{"title":"学习无定形表面的吸附模式","authors":"Mattia Turchi, Sandra Galmarini, Ivan Lunati","doi":"10.1021/acs.jctc.4c00702","DOIUrl":null,"url":null,"abstract":"<p><p>The physicochemical heterogeneity found on amorphous surfaces leads to a complex interaction of adsorbate molecules with topological and undercoordinated defects, which enhance the adsorption capacity and can participate in catalytic reactions. The identification and analysis of the adsorption structure observed on amorphous surfaces require novel tools that allow the segmentation of the surfaces into complex-shaped regions that contrast with the periodic patterns found on crystalline surfaces. We propose a Random Forest (RF) classifier that segments the surface into regions that can then be further analyzed and classified to reveal the dynamics of the interaction with the adsorbate. The RF segmentation is applied to the surface density map of the adsorbed molecules and employs multiple features (intensity, gradient, and the eigenvalues of the Hessian matrix) which are nonlocal and allow a better identification of the adsorption structures. The segmentation depends on a set of parameters that specify the training set and can be tailored to serve the specific purpose of the segmentation. Here, we consider an example in which we aim to separate highly heterogeneous regions from weakly heterogeneous regions. We demonstrate that the RF segmentation is able to separate the surface into a fully connected weakly heterogeneous region (whose behavior is somehow similar to crystalline surfaces and has an exponential distribution of the residence time) and a very heterogeneous region characterized by a complex residence-time distribution, which is generated by the undercoordinated defects and is responsible for the peculiar characteristics of the amorphous surface.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"7597-7610"},"PeriodicalIF":5.5000,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11391580/pdf/","citationCount":"0","resultStr":"{\"title\":\"Learning Adsorption Patterns on Amorphous Surfaces.\",\"authors\":\"Mattia Turchi, Sandra Galmarini, Ivan Lunati\",\"doi\":\"10.1021/acs.jctc.4c00702\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The physicochemical heterogeneity found on amorphous surfaces leads to a complex interaction of adsorbate molecules with topological and undercoordinated defects, which enhance the adsorption capacity and can participate in catalytic reactions. The identification and analysis of the adsorption structure observed on amorphous surfaces require novel tools that allow the segmentation of the surfaces into complex-shaped regions that contrast with the periodic patterns found on crystalline surfaces. We propose a Random Forest (RF) classifier that segments the surface into regions that can then be further analyzed and classified to reveal the dynamics of the interaction with the adsorbate. The RF segmentation is applied to the surface density map of the adsorbed molecules and employs multiple features (intensity, gradient, and the eigenvalues of the Hessian matrix) which are nonlocal and allow a better identification of the adsorption structures. The segmentation depends on a set of parameters that specify the training set and can be tailored to serve the specific purpose of the segmentation. Here, we consider an example in which we aim to separate highly heterogeneous regions from weakly heterogeneous regions. We demonstrate that the RF segmentation is able to separate the surface into a fully connected weakly heterogeneous region (whose behavior is somehow similar to crystalline surfaces and has an exponential distribution of the residence time) and a very heterogeneous region characterized by a complex residence-time distribution, which is generated by the undercoordinated defects and is responsible for the peculiar characteristics of the amorphous surface.</p>\",\"PeriodicalId\":45,\"journal\":{\"name\":\"Journal of Chemical Theory and Computation\",\"volume\":\" \",\"pages\":\"7597-7610\"},\"PeriodicalIF\":5.5000,\"publicationDate\":\"2024-09-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11391580/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Chemical Theory and Computation\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://doi.org/10.1021/acs.jctc.4c00702\",\"RegionNum\":1,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/8/26 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q2\",\"JCRName\":\"CHEMISTRY, PHYSICAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Theory and Computation","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/acs.jctc.4c00702","RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/8/26 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
Learning Adsorption Patterns on Amorphous Surfaces.
The physicochemical heterogeneity found on amorphous surfaces leads to a complex interaction of adsorbate molecules with topological and undercoordinated defects, which enhance the adsorption capacity and can participate in catalytic reactions. The identification and analysis of the adsorption structure observed on amorphous surfaces require novel tools that allow the segmentation of the surfaces into complex-shaped regions that contrast with the periodic patterns found on crystalline surfaces. We propose a Random Forest (RF) classifier that segments the surface into regions that can then be further analyzed and classified to reveal the dynamics of the interaction with the adsorbate. The RF segmentation is applied to the surface density map of the adsorbed molecules and employs multiple features (intensity, gradient, and the eigenvalues of the Hessian matrix) which are nonlocal and allow a better identification of the adsorption structures. The segmentation depends on a set of parameters that specify the training set and can be tailored to serve the specific purpose of the segmentation. Here, we consider an example in which we aim to separate highly heterogeneous regions from weakly heterogeneous regions. We demonstrate that the RF segmentation is able to separate the surface into a fully connected weakly heterogeneous region (whose behavior is somehow similar to crystalline surfaces and has an exponential distribution of the residence time) and a very heterogeneous region characterized by a complex residence-time distribution, which is generated by the undercoordinated defects and is responsible for the peculiar characteristics of the amorphous surface.
期刊介绍:
The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.