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With a user-specified threshold of T = 2 for the first iteration step, the threshold value remains - log2 (0.5) in all subsequent steps, and with a chosen threshold value of T = 1, the value for the subsequent iteration steps is set to - log2 (0.75).
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The default parameters were used and the number of annealing steps was set to 10,000,000.
The maximum number of Monte Carlo steps was set to 5000.
During the simulations, the time steps were set to 1 × 107, with a fixed time step of 1 fs.
Δt, the time step of FDTD, equals 16.667 ps, and the total computation time steps are set to 11,070.
For application of the IZZI-Thellier method, temperature steps were set to be every 50 °C between room temperature and 500 °C and every 35 °C between 500 and 600 °C.
Camera wells were not binned, yielding a pixel size of 0.07 µm in x and y. z steps were set to 0.07 µm, yielding cubic voxels.
Incubation volumes for all ISH steps were set to 250 μl.
Upper and lower bounds for parameter optimization steps were set to the following ranges: bottleneck proportion or magnitude of population decline (BG and NEGG models; 0.001-1), magnitude of population growth (BG and POSG models; 1-100), timing of demographic events (BG, POSG, NEGG models; 0.01-5 0.01-5
The temperature is kept at 10 K so as to minimize thermal fluctuations and the time step is set to 0.5 fs.
In the test on the stiff Markov ionic channel model, the Hybrid blows up if the allowable time step is set to be greater than 0.1 ms.
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