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 Pattern mining and visualization for molecular dynamics simulation.


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Type of Resource: text

Genre: Electronic Thesis or Dissertation

Issuance: single unit

Date Created: Summer 2014

Date Issued: 2014

Publisher: Florida Atlantic University

Physical Form: Online Resource

Extent: 88 p.

Language(s): English

Summary: Molecular dynamics is a computer simulation technique for expressing theultimate details of individual particle motions and can be used in many fields, such aschemical physics, materials science, and the modeling of biomolecules. In this thesis, westudy visualization and pattern mining in molecular dynamics simulation. The moleculardata set has a large number of atoms in each frame and range of frames. The features ofthe data set include atom ID; frame number; position in x, y, and z plane; charge; andmass. The three main challenges of this thesis are to display a larger number of atoms andrange of frames, to visualize this large data set in 3-dimension, and to cluster theabnormally shifting atoms that move with the same pace and direction in different frames.Focusing on these three challenges, there are three contributions of this thesis. First, wedesign an abnormal pattern mining and visualization framework for molecular dynamicssimulation. The proposed framework can visualize the clusters of abnormal shifting atomgroups in a three-dimensional space, and show their temporal relationships. Second, we propose a pattern mining method to detect abnormal atom groups which share similarmovement and have large variance compared to the majority atoms. We propose ageneral molecular dynamics simulation tool, which can visualize a large number of atoms,including their movement and temporal relationships, to help domain experts studymolecular dynamics simulation results. The main functions for this visualization andpattern mining tool include atom number, cluster visualization, search across differentframes, multiple frame range search, frame range switch, and line demonstration for atommotions in different frames. Therefore, this visualization and pattern mining tool can beused in the field of chemical physics, materials science, and the modeling ofbiomolecules for the molecular dynamic simulation outcomes.

Identifier: FA00004212 (IID)

Note(s): Includes bibliography.Thesis (M.S.)--Florida Atlantic University, 2014.

Subject(s): Data miningInformation visualizationMolecular dynamics -- Computer simulationMolecules -- Mathematical modelsPattern perception

Held by: Florida Atlantic University Digital Library

Sublocation: Boca Raton, Fla.

Persistent Link to This Record: http://purl.flvc.org/fau/fd/FA00004212

Restrictions on Access: All rights reserved by the source institution

Owner Institution: FAU



Author: Kong, Xue, author Zhu, Xingquan Dr., Thesis advisor College of Computer Science and Engineering, Degree grantor

Source: http://fau.digital.flvc.org/islandora/object/fau%3A13682



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