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Visual Mining and Spatio-Temporal Querying in Molecular Dynamics

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Continuously increasing power of computers makes it possible to model dynamic behaviour of the systems studied by experimental nanoscience (e.g., single-molecule mechanics, electron and atomic force microscopy) with explicit all-atom presentation by applying various molecular dynamics approximations. Computer simulation in molecular dynamics usually results in gigabytes of time-dependent data. Computational and querying tools could help to analyze such information. We propose a novel geometric querying method for data analysis in molecular dynamics. This method is based on a novel geometric model for querying of spatio-temporal data. In our model, data from database or file are interpreted geometrically as multidimensional points with time dimension. A geometric query is a query solid of any shape specified by its parameters, location and time. These queries are formulated with geometric objects and operations over them to form the query solid changing over time. The geometric objects and operations are described with implicit functions. We propose spatio-temporal queries for data analysis in molecular dynamics that allow formulation of new hypotheses of nanoscale structures and interactions between molecules. The geometric queries in our model can be considered as motion classifiers. The resulting datasets are coordinates of molecules and atoms inside the particular shape changing over time. With the uniform geometric model we integrate visual mining and querying of time-dependent data employing 3D visualization tools. This query system should be useful in detailed studies on structure and movement of large molecule complexes of interest in various nanotechnology applications.
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Keywords: GOPENMOL; IMPLICIT FUNCTIONS; MOLECULAR DYNAMICS; SPATIO-TEMPORAL QUERIES; VISUAL MINING

Document Type: Research Article

Publication date: December 1, 2005

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  • Journal of Computational and Theoretical Nanoscience is an international peer-reviewed journal with a wide-ranging coverage, consolidates research activities in all aspects of computational and theoretical nanoscience into a single reference source. This journal offers scientists and engineers peer-reviewed research papers in all aspects of computational and theoretical nanoscience and nanotechnology in chemistry, physics, materials science, engineering and biology to publish original full papers and timely state-of-the-art reviews and short communications encompassing the fundamental and applied research.
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