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In the simulation, the free RNA samples various distinct conformations in accordance with the earlier findings.
According to our simulation, the free energy threshold provided by He's model is inferior to -40 kcal/mol threshold with Zuker's model.
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It can be seen that in most simulations the free energies of binding converge within 20 ns, as the running averages become reasonably stable.
That is, for the case of anticipatory responding simulations, the free parameters are derived according to the training days (the first 8 days of the experiment), and then are used for predicting the extinction days, as well as the re-acquisition day.
The side chain of Phe82 in Loop 2 had three kinds of orientations during the MD simulation for the free enzyme with two conformations occupied most of the simulation time (black line in Figure 8B).
The fluid flows and hydrodynamic pressures are simulated by a Large Eddy Simulation model, and the free surface is tracked by the Volume-of-Fluid (VOF) method.
The Lagrangian moving grid method is employed for the simulation of the free surface.
Simulation of the free TcB-TcC complex started from the open state, where the β-propeller undergoes the full transition to the closed state.
The second is regarding the simulation of the free surface, which requires special techniques in the traditionally used Eulerian framework.
A quantum-mechanical simulation of the free radical recombination reaction, during which the singlet dioxygen is generated, was carried out.
As a result, a multiple scale UGKS-AS is developed and used for the flow simulation from the free molecular transport to the Navier Stokes solutions.
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