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Kinetically determined transition midpoints match well with their thermodynamic counterparts.
One of these regions was located near the experimentally determined transition state.
This resulted in an increase in the size of the encounter region located near the experimentally determined transition state, as well as a decrease in the energy of this region and an increase in the number of successful trajectories (i.e., encounters that develop into complex).
The boxes in Figure 1 display the various TB states that are tracked for each individual and the arrows depict the stochastically determined transition probabilities.
We thus define the experimentally determined transition rate for calcein (with a concentration difference of 125 μM) as kExp = 1/ τExp = 226 s−1.
In order to use the best parameters for our simulations, we determined transition and emission probabilities from the underlying true copy number status of the simulated data for each run.
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Using the Poisson Boltzmann equation, we considered the effects of colloidal charge repulsion among monomers, when confined in different aggregate morphologies (oligomers or precipitates), as the basis for the observed salt- and protein-concentration dependence of the experimentally determined transitions.
The trapezoidal membership functions are used to determine transition zones.
The cage speeds can be used to determine transition speed.
These methods derive from a more general approach for determining transition temperatures.
Vibration spectroscopy is applied in order to determine transition band frequencies and related shifts with ligand incorporation.
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