Accurate implementation of leaping in space: The spatial partitioned-leaping algorithm
نویسندگان
چکیده
منابع مشابه
Accurate implementation of leaping in space: the spatial partitioned-leaping algorithm.
There is a great need for accurate and efficient computational approaches that can account for both the discrete and stochastic nature of chemical interactions as well as spatial inhomogeneities and diffusion. This is particularly true in biology and nanoscale materials science, where the common assumptions of deterministic dynamics and well-mixed reaction volumes often break down. In this arti...
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We propose the S-leaping algorithm for the acceleration of Gillespie’s stochastic simulation algorithm that combines the advantages of the two main accelerated methods; the τ -leaping and R-leaping algorithms. These algorithms are known to be efficient under different conditions; the τ -leaping is efficient for non-stiff systems or systems with partial equilibrium, while the R-leaping performs ...
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Clustering is one of the known techniques in the field of data mining where data with similar properties is within the set of categories. K-means algorithm is one the simplest clustering algorithms which have disadvantages sensitive to initial values of the clusters and converging to the local optimum. In recent years, several algorithms are provided based on evolutionary algorithms for cluster...
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"Leaping" methods show great promise for significantly accelerating stochastic simulations of complex biochemical reaction networks. However, few practical applications of leaping have appeared in the literature to date. Here, we address this issue using the "partitioned leaping algorithm" (PLA) [L. A. Harris and P. Clancy, J. Chem. Phys. 125, 144107 (2006)], a recently introduced multiscale le...
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One of the most severe problems for ray casting architectures is the waste of computation cycles and I/O bandwidth, due to redundant sampling of empty space. While several techniques exist for software implementations to skip these empty regions, few are suitable for hardware implementation. The few which have been presented either require a tremendous amount of logic or are not feasible for hi...
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ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2010
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.3310808