Structure simulation models using annealing techniques

Despite such restrictions, real space crystallographic methods based on genetic algorithms, Monte-Carlo methods, or simulated annealing techniques have proved to be powerful means for structure solutions from X-ray powder patterns. Provided with the unit cell, the composition and configuration of the asymmetric unit, and sufficiently texture-free diffraction data, refinable structure models can be obtained within minutes on a personal computer, even for molecules with multiple internal degrees of freedom. The resulting structure models are then refined by Rietveld techniques, which use the whole profile of the X-ray diffraction pattern for refinement . ... 

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.

In the recent years, sophisticated modeling tools have become available, such as the Cerius (8), where various modules aUow the analysis of crystallization, crystal growth, and material form characterization. In brief, this technique uses a simulated annealing and a rigid-body Rietveld refinement procedure, whereby the calculated and measured XRPD patterns are compared if they agree sufficiently, the structure is deemed to be solved. Other modules offered by Cerus include ... 

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