The Silica-Water Interface from the Analysis of Molecular Dynamic Simulations

Handle URI:
http://hdl.handle.net/10754/293859
Title:
The Silica-Water Interface from the Analysis of Molecular Dynamic Simulations
Authors:
Lardhi, Sheikha F. ( 0000-0001-9061-8397 )
Abstract:
Surface chemistry is an emerging field that can give detailed insight about the elec- tronic properties and the interaction of complex material surfaces with their neigh- bors. This is for both solid-solid and solid-liquid interfaces. Among the latter class, the silica-water interface plays a major role in nature. Silica is among the most abundant materials on earth, as well in advanced technological applications such as catalysis and nanotechnology. This immediately indicates the relevance of a detailed understanding of the silica-water interface. In this study, we investigate the details of this interaction at microscopic level by analyzing trajectories obtained with ab initio molecular dynamic simulations. The system we consider consists of bulk liquid water confined between two β-cristobalite silica surfaces. The molecular dynamics were generated with the CP2K, an ab initio molecular dynamic simulation tool. The simulations are 25 picoseconds long, and the CP2K program was run on 64 cores on a supercomputer cluster. During the simulations the program integrates Newton’s equations of motion for the system and generates the trajectory for analysis. For analysis, we focused on the following properties that characterize the silica water interface. We calculated the density profile of the water layers from the silica surface, and we also calculated the radial distribution function (RDF) of the hydrogen bond at the silanols on the silica surface. The main focus of this thesis is to write the programs for calculating the atom density profile and the RDF from the generated MD trajectories. The atomic probability density profile shows that water is strongly adsorbed on the (001) cristobalite surface, while the RDF indicates differently ad- sorbed water molecules in the first adsorption layer. As final remark, the protocol and the tools developed in this thesis can be applied to the study of basically any crystal-water interface.
Advisors:
Cavallo, Luigi ( 0000-0002-1398-338X )
Committee Member:
Keyes, David E. ( 0000-0002-4052-7224 ) ; Moshkov, Mikhail ( 0000-0003-0085-9483 )
KAUST Department:
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Program:
Computer Science
Issue Date:
May-2013
Type:
Thesis
Appears in Collections:
Theses; Computer Science Program; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.advisorCavallo, Luigien
dc.contributor.authorLardhi, Sheikha F.en
dc.date.accessioned2013-06-12T09:29:41Z-
dc.date.available2013-06-12T09:29:41Z-
dc.date.issued2013-05en
dc.identifier.urihttp://hdl.handle.net/10754/293859en
dc.description.abstractSurface chemistry is an emerging field that can give detailed insight about the elec- tronic properties and the interaction of complex material surfaces with their neigh- bors. This is for both solid-solid and solid-liquid interfaces. Among the latter class, the silica-water interface plays a major role in nature. Silica is among the most abundant materials on earth, as well in advanced technological applications such as catalysis and nanotechnology. This immediately indicates the relevance of a detailed understanding of the silica-water interface. In this study, we investigate the details of this interaction at microscopic level by analyzing trajectories obtained with ab initio molecular dynamic simulations. The system we consider consists of bulk liquid water confined between two β-cristobalite silica surfaces. The molecular dynamics were generated with the CP2K, an ab initio molecular dynamic simulation tool. The simulations are 25 picoseconds long, and the CP2K program was run on 64 cores on a supercomputer cluster. During the simulations the program integrates Newton’s equations of motion for the system and generates the trajectory for analysis. For analysis, we focused on the following properties that characterize the silica water interface. We calculated the density profile of the water layers from the silica surface, and we also calculated the radial distribution function (RDF) of the hydrogen bond at the silanols on the silica surface. The main focus of this thesis is to write the programs for calculating the atom density profile and the RDF from the generated MD trajectories. The atomic probability density profile shows that water is strongly adsorbed on the (001) cristobalite surface, while the RDF indicates differently ad- sorbed water molecules in the first adsorption layer. As final remark, the protocol and the tools developed in this thesis can be applied to the study of basically any crystal-water interface.en
dc.language.isoenen
dc.subjectmolecularen
dc.subjectdynamicsen
dc.subjecthydrogenen
dc.subjectsilicaen
dc.subjectsimulationen
dc.titleThe Silica-Water Interface from the Analysis of Molecular Dynamic Simulationsen
dc.typeThesisen
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
thesis.degree.grantorKing Abdullah University of Science and Technologyen_GB
dc.contributor.committeememberKeyes, David E.en
dc.contributor.committeememberMoshkov, Mikhailen
thesis.degree.disciplineComputer Scienceen
thesis.degree.nameMaster of Scienceen
dc.person.id118458en
All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.