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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
Computational and Structural Biotechnology Journal ( IF 6 ) Pub Date : 2024-03-12 , DOI: 10.1016/j.csbj.2024.03.011
Panagiotis D. Kolokathis , Evangelos Voyiatzis , Nikolaos K. Sidiropoulos , Andreas Tsoumanis , Georgia Melagraki , Kaido Tämm , Iseult Lynch , Antreas Afantitis

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 TiO (both Anatase and Rutile forms) in vacuum, integrated into the Enalos Cloud Platform (). 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, TiO-Anatase, TiO-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.

中文翻译:

ASCOT:一种网络工具,用于数字化构建能量最小化的 Ag、CuO、TiO2 球形纳米颗粒并计算其原子描述符

ASCOT(源自 Ag-Silver、Copper Oxide、Titanium Oxide 的缩写)是一种用户友好的网络工具,用于数字化构建 Ag、CuO 和 TiO(锐钛矿型和金红石型)的电中性、能量最小化球形纳米颗粒 (NP)形式)在真空中集成到 Enalos 云平台 () 中。 ASCOT 计算关键的原子描述符,例如每个原子的平均势能、平均配位数、公共邻居参数(用于结晶相模拟中的结构分类)和六方序参数(测量粒子周围的局部环境与完美六方的相似程度)对称性)适用于纳米粒子的核心(距表面超过 4 Å)和壳(距表面 4 Å 以内)区域。这些原子描述符有助于根据最低的每原子能量预测最稳定的纳米颗粒尺寸,并作为开发机器学习模型的输入来预测这些纳米材料的毒性。 ASCOT 的自动化后端需要最少的用户输入来构建数字 NP:所需的输入包括材料类型(Ag、CuO、TiO-锐钛矿、TiO-金红石)、目标直径、预先验证列表中的力场以及能量最小化参数,该工具为新手用户提供一组默认值。
更新日期:2024-03-12
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