Cloning algorithm

This repository contains:

• c++ code used in reference [1] for the evaluation of the scaled cumulant generating functions (SCGFs) in:

  • Non-Markovian TASEP (Totally Asymmetric Simple Exclusion Process) \nonMarkovTASEP,
  • Semi-Markov model for ion-channel gating with direction-time independence (DTI) \SemiMarkovDTI,
  • Semi-Markov model for ion-channel gating without DTI \SemiMarkovNonDTI,
  • Discrete-time random walk on a ring (with heap sort) \RingDiscreteMarkov.

• cloning.py, a Python implementation of the cloning algorithm for non-Markovian processes with heap sort, based on the examples at https://www.lpsm.paris//pageperso/lecomte/warwick-summer-school_2013.html. A basic Jupyter notebook demonstration (with Process-based parallelism) is here.

If you find any use of these codes, please do not forget to cite the paper [1].

[1] Cavallaro, M., & Harris, R. J., A framework for the direct evaluation of large deviations in non-Markovian processes, Journal of Physics A: Mathematical and Theoretical, 49, 47LT02 (2016) 171–176 (ArXiv:1603.05634).