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Another close, transitioned trans friend always finds a delicate way to ask me this too; I recognize it as a sign of love.
The next step is to use the kinetic rates to calculate the probability of state ("open" or "close") transition by means of a Monte Carlo model.
To perform normal mode analysis (NMA) to examine the modal description of the opening and closing transitions, we first had to define the open and closed states of E. coli SecA in the monomer and dimer forms.
Recombination sites found in EXT repeats are associated with open-close transitions of more than 3 °C (Fig. 6b).
When we compare the dimer and monomer closing transitions, the dimer has slightly larger projections, indicating the transition for the dimer requires less energy.
Under such conditions, discrete opening and closing transitions of single BK channels would be readily visible; not only at 100 mV, but even more so at voltages < 100 mV.
What we can observe from Figure 7A is that the open to closed transition is more robustly described by the low-frequency modes than the closed to open transition, indicating that the closing transition requires less energy (lower-frequency modes) than the opening transition.
After the initial paths were converged, the highest energy points were optimized to the closest transition state (TS).
From these results, we predict mutations that will perturb the opening and/or closing transition rates by changing the entropy of dihedrals and/or the enthalpy of contacts.
This residue is known as the "mobile Asn" because it moves by 10 Å during the closing transition.
The transition zones from the torsion angle profiles appear to be in perfect harmony with the opening and closing transition movement of catalytic loops.
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