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The stochastic simulation is allowed to run for a sufficient number of time steps so that the mean fitness of the population does not change significantly, at which point the system is assumed to be at steady-state.
The simulation is allowed to run with no external wind, that is, cells move only according to the landscape and stochastic variability.
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The simulation was allowed a "warm-up" period of 24 hours, then observations were made during the following 24 hours.
For each experiment and at each value of μ, the simulation was allowed to run for 1000 generations; in some cases, the population became extinct before 1000 generations were reached.
For treatment planning, both conventional 2-D X-ray simulation and 3-D CT simulation were allowed.
Prior to data collection, the simulation was allowed to run for 200 host generations; this allowed for establishment of long-term coevolutionary dynamics arising from the host-parasite interaction.
Two independent runs of Markov chain Monte Carlo (MCMC) simulation were allowed for 1.2 or 2.2 million generations each (for nuclear and chloroplast datasets, respectively), with trees sampled every 1000 generations, to achieve independence among samples.
In the initial phase, simulations were allowed to run for 25,000 generations (µ = 10−4) or 85,000 generations (µ = 2.5*10−5) to permit quasi-equilibrium patterns of spatial genetic structure and diversity to evolve.
Simulations are allowed to proceed until the desired simulation time is reached (50 s for H2, 200 s for D2, same as the dosing times in the experiments).
The MD simulations were allowed to continue for another 70 ps at 298 K and from the last 50 ps, snapshots were collected to create an average structure that was visually inspected.
An undergraduate history course incorporating strategy games is just the beginning: computer simulations are allowing people to study the past in ways that have never been possible.
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CEO of Professional Science Editing for Scientists @ prosciediting.com