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    14 repositories

    • ActinRingsMC.jl

      Public
      A Julia simulation package with functions for running adaptive umbrella sampling Monte Carlo simulations of crosslinked actin rings.
      Julia
      •
      MIT License
      •0•0•0•0•Updated Jul 18, 2026Jul 18, 2026

    • 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 …
      Jupyter Notebook
      •0•0•0•0•Updated Jul 3, 2024Jul 3, 2024

    • Tradeoffs-cellular-prediction

      Public
      Reproduce the figures of 'Trade-offs between cost and information in cellular prediction'
      Mathematica
      •0•0•0•0•Updated Oct 13, 2023Oct 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.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Aug 24, 2023Aug 24, 2023

    • actinfrictionpy

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 24, 2023Mar 24, 2023

    • actinrings

      Public
      Python package that implements the analytical model from "Constriction of actin rings by passive crosslinker".
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 24, 2023Mar 24, 2023

    • PathWeightSampling-Langevin

      Public
      Path Weight Sampling implementation for Langevin systems in presence of feedback
      Python
      •0•0•0•0•Updated Mar 16, 2023Mar 16, 2023

    • filament-sliding

      Public
      A program to simulate the sliding of crosslinked filaments, based on the code of Harmen Wierenga.
      C++
      •
      MIT License
      •0•0•0•0•Updated Apr 21, 2022Apr 21, 2022

    • PathWeightSampling.jl

      Public
      Julia implementation of Path Weight Sampling (PWS) to compute information transmission rates
      Julia
      •
      MIT License
      •1•0•0•0•Updated Apr 12, 2022Apr 12, 2022

    • linear_cell_complex_to_incidence_graph

      Public
      Some utilities for checking adjacency and incidence and computing the incidence graph.
      C++
      •
      MIT License
      •1•0•0•0•Updated Apr 8, 2022Apr 8, 2022

    • elastic-rings

      Public
      A program for solving geometrically non-linear elastic rings with the deal.II finite element method (FEM) library.
      C++
      •
      GNU Lesser General Public License v2.1
      •0•0•0•0•Updated Apr 7, 2022Apr 7, 2022

    • simple_spherical_shell_partitioner

      Public
      Constructs the convex hull of points on the sphere, then uses duality and extrusion to create cells partitioning a spherical shell.
      C++
      •
      MIT License
      •1•0•0•0•Updated Apr 6, 2022Apr 6, 2022

    • Cellcycle

      Public
      This code implements different mechanistic models of the regulation of replication initiation in E. coli.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Jan 28, 2022Jan 28, 2022

    • egfrd

      Public
      A modern C++ implementation of eGFRD.
      C++
      •
      GNU General Public License v2.0
      •8•0•0•0•Updated Dec 5, 2020Dec 5, 2020
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