Lab Stuff

  • General Instructions (todo) link
  • How to use the computing cluster link + script
    See also School wiki (for first time users!)
  • LAMMPS intro:
    Tutorial0-nve LJ fluids NVE
    Tutorial0-nvt LJ fluids NVT
    Tutorial1 Polymers
    Tutorial2 Knots
    Tutorial3 Topo2+Knots
    Tutorial3a Topo2+Links
    Tutorial4 Dynamic Topo2 w external c++ code
    Example Switching protein types with external c++ code
    Tutorial5 Reconnections w custom lammps module
    Tutorial6 Polymer Recolouring w custom Lammps module
    Tutorial7 Ligating polymers of different lengths
    Slides from EUTOPIA TRAINING
    Recording Part I
    Recording Part II
  • How to keep a lab book (todo) link
  • Intro to Knot Theory (work in progress) link
  • Intro to Polymer Physics (work in progress) link
  • Tips for presentations and reports (todo) link
  • Tips for proposals (todo) link
  • Stocks and Materials (todo) link
  • Codes:
  • Living polymers: Code to mimic relaxation of (non-equilibrium) living polymers in 1D (from Michieletto, Entropy 2020)

    Supercoiled plasmids: Code to model DNA plasmids as twistable chains in LAMMPS. Needs rigid and molecular packages installed (from Smrek et al, Science Advances 2021)

    SuperStructure: Parameter-free algorithm to quantify clustered structures in SMLM (STORM) datasets (from Marenda et al, Journal of Cell Biology, 2021)

    Topoisomerase on LAMMPS: A LAMMPS fix to simulate a moving Topoisomerase (from Michieletto et al, NAR 2021)

    AFM-steered MD simulations of kDNA: Bash and LAMMPS scripts to convert AFM images into a tool to guide MD simulations of corssable DNA rings. (From He et al Phys. Rev. X 2023)

    GitLab: For a complete collection of our codes see this GitLab repo