CS6404 Project List

Yang Cao


Note: This list will provide some examples for possible projects. Students can choose their own presentation topic and projects. However, if you do not have any idea about how a project should be, the following list may serve as a reference list.


    Comparison between StochSim and Gillespie Algorithm. This project will have some programing work, including evaluation of code efficiency and accuracy. You need to find some interesting model as a test problem.

    Paper References:

    1. GILLESPIE DT, EXACT STOCHASTIC SIMULATION OF COUPLED CHEMICAL-REACTIONS, JOURNAL OF PHYSICAL CHEMISTRY 81 (25): 2340-2361 1977.

    2. GILLESPIE DT, GENERAL METHOD FOR NUMERICALLY SIMULATING STOCHASTIC TIME EVOLUTION OF COUPLED CHEMICAL-REACTIONS 
      JOURNAL OF COMPUTATIONAL PHYSICS 22 (4): 403-434 1976.

    3. Morton-Firth CJ, Bray D Predicting temporal fluctuations in an intracellular signaling pathway JOURNAL OF THEORETICAL BIOLOGY 192 (1): 117-128 MAY 7 1998



    1. Korobkova E, Emonet T, Vilar JMG, et al. From molecular noise to behavioural variability in a single bacterium NATURE 428 (6982): 574-578 APR 1 2004



    1. Pedraza JM, van Oudenaarden A Noise propagation in gene networks SCIENCE 307 (5717): 1965-1969 MAR 25 2005

    2. Rosenfeld N, Young JW, Alon U, et al. Gene regulation at the single-cell level SCIENCE 307 (5717): 1962-1965 MAR 25 2005

Chemotaxis is a fascinating mechanism for bacterium, and also maybe it is one of the best understood mechanisms in cells. There are many experimental data related to it (even movies). There are also several interesting models. In this project you can construct a Gillespie type of model for this system. Run the ODE simulation and Stochastic simulation based on your model and compare with the experimental data. Note that there are plenty of references you can get help from.

Paper References:

    1. SPUDICH JL NON-GENETIC INDIVIDUALITY - CHANCE IN SINGLE CELL, NATURE 262 : 467 1976

    2. Korobkova E, Emonet T, Vilar JMG, et al. From molecular noise to behavioural variability in a single bacterium NATURE 428 (6982): 574-578 APR 1 2004

    3. MORTONFIRTH CJ, A free-energy-based stochastic simulation of the Tar receptor complex, JOURNAL OF MOLECULAR BIOLOGY 286 : 1059 1999