Advancing scanning probe microscopy simulations: A decade of development in probe-particle models

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68378271%3A_____%2F24%3A00599574" target="_blank" >RIV/68378271:_____/24:00599574 - isvavai.cz</a>

Výsledek na webu

<a href="https://hdl.handle.net/11104/0357016" target="_blank" >https://hdl.handle.net/11104/0357016</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.cpc.2024.109341" target="_blank" >10.1016/j.cpc.2024.109341</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Advancing scanning probe microscopy simulations: A decade of development in probe-particle models

Popis výsledku v původním jazyce

The Probe-Particle Model combines theories designed for the simulation of scanning probe microscopy experiments, employing non-reactive, flexible tip apices to achieve sub-molecular resolution. In the article, we present the latest version of the Probe-Particle Model implemented in the open-source ppafm package, highlighting substantial advancements in accuracy, computational performance, and user-friendliness. To demonstrate this we provide a comprehensive review of approaches for simulating non-contact Atomic Force Microscopy. They vary in complexity from simple Lennard-Jones potential to the latest full-density-based model. We compared those approaches with ab initio calculated references, showcasing their respective merits. All parts of the ppafm package have undergone acceleration by 1-2 orders of magnitude using OpenMP and OpenCL technologies. The updated package includes an interactive graphical user interface and seamless integration into the Python ecosystem via pip, facilitating advanced scripting and interoperability with other software. This adaptability positions ppafm as an ideal tool for high-throughput applications, including the training of machine learning models for the automatic recovery of atomic structures from nc-AFM measurements. We envision significant potential for this application in future single-molecule analysis, synthesis, and advancements in surface science in general. Additionally, we discuss simulations of other sub-molecular scanning-probe imaging techniques, such as bond-resolved scanning tunneling microscopy and Kelvin probe force microscopy, all built on the robust foundation of the Probe-Particle Model. Altogether this demonstrates the broad impact of the model across diverse domains of on-surface science and molecular chemistry.

Název v anglickém jazyce

Advancing scanning probe microscopy simulations: A decade of development in probe-particle models

Popis výsledku anglicky

The Probe-Particle Model combines theories designed for the simulation of scanning probe microscopy experiments, employing non-reactive, flexible tip apices to achieve sub-molecular resolution. In the article, we present the latest version of the Probe-Particle Model implemented in the open-source ppafm package, highlighting substantial advancements in accuracy, computational performance, and user-friendliness. To demonstrate this we provide a comprehensive review of approaches for simulating non-contact Atomic Force Microscopy. They vary in complexity from simple Lennard-Jones potential to the latest full-density-based model. We compared those approaches with ab initio calculated references, showcasing their respective merits. All parts of the ppafm package have undergone acceleration by 1-2 orders of magnitude using OpenMP and OpenCL technologies. The updated package includes an interactive graphical user interface and seamless integration into the Python ecosystem via pip, facilitating advanced scripting and interoperability with other software. This adaptability positions ppafm as an ideal tool for high-throughput applications, including the training of machine learning models for the automatic recovery of atomic structures from nc-AFM measurements. We envision significant potential for this application in future single-molecule analysis, synthesis, and advancements in surface science in general. Additionally, we discuss simulations of other sub-molecular scanning-probe imaging techniques, such as bond-resolved scanning tunneling microscopy and Kelvin probe force microscopy, all built on the robust foundation of the Probe-Particle Model. Altogether this demonstrates the broad impact of the model across diverse domains of on-surface science and molecular chemistry.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10302 - Condensed matter physics (including formerly solid state physics, supercond.)

Projekt

<a href="/cs/project/GM22-06008M" target="_blank" >GM22-06008M: Počítačový návrh templatoveho sestavování, replikace a syntézy na iontových površích</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2024

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Computer Physics Communications

ISSN

0010-4655

e-ISSN

1879-2944

Svazek periodika

305

Číslo periodika v rámci svazku

Dec

Stát vydavatele periodika

NL - Nizozemsko

Počet stran výsledku

12

Strana od-do

109341

Kód UT WoS článku

001295853800001

EID výsledku v databázi Scopus

2-s2.0-85201066796