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Scientific simulation is a most challenging task in, which the basic components of large systems are treated as classical entities (i.e. particles) the structure of the system, movement and function are explore by Molecular Simulation (MS) data, which analyzing the behavior of natural systems. Data generated by such simulations impose great challenges to database storage and query processing. One of the queries against particle simulation data is Spatial Distance Histogram (SDH), which asks for the distances of all pairs of particles in the simulated system.