A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms
Fig 2
Exploration of model space using Markov-chain Monte Carlo.
The plot shows a ModelExplorer trajectory based on a symporter energy function during a 1e6 MC step simulation. Note that each point represents a different fully specified model. Energy minima correspond to models that are more fit, using EMC = −Jsubstrate as a fitness function in this case, where Jsubstrate is the flux of substrate. Models are initially at a high energy but quickly find local minima. A tempering schedule (see S1 Text) of alternating temperature increases and decreases prevents the simulation from being trapped in local minima.