Generation Algorithm for

A R, D P Dolata and K Prout 1990. Automated Conformational Analysis and Structure Generation Algorithms for Molecular Perception. Journal of Chemical Information and Computer Science 30 316-324. 

It is also possible to extend the Liouville operator-splitting approach to generate algorithms for MD in these ensembles examples of explicit, reversible, integrators are given by Martyna et al [91],... 

A local algorithm for Metropolis Monte Carlo trajectories must be constructed carefully. Due to the finite probability of exactly repeated states in these paths, the corresponding transition probability includes a singular term [see Eq. (1.14)]. The generation algorithm for local path moves must take this singularity into account properly. Appropriate acceptance probabilities are given in [5]. (H. C. Andersen has drawn our attention to an omission in [5]. In Metropolis Monte Carlo trajectories sequences of multiple rejections can occur. Attempts to modify time slices in the interior... 

Tokuda, K., Yoshimura, T., Masuko, T., Kobayashi, T., and Kitamura, T. Speech parameter generation algorithms for HMM-based speech synthesis. In Proceedings International Conference on Acoustics Speech and Signal Processing 2000 (2000). 

Floating search method proposed by Pudil et al. [112] is used as feature subset generation procedure, and has been proved to be one of the best subset generation algorithms for moderately large or small data sets. Backward floating search (BFS) method needs more computer time than forward floating search method, but it can treat interactive features well, so we combine it with SVM based on wrapper method and name it SVM-BFS method. 

The Boltzmaim weight appears implicitly in the way the states are chosen. The fomi of the above equation is like a time average as calculated in MD. The MC method involves designing a stochastic algorithm for stepping from one state of the system to the next, generating a trajectory. This will take the fomi of a Markov chain, specified by transition probabilities which are independent of the prior history of the system. 

L. Holm and C. Sander, Database algorithm for generating protein backbone and side-chain co-ordinates from a trace, J. Mol. Biol. 218 (1991), 183-194. 

A related algorithm can be written also for the Brownian trajectory [10]. However, the essential difference between an algorithm for a Brownian trajectory and equation (4) is that the Brownian algorithm is not deterministic. Due to the existence of the random force, we cannot be satisfied with a single trajectory, even with pre-specified coordinates (and velocities, if relevant). It is necessary to generate an ensemble of trajectories (sampled with different values of the random force) to obtain a complete picture. Instead of working with an ensemble of trajectories we prefer to work with the conditional probability. I.e., we ask what is the probability that a trajectory being at... 

Fig. 5.29 Method for correcting the path followed by a steepest descents algorithm to generate the intrinsic reaction coordinate. The solid line shows the real path and the dotted line shows the algorithmic approximation to it. (Figure redrawn from Gonzalez C and H B Schlegel 1988. An Improved Algorithm for Reaction Path Following. Journal of Chemical Physics 90 2154-2161.)...

P Willett, J Bradshaw and D V S Green 1999. Selecting Combinatorial Libraries to Optimize rsity and Physical Properties. Journal of Chemical Information and Computer Science 39 169-177. 1 and A W R Payne 1995. A Genetic Algorithm for the Automated Generation of Molecules in Constraints. Journal of Computer-Aided Molecular Design 9 181-202. 

Siace the columns of any complete B-matrix are a basis for the null space of the dimensional matrix, it follows that any two complete B-matrices are related by a nonsingular transformation. In other words, a complete B-matrix itself contains enough information as to which linear combiaations should be formed to obtain the optimized ones. Based on this observation, an efficient algorithm for the generation of an optimized complete B-matrix has been presented (22). No attempt is made here to demonstrate the algorithm. Instead, an example is being used to illustrate the results. 

An algorithm for performing a constant-pressure molecular dynamics simulation that resolves some unphysical observations in the extended system (Andersen s) method and Berendsen s methods was developed by Feller et al. [29]. This approach replaces the deterministic equations of motion with the piston degree of freedom added to the Langevin equations of motion. This eliminates the unphysical fluctuation of the volume associated with the piston mass. In addition, Klein and coworkers [30] present an advanced constant-pressure method to overcome an unphysical dependence of the choice of lattice in generated trajectories. 

Algorithms for machine-generated syntheses by application of connective transforms to target structures containing appendages, medium-sized rings, etc. have been described. ... 

Li s algorithm for generating closed form solutions for the power spectra of CA attractors consists essentially of five main parts ([li87], [li89b]) ... 

Two alternatives present themselves in formulating algorithms for the tracking of segments of stable and unstable manifolds. The first involves observing the initial value problem for an appropriately chosen familv of initial conditions, henceforth referred to as simulation of invariant manifolds. A second generation of algorithms for the computation of invariant manifolds involves numerical fixed point techniques. 

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