attempted PID controller with Kepler

I wanted to check out the Kepler scientific workflow system (https://kepler-project.org/), and decided to build a PID controller model with it. Here I report on my results. The following schematic, taken from the Wikipedia entry http://en.wikipedia.org/wiki/PID_controller, shows the basic configuration of a PID controller. PID stands for “proportional integral derivative”, reflecting the fact that the […]

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monte-carlo simulation in C++ with MCS-libre

Monte-Carlo simulation is a sometimes elegant (and sometimes crude) method for simulating complex systems. Parameters that affect the system are selected from random distributions and the system response to these values is then calculated. Repeating this process many times produces often useful information about the system. The method is especially useful for examining non-linear systems […]

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simulating a synthetic biology circuit with system dynamics

McAdams and Arkin report the following synthetic biology oscillator circuit in their paper “Gene regulation: Towards a circuit engineering discipline” [1]: The circuit works by having gene R1’s protein inhibit production of R3, who’s protein inhibits production of R2, which in turn inhibits production of R1. Delays in the inhibition processes cause sufficient expression of […]

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