Visual Query Interface for Molecular Dynamics Application

Abstract

Visual data mining opens new possibilities for scientific research on the Web. In this paper, we propose new types of spatio-temporal queries for molecular dynamics application. A new visual spatio-temporal query interface is designed and implemented. The Molecular Visual Dynamics Query System (MDVQS) is described. The system reads and visualizes the molecular dynamics file as a sequence of time frames. The queries are defined as geometric shapes changing over time. The queries are formulated with geometric objects and operations over them at the first time frame. The atoms coordinates or the distance between atoms can be chosen as time-dependent parameters of the query solid that defines the shape of the spatio-temporal range query. Then, the resulting region inside the spatio-temporal query is visualized as an animated sequence or frame-by-frame. The system application in analysis of molecular dynamics simulation results is discussed. The temporal range queries in our model can be considered as motion classifiers. The resulting sets are coordinates of molecules and atoms inside the particular shape changing over time.