arXiv subjects

Niko Oinonen

Publications and source records attributed to Niko Oinonen.

4 recordsLinked to original sources

arXiv2025

Improving atomic force microscopy structure discovery via style-translation

Atomic force microscopy (AFM) is a key tool for characterising nanoscale structures, with functionalised tips now offering detailed images of the atomic structure. In parallel, AFM simulations using the particle probe model provide a cost-effective approach for rapid AFM image generation. Using state-of-the-art machine learning models and substantial simulated datasets, properties such as molecular structure, electrostatic potential, and molecular graph can be predicted from AFM images. However, transferring model performance from simulated to experimental AFM images poses challenges due to the subtle variations in real experimental data compared to the seemingly flawless simulations. In this study, we explore style translation to augment simulated images and improve the predictive performance of machine learning models in surface property analysis. We reduce the style gap between simulated and experimental AFM images and demonstrate the method's effectiveness in enhancing structure discovery models through local structural property distribution comparisons. This research presents a novel approach to improving the efficiency of machine learning models in the absence of labelled experimental data.

cond-mat.mtrl-sci↗

arXiv2024

Advancing Scanning Probe Microscopy Simulations: A Decade of Development in Probe-Particle Models

The Probe-Particle Model combine 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 userfriendliness. 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 n 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 on-surface science in general. Additionally, we discuss simulations of other sub-molecular scanning-probe imaging techniques, such as bond-resolved scanning tunnelling 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 surface science and molecular chemistry.

cond-mat.mes-hall↗

arXiv2023

Automated Structure Discovery for Scanning Tunneling Microscopy

Scanning tunnelling microscopy (STM) with a functionalized tip apex reveals the geometric and electronic structure of a sample within the same experiment. However, the complex nature of the signal makes images difficult to interpret and has so far limited most research to planar samples with a known chemical composition. Here, we present automated structure discovery for STM (ASD-STM), a machine learning tool for predicting the atomic structure directly from an STM image, by building upon successful methods for structure discovery in non-contact atomic force microscopy (nc-AFM). We apply the method on various organic molecules and achieve good accuracy on structure predictions and chemical identification on a qualitative level, while highlighting future development requirements to ASD-STM. This method is directly applicable to experimental STM images of organic molecules, making structure discovery available for a wider SPM audience outside of nc-AFM. This work also opens doors for more advanced machine learning methods to be developed for STM discovery.

cond-mat.mtrl-sci↗

arXiv2021

Electrostatic Discovery Atomic Force Microscopy

While offering unprecedented resolution of atomic and electronic structure, Scanning Probe Microscopy techniques have found greater challenges in providing reliable electrostatic characterization at the same scale. In this work, we introduce Electrostatic Discovery Atomic Force Microscopy, a machine learning based method which provides immediate quantitative maps of the electrostatic potential directly from Atomic Force Microscopy images with functionalized tips. We apply this to characterize the electrostatic properties of a variety of molecular systems and compare directly to reference simulations, demonstrating good agreement. This approach opens the door to reliable atomic scale electrostatic maps on any system with minimal computational overhead.

cond-mat.mes-hall↗