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Temporal databases and data warehouses are essential components of intelligent information systems in cyberworlds. We describe a geometric model for querying time-dependent data in databases and warehouses. An implementation and application of the model for querying of results of numerical simulation in molecular dynamics is discussed. Data 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. The geometric objects and operations are described with implicit functions. With the uniform geometric model for querying time-dependent data, 3D visualization tools can be naturally incorporated into the molecular dynamics visualization system to pose the queries.