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The docked models were relaxed and refined by a short 500 ps solvated simulation.
All the pilin models were relaxed by Rosetta Relax protocol to eliminate steric clashes, before the calculations.
These models were scored by Rosetta, and the top models were relaxed iteratively (see Figure 2 and Figures S3 and S4 of the Supporting Information).
The initial models were relaxed by energy minimization using the CVFF force-field in Discover (2.98 version; Accelrys) for a total of 4000 conjugate gradient steps.
The models were relaxed using a quick minimization routine with Amber force field and molecular surfaces were generated using the Molecular Operating Environment (MOE) (Chemical Computing Group, Montreal, Canada).
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Motivated by this recognition and the fact that the separation of parameter dependencies increases the complexity and computational cost, the definition of Polytopic TP representation for LPV/qLPV models is relaxed.
The proposed filter has an advantage in which the restrictive assumptions of statistical models for process noise, measurement noise, and motion models are relaxed.
The zero-kinetic-energy models are relaxed over 2.5 dynamical timescales of the gas using critical damping on the velocities of the particles, where at each step the magnitude of damping is reduced so that in the final step no constraint on the velocity is imposed (for a similar approach, see de Vries et al. 2014).
Then the differentiation rules in the model were relaxed and the intact virtual epidermis was simulated for 100 iterations under high cell proliferation (stem cell 10%, TA cell 20%) and default cell proliferation (stem cell 1%, TA cell 2%) conditions.
However, this was not obvious under default cell proliferation conditions even when the differentiation rules in the model were relaxed and the intact virtual epidermis was also simulated for 100 iterations (Table 1), suggesting psoriasis might be related to both cell proliferation and differentiation.
First, the model is relaxed about 50 ps relaxation process using a canonical ensemble (NVT) MD simulation in order that the system lies in local potential minimum.
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CEO of Professional Science Editing for Scientists @ prosciediting.com