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ASCOT: A web tool for the digital construction of energy minimized Ag, CuO, TiO2 spherical nanoparticles and calculation of their atomistic descriptors

Authors :
Panagiotis D. Kolokathis
Evangelos Voyiatzis
Nikolaos K. Sidiropoulos
Andreas Tsoumanis
Georgia Melagraki
Kaido Tämm
Iseult Lynch
Antreas Afantitis
Source :
Computational and Structural Biotechnology Journal, Vol 25, Iss , Pp 34-46 (2024)
Publication Year :
2024
Publisher :
Elsevier, 2024.

Abstract

ASCOT (an acronym derived from Ag-Silver, Copper Oxide, Titanium Oxide) is a user-friendly web tool for digital construction of electrically neutral, energy-minimized spherical nanoparticles (NPs) of Ag, CuO, and TiO2 (both Anatase and Rutile forms) in vacuum, integrated into the Enalos Cloud Platform (https://www.enaloscloud.novamechanics.com/sabydoma/ascot/). ASCOT calculates critical atomistic descriptors such as average potential energy per atom, average coordination number, common neighbour parameter (used for structural classification in simulations of crystalline phases), and hexatic order parameter (which measures how closely the local environment around a particle resembles perfect hexatic symmetry) for both core (over 4 Å from the surface) and shell (within 4 Å of the surface) regions of the NPs. These atomistic descriptors assist in predicting the most stable NP size based on lowest per atom energy and serve as inputs for developing machine learning models to predict the toxicity of these nanomaterials. ASCOT's automated backend requires minimal user input in order to construct the digital NPs: inputs needed are the material type (Ag, CuO, TiO2-Anatase, TiO2-Rutile), target diameter, a Force-Field from a pre-validated list, and the energy minimization parameters, with the tool providing a set of default values for novice users.

Details

Language :
English
ISSN :
20010370
Volume :
25
Issue :
34-46
Database :
Directory of Open Access Journals
Journal :
Computational and Structural Biotechnology Journal
Publication Type :
Academic Journal
Accession number :
edsdoj.1488a2a921a4395b2e77edd5f193313
Document Type :
article
Full Text :
https://doi.org/10.1016/j.csbj.2024.03.011