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In addition to estimating changes in preferences for service packages for the full sample, simulations were stratified by the SDC variables used in the main analysis.
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Our analytical results and our sample simulations are quite meaningful as we work with the current HIV trend in South Africa.
In addition to the 2D umbrella sampling simulations, one-dimensional (1D) umbrella sampling simulations were also performed for both C5 C8 and C5 O6 as single-reaction pathways.
Preliminary umbrella sampling simulations were performed with the His523 Nε atom either protonated or unprotonated, to identify the most likely protonation state of this residue.
The active site structures from the 15 ps unrestrained QM/MM MD simulations performed prior to umbrella sampling simulations were very similar (in terms of interatomic distances, hydrogen bonding, etc).
The STH sampling simulations were run according to the previous protocol, with the number of clusters calculated based on a cut-off of 2% antigenemia prevalence determined by the principle LF vector in Kenya, which is Anopheles.
Starting structures of the corresponding umbrella sampling simulations were extracted from the corresponding steered MD trajectories at an interval of 0.1 Å between adjacent windows for both the O5 C6 and C5 C8 reaction coordinates in the 1D PMF calculations.
A sample simulation is included in the Appendix.
A statistical model based on large sample simulation is established to study the relationship between random telegraph signal (RTS) noise and the number of time delay integration (TDI) stages in TDI CMOS image sensor (CIS).
To accelerate conformational sampling, simulations are performed at elevated temperatures and peptide concentrations.
Since the curvature measures depend on the parameter set θ and also on the noise samples, simulations are performed for a fixed channel model at different SNRs.
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