Algorithmic considerations

A few groups replace the Lennard-Jones interactions by interactions of a different form, mostly ones with a much shorter interaction range [144,146]. Since most of the computation time in an off-lattice simulation is usually spent on the evaluation of interaction energies, such a measure can speed up the algorithm considerably. For example, Viduna et al. use a potential in which the interaction range can be tuned... 

Our results from oif-lattice simulations of dense polymer phases, obtained with a combination of newly available simulation tools, demonstrate that the Concerted-Rotation MC algorithm, introduced recently by Dodd et al. [47], is a valuable tool for the simulation of realistic polymer modds. While CONROT does not constitute an improvement over existing methods for systems with many chain ends, CONROT-based algorithms considerably extend the ran trf systems and problems that can be studied with MC methods. Such algorithms are particularly powerful when the >lutions to the geometric CONROT problem are selected with bias. 

In traditional Fan-Beam CT the radiation emitted from the X-ray tube is collimated to a planar fan, and so most of the intensity is wasted in the collimator blades (Fig. 2a). Cone-Beam CT, where the X-rays not only diverge in the horizontal, but also in the vertical direction, allows to use nearly the whole emitted beam-profile and so makes best use of the available LINAC photon flux (Fig. 2b). So fast scanning of the samples three-dimensional structure is possible. For Cone-Beam 3D-reconstruction special algorithms, taking in consideration the vertical beam divergence of the rays, were developed. 

However, by constructing a nested sequence of successively larger discrete spaces and approximations therein we hope to end up with some approximation of a unique invariant measure, which is then implicitly defined via the constructed sequence of subspaces. An expression of this mathematical consideration is the multilevel structure of the suggested algorithm - details see below (Section 3.2). In physical terms, we hope that the perturbations introduced by discretization induce a unique and smooth invariant measure but are so weak that they do not destroy the essential physical structure of the problem. 

Extending time scales of Molecular Dynamics simulations is therefore one of the prime challenges of computational biophysics and attracted considerable attention [2-5]. Most efforts focus on improving algorithms for solving the initial value differential equations, which are in many cases, the Newton s equations of motion. 

There is no correct method of performing cluster analysis and a large number of algorithms have been devised from which one must choose the most appropriate approach. There can also be a wide variation in the efficiency of the various cluster algorithms, which may be an important consideration if the data set is large. 

Another important consideration is the amount of labor necessary on the part of the user. One major difference between different software packages is the developer s choices between ease of use and efficiency of operation. For example, the Spartan program is extremely easy to use, but the price for this is that the algorithms are not always the most efficient available. Many chemistry users begin with software that is very simple, but when more sophisticated problems need to be solved, it is often easier to learn to use more complicated software than to purchase a supercomputer to solve a problem that could be done by a workstation with different software. 

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