Literature Database Entry


Jonathan Simon Burggraf, "Modeling and Simulating Chemotaxis Bacteria Networks in MATLAB," Master's Thesis, School of Electrical Engineering and Computer Science (EECS), TU Berlin (TUB), July 2022. (Advisor: Jorge Torres Gómez; Referees: Falko Dressler and Thomas Sikora)


To reduce costs and difficulty of researching bionanomachines nanonetwork forma- tion via molecular communication, we present a simulation model of chemotactic nanonetwork formation among bacteria, written in MATLAB. Expanding on the model presented by Wei, Bogdan, and Marculescu [1], we implement a stochastic model based on the Gillespie’s algorithm to simulate the random walk behaviour of E. coli bacteria. We added the ability to simulate movement of the target, by modifying the chemotactic gradient calculation. We change the functions repre- senting the generation rate of attractant molecules, allowing for the calculation of multiple component chemotactic gradients for the different target locations. These can then be overlaid to form a chemotactic gradient that simulates target movement. Evaluations with the Mean Squared Distance to Target (MSDT) metric show the models ability to achieve a high degree of clustering around a moving target.

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Jonathan Simon Burggraf

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    author = {Burggraf, Jonathan Simon},
    title = {{Modeling and Simulating Chemotaxis Bacteria Networks in MATLAB}},
    advisor = {Torres G{\'{o}}mez, Jorge},
    institution = {School of Electrical Engineering and Computer Science (EECS)},
    location = {Berlin, Germany},
    month = {7},
    referee = {Dressler, Falko and Sikora, Thomas},
    school = {TU Berlin (TUB)},
    type = {Master's Thesis},
    year = {2022},

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