Selected article for: "energy function and free energy"
Author: Naoto Hori; Natalia A. Denesyuk; D. Thirumalai
Title: Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension
  • Document date: 2016_4_15
    • ID: 08mep8hm_17
    Snippet: A much richer diagram of states emerges when the G(R g ) = −k B T log P (R g ) is examined. The G(R g ) profile at C = 10 mM is similar to G(R ee ). However, at higher concentrations, there is clear signature of three states (especially at f = 12.5 pN) corresponding to the folded PK, an intermediate state, and the E state. The free energy profiles show that under force, there are minimally three states, which are F, I, and E. Because R ee canno.....
    Document: A much richer diagram of states emerges when the G(R g ) = −k B T log P (R g ) is examined. The G(R g ) profile at C = 10 mM is similar to G(R ee ). However, at higher concentrations, there is clear signature of three states (especially at f = 12.5 pN) corresponding to the folded PK, an intermediate state, and the E state. The free energy profiles show that under force, there are minimally three states, which are F, I, and E. Because R ee cannot capture the complexity of the states populated as C and f are varied, it is important to consider R g as well to fully capture the phase diagram of the PK. We also computed the free energy profiles as a function of root-mean-square-deviations (RMSD). In terms of the number and relative positions of basins, the profiles based on RMSD are qualitatively similar to one of R g (Fig. S4 ).

    Search related documents: