Modelling methods simulated annealing

This criterion resumes all the a priori knowledge that we are able to convey concerning the physical aspect of the flawed region. Unfortunately, neither the weak membrane model (U2 (f)) nor the Beta law Ui (f)) energies are convex functions. Consequently, we need to implement a global optimization technique to reach the solution. Simulated annealing (SA) cannot be used here because it leads to a prohibitive cost for calculations [9]. We have adopted a continuation method like the GNC [2]. 

Figure 5 Optimization of the objective function in Modeller. Optimization of the objective function (curve) starts with a random or distorted model structure. The iteration number is indicated below each sample structure. The first approximately 2000 iterations coiTespond to the variable target function method [82] relying on the conjugate gradients technique. This approach first satisfies sequentially local restraints, then slowly introduces longer range restraints until the complete objective function IS optimized. In the remaining 4750 iterations, molecular dynamics with simulated annealing is used to refine the model [83]. CPU time needed to generate one model is about 2 mm for a 250 residue protein on a medium-sized workstation.

Roitberg, A. Elber, R., Modeling side chains in peptides and proteins application of the locally enhanced sampling technique and the simulated annealing methods to find minimum energy conformations, J. Chem. Phys. 1991, 95, 9277-9287... 

Several methods have been developed to aid in the selection of descriptors to create a QSAR model. The use of brute computational force to test every possible combination of the above problem is wasteful. Methods such as the Stepwise Searches (45), Simulated Annealing (94), and Genetic Algorithms... 

The subtractive phase is followed by an optimization phase where simulated annealing is used to improve the predictive power of the hypotheses. Small changes are made to the models and they are scored according to the accuracy in activity estimation. Finally, the simplest models that correctly estimate activity are selected (Occam s Razor) and the top N solutions are reported to the user. The method has been described in more detail elsewhere [39, 40]. 

Operations like pressure swing adsorption involve the condensation of the liquid in the porous medium. Several researchers developed predictive models of the configuration of liquid phase in the wet, unsaturated, porous media. The method developed by Silverstein and Fort (2000) is based on simulated annealing with random swapping of gas and liquid elements in the system to achieve a global energy minimum defined by... 

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