Abstract: Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models (i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a `tree search with pruning' approach. This method, as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard `automated MR' mode and two case studies are used to show how to modify the automated search strategy for problematic cases.

Abstract: A cam phaser diagnostic system is provided. The system includes: a first sample variance module that computes a first variance based on a desired cam phaser position. A second sample variance module computes a second variance based on a measured cam phaser position. An evaluation module diagnoses faulty cam phaser operation based on the first variance and the second variance.

Abstract: A method for controlling dual independent camshaft phasers in an internal combustion engine. The method has three basic steps: a) first, determining if rate balancing between the two phasers is required; b) second, determining the optimal rate balancing commands; and c) third, applying the determined rate balancing commands to the appropriate phaser(s). In determining the rate balancing commands, there are three possible phaser options: the intake phaser requires priority; the exhaust phaser requires priority; or neither phaser requires priority. Lookup tables are stored in the engine controller for each option. When either phaser has priority, the other phaser is actuated after a delay based upon the position error of the priority phaser, generally at a lower phase rate. When neither phaser has priority, both phasers are actuated at a rate consistent with oil-delivery capabilities of the engine.

Abstract: There are two likelihood functions in Phaser for use in experimental phasing: one for MIR/MIRAS/MAD phasing, and one specially developed for SAD (single-wavelength anomalous dispersion) phasing. The MIR/ MIRAS/MAD function involves a two-dimensional (2D) integration over the complex plane. 2D integration is a slow process, and in the course of a typical experimental phasing run needs to be performed millions of times. We review here how both likelihood functions are derived, and discuss methods for overcoming the computational bottleneck in the integration of the MIR/MIRAS/MAD function, as implemented in the program Phaser.

Abstract: We present results of cellular automata based investigations of rotating spiral autowaves in a nonequilibrium excitable medium which models three-level paramagnetic microwave phonon laser (phaser). The computational model is described in arXiv:cond-mat/0410460v2 and arXiv:cond-mat/0602345v1 . We have observed several new scenarios of self-organization, competition and dynamical stabilization of rotating spiral autowaves under conditions of cross-relaxation between three-level active centers. In particular, phenomena of inversion of topological charge, as well as processes of regeneration and replication of rotating spiral autowaves in various excitable media were revealed and visualized for mesoscopic-scale areas of phaser-type active systems, which model real phaser devices.