Topic outline

◄THE FANO FACTOR
►Topic 13

  • GILLESPIE ALGORITHM AND ENZYME KINETICS

    Lectures n. 22 and 23 and 24, wed 16 and fri 18 of may 2018 and  monday 21st of may 2018

    Gillespie' algorithm is a stochastic simulation algorithm, based on a montecarlo procedure that

    is currently used in systems biology to numerically simulate kinetic master-equations.

    Kinetic deterministic rate equations are the model for chemical kinetics in large volumes, whereas SME are the

    probabilistic models for chemical reactivity in confined volumes where fluctuations cannot be neglected.


    The Michaelis-Menten approximation for the rate equations of enzymic catalysis has been the

    main theoretical approach in vitro. In vivo stochastic effects play a role and the Gillespie algorithm is the natural extension

    of the classic MM approach.

    Rate equations for the rapid equilibrium model (PBoC 15.2.6)

    Michaelis-Menten Kinetics of enzymatic catalysis (Proc 15.2.7)

    Reverse Michaelis-Menten (Fabrini2011, Tang2015)

    List of computational tools for chemical kinetic (Deterministic and Stochastic Simulations)

    COPASI (copasi.org)

    StochPy (Marleeveld2013)

    You can download the programming tools here below from Sapienza with your INFOSTUD ID

    (https://campus3.uniroma1.it/campus/indexlogin.php)

    in particular: Mathematica & Matlab.




◄THE FANO FACTOR
►Topic 13