Exploiting graph theory in MD simulations for extracting chemical and physical properties of materials

Sana Bougueroua; A.A. Kolganov; Chloe Helain; Coralie  Zens; Dominique  Barth; E.A. Pidko; Marie Pierre Gaigeot

doi:10.1039/D4CP02764G

Exploiting graph theory in MD simulations for extracting chemical and physical properties of materials

Sana Bougueroua^*, A.A. Kolganov, Chloe Helain, Coralie Zens, Dominique Barth, E.A. Pidko, Marie Pierre Gaigeot

^*Corresponding author for this work

ChemE/Inorganic Systems Engineering

Research output: Contribution to journal › Article › Scientific › peer-review

Abstract

Some of our recent developments and applications of algorithmic graph theory for extracting the physical and chemical properties of materials from molecular dynamics simulations are presented. From the chemical viewpoint, the power of graph theory is illustrated in the search for a catalyst's active sites at a silica solid surface. From the physical viewpoint, we present graph algorithms that recognize the structural motifs that exist at the silica/liquid water interface. Statistical analyses of the instances of these surface–water motifs provide a detailed understanding of the structures and dynamics at the aqueous interface.

Original language	English
Pages (from-to)	1298-1309
Number of pages	12
Journal	Physical chemistry chemical physics (PCCP)
Volume	27
Issue number	3
DOIs	https://doi.org/10.1039/D4CP02764G
Publication status	Published - 2024

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Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care
Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.

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title = "Exploiting graph theory in MD simulations for extracting chemical and physical properties of materials",

abstract = "Some of our recent developments and applications of algorithmic graph theory for extracting the physical and chemical properties of materials from molecular dynamics simulations are presented. From the chemical viewpoint, the power of graph theory is illustrated in the search for a catalyst's active sites at a silica solid surface. From the physical viewpoint, we present graph algorithms that recognize the structural motifs that exist at the silica/liquid water interface. Statistical analyses of the instances of these surface–water motifs provide a detailed understanding of the structures and dynamics at the aqueous interface.",

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note = "Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.",

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doi = "10.1039/D4CP02764G",

language = "English",

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AU - Bougueroua, Sana

AU - Kolganov, A.A.

AU - Helain, Chloe

AU - Zens, Coralie

AU - Barth, Dominique

AU - Pidko, E.A.

AU - Gaigeot, Marie Pierre

N1 - Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.

PY - 2024

Y1 - 2024

N2 - Some of our recent developments and applications of algorithmic graph theory for extracting the physical and chemical properties of materials from molecular dynamics simulations are presented. From the chemical viewpoint, the power of graph theory is illustrated in the search for a catalyst's active sites at a silica solid surface. From the physical viewpoint, we present graph algorithms that recognize the structural motifs that exist at the silica/liquid water interface. Statistical analyses of the instances of these surface–water motifs provide a detailed understanding of the structures and dynamics at the aqueous interface.

AB - Some of our recent developments and applications of algorithmic graph theory for extracting the physical and chemical properties of materials from molecular dynamics simulations are presented. From the chemical viewpoint, the power of graph theory is illustrated in the search for a catalyst's active sites at a silica solid surface. From the physical viewpoint, we present graph algorithms that recognize the structural motifs that exist at the silica/liquid water interface. Statistical analyses of the instances of these surface–water motifs provide a detailed understanding of the structures and dynamics at the aqueous interface.

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Exploiting graph theory in MD simulations for extracting chemical and physical properties of materials

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