Contact / obtain code and data
Royal School of Mines Room 4.37
Department of Bioengineering
Imperial College London, South Kensington Campus
We're happy to share all of our code and data with anyone who's interested; please email Tom for information.
- If you're interested in the oxDNA model, please head to this wiki. You'll find the model implemented with simulation code and plenty of documentation.
- For the adventurous, the code for our domain-level model of origami folding can be found here.
Code and data for specific publications:
- Code to reproduce the figures in "Optimizing enzymatic catalysts for rapid turnover of substrates with low enzyme sequestration" can be found here: https://doi.org/10.5281/zenodo.2656526.
- Code for the simulations in Coarse-grained modelling of strong DNA bending II: Cyclization can be downloaded from https://doi.org/10.5281/zenodo.1753767
- Code for data generation and analysis in Biochemical Szilard engines for memory-limited inference can be downloaded from https://zenodo.org/record/2536384
- Code for the data and analysis of "Designing the Optimal Bit: Balancing Energetic Cost, Speed and Reliability" can be downloaded from here.
- Code for the data and analysis of "High rates of fuel consumption are not required by insulating motifs to suppress retroactivity in biochemical circuits" can be downloaded from here.