{"title":"压力对非晶硅原子结构的影响","authors":"Nicolás Amigo","doi":"10.1007/s00894-025-06470-0","DOIUrl":null,"url":null,"abstract":"<div><h3>Context</h3><p>This study explores how hydrostatic pressure influences the atomic structure of amorphous silicon. As pressure increases, the material undergoes densification, reflected in the shift of radial distribution functions and bond angle distributions. While the short-range order undergoes relatively small structural variations, the medium-range order exhibits significant structural rearrangements, including changes in coordination numbers and atomic connectivity. These pressure-induced transformations favor simpler, more compact atomic configurations. The resulting structural reorganization leads to increased internal energy and reduced atomic volume, revealing the energetic cost of compression. Overall, the findings offer insights into the fundamental behavior of amorphous silicon under extreme conditions.</p><h3>Methods</h3><p>Molecular dynamics simulations were conducted using the Tersoff potential for LAMMPS to study amorphous silicon. The samples were prepared using a cooling rate of 10<span>\\(^{11}\\)</span> K/s and then relaxed at 100 K at six different pressures: 0, 2, 4, 6, 8, 10 GPa. Structural properties were calculated using radial distribution functions, bond angle distribution, Voronoi analysis, and atomic volumes, and network analysis was conducted to quantify connectivity among four-coordinated atoms. Calculations were performed using the OVITO software and Python programming language.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5000,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Pressure effect on the atomic structure of amorphous silicon\",\"authors\":\"Nicolás Amigo\",\"doi\":\"10.1007/s00894-025-06470-0\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Context</h3><p>This study explores how hydrostatic pressure influences the atomic structure of amorphous silicon. As pressure increases, the material undergoes densification, reflected in the shift of radial distribution functions and bond angle distributions. While the short-range order undergoes relatively small structural variations, the medium-range order exhibits significant structural rearrangements, including changes in coordination numbers and atomic connectivity. These pressure-induced transformations favor simpler, more compact atomic configurations. The resulting structural reorganization leads to increased internal energy and reduced atomic volume, revealing the energetic cost of compression. Overall, the findings offer insights into the fundamental behavior of amorphous silicon under extreme conditions.</p><h3>Methods</h3><p>Molecular dynamics simulations were conducted using the Tersoff potential for LAMMPS to study amorphous silicon. The samples were prepared using a cooling rate of 10<span>\\\\(^{11}\\\\)</span> K/s and then relaxed at 100 K at six different pressures: 0, 2, 4, 6, 8, 10 GPa. Structural properties were calculated using radial distribution functions, bond angle distribution, Voronoi analysis, and atomic volumes, and network analysis was conducted to quantify connectivity among four-coordinated atoms. Calculations were performed using the OVITO software and Python programming language.</p></div>\",\"PeriodicalId\":651,\"journal\":{\"name\":\"Journal of Molecular Modeling\",\"volume\":\"31 9\",\"pages\":\"\"},\"PeriodicalIF\":2.5000,\"publicationDate\":\"2025-08-11\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Molecular Modeling\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://link.springer.com/article/10.1007/s00894-025-06470-0\",\"RegionNum\":4,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Molecular Modeling","FirstCategoryId":"92","ListUrlMain":"https://link.springer.com/article/10.1007/s00894-025-06470-0","RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
Pressure effect on the atomic structure of amorphous silicon
Context
This study explores how hydrostatic pressure influences the atomic structure of amorphous silicon. As pressure increases, the material undergoes densification, reflected in the shift of radial distribution functions and bond angle distributions. While the short-range order undergoes relatively small structural variations, the medium-range order exhibits significant structural rearrangements, including changes in coordination numbers and atomic connectivity. These pressure-induced transformations favor simpler, more compact atomic configurations. The resulting structural reorganization leads to increased internal energy and reduced atomic volume, revealing the energetic cost of compression. Overall, the findings offer insights into the fundamental behavior of amorphous silicon under extreme conditions.
Methods
Molecular dynamics simulations were conducted using the Tersoff potential for LAMMPS to study amorphous silicon. The samples were prepared using a cooling rate of 10\(^{11}\) K/s and then relaxed at 100 K at six different pressures: 0, 2, 4, 6, 8, 10 GPa. Structural properties were calculated using radial distribution functions, bond angle distribution, Voronoi analysis, and atomic volumes, and network analysis was conducted to quantify connectivity among four-coordinated atoms. Calculations were performed using the OVITO software and Python programming language.
期刊介绍:
The Journal of Molecular Modeling focuses on "hardcore" modeling, publishing high-quality research and reports. Founded in 1995 as a purely electronic journal, it has adapted its format to include a full-color print edition, and adjusted its aims and scope fit the fast-changing field of molecular modeling, with a particular focus on three-dimensional modeling.
Today, the journal covers all aspects of molecular modeling including life science modeling; materials modeling; new methods; and computational chemistry.
Topics include computer-aided molecular design; rational drug design, de novo ligand design, receptor modeling and docking; cheminformatics, data analysis, visualization and mining; computational medicinal chemistry; homology modeling; simulation of peptides, DNA and other biopolymers; quantitative structure-activity relationships (QSAR) and ADME-modeling; modeling of biological reaction mechanisms; and combined experimental and computational studies in which calculations play a major role.