the bacterial cell cycle and is used to study the degree of synchrony of replication initiation in the bacterium E. coli.

    Biochemical-Networks/Synchronous-Replication-Initiation’s past year of commit activity
    Jupyter Notebook 0 CC0-1.0 0 0 0 Updated Aug 24, 2023
  • DNA_replication_muriel Public
    Biochemical-Networks/DNA_replication_muriel’s past year of commit activity
    Mathematica 0 0 0 0 Updated Jul 21, 2023
  • actinfrictionpy Public
    Biochemical-Networks/actinfrictionpy’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Mar 24, 2023
  • actinrings Public

    Python package that implements the analytical model from "Constriction of actin rings by passive crosslinker".

    Biochemical-Networks/actinrings’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Mar 24, 2023
  • PathWeightSampling-Langevin Public

    Path Weight Sampling implementation for Langevin systems in presence of feedback

    Biochemical-Networks/PathWeightSampling-Langevin’s past year of commit activity
    Python 0 0 0 0 Updated Mar 16, 2023
  • filament-sliding Public

    A program to simulate the sliding of crosslinked filaments, based on the code of Harmen Wierenga.

    Biochemical-Networks/filament-sliding’s past year of commit activity
    C++ 0 MIT 0 0 0 Updated Apr 21, 2022
  • PathWeightSampling.jl Public Forked from manuel-rhdt/PathWeightSampling.jl

    Julia implementation of Path Weight Sampling (PWS) to compute information transmission rates

    Biochemical-Networks/PathWeightSampling.jl’s past year of commit activity
    Julia 0 MIT 1 0 0 Updated Apr 12, 2022
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