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_48
Snippet: To analyze the structural transitions from which the phase diagrams are determined, we stored snapshots every 10 4 time steps from all the trajectories. We computed the radius of gyration (R g ) and the end-to-end distance (R ee ) using the stored snapshots. The fraction of native contacts, Q, is calculated by counting the number of hydrogen bond (HB) interaction pairs. The assessment of HB formation is based on the instantaneous value of the HB .....
Document: To analyze the structural transitions from which the phase diagrams are determined, we stored snapshots every 10 4 time steps from all the trajectories. We computed the radius of gyration (R g ) and the end-to-end distance (R ee ) using the stored snapshots. The fraction of native contacts, Q, is calculated by counting the number of hydrogen bond (HB) interaction pairs. The assessment of HB formation is based on the instantaneous value of the HB interaction energy, U HB . In our model, each HB interaction pair contributes up to nU 0 HB toward stability, where U 0 HB is -2.43 kcal/mol, corresponding to the stability of one HB, and n represents number of HB associated in the interaction [37] . A cutoff value nU C HB is defined to pick out contacts that are established. We use a value, U C HB = −1.15 kcal/mol to obtain the diagram using Q as an order parameter. Modest changes in U C HB do not affect the results qualitatively.
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