Scanning Probe Microscopy Imaging Research Articles

Real-Time Imaging of On-Surface Ullmann Polymerization Reveals an Inhibiting Effect of Adatoms.

Ullmann coupling is a widely used reaction for the on-surface growth of low-dimensional carbon nanomaterials. The irreversible nature of this reaction prevents the "self-healing" of defects, and a detailed knowledge of its mechanism is therefore essential to enable the growth of extended ordered structures. However, the dynamics of the Ullmann polymerization remain largely unexplored, as coupling events occur on a timescale faster than conventional scanning probe microscopy imaging frequencies. Here, we reveal the dynamics of these surface events using high-speed variable-temperature scanning tunneling microscopy (STM) (10 frames per second). Performing the measurements at the onset reaction temperatures provides an unprecedented description of the evolution of organometallic (OM) and covalent surface species during the Ullmann polymerization of para-dibromobenzene on Cu(110). Our results demonstrate the existence of an intermediate OM phase with Cu adatoms that inhibits the polymerization. These observations now complete the picture of the pathways of on-surface Ullmann polymerization, which includes the complex interplay of the phenylene moieties and metal atoms. Our work demonstrates the unique capability of high-speed STM to capture the dynamics of molecular self-assembly and coupling.

Mechanical Properties of Mullite Investigated by Nanoindentation

The mechanical behavior of sintered mullite material was studied using nanoindentation tests. Mullite compact was obtained by cold pressing sol-gel synthesized mullite precursor powder and sintering at 1550 °C. Analysis of the microstructural parameters and phase composition was done by XRD (X-ray diffraction) and SEM-EDS (scanning electron microscopy with energy dispersive X-ray spectrometry). A Berkovich indenter was employed for nanoindentation measurements at various loads (1000-9000 µN). After each test, in situ SPM (scanning probe microscopy) imaging was performed. The XRD pattern of sintered mullite displayed peaks of mullite (93.3%) and corundum (6.7%). Results revealed average values of hardness and elastic modulus of sintered mullite as 15.55 GPa and 174.37 GPa, respectively. Moreover, nanoindentation results indicated that mullite follows the Hall-Petch hardening relation due to the presence of grains with a size range of 0.2-2 µm. Indentation in areas with smaller grains exhibits higher hardness values. Post-test SPM images disclosed the presence of pile-ups around the indents, which were formed under loads higher than 3000 µN.

Advances in probing single biomolecules: From DNA bases to glycans

AbstractImaging biomolecules in real space is crucial for gaining a comprehensive understanding of the properties and functions of biological systems at the most fundamental level. Among the various imaging techniques available for biomolecules and their assembled nanostructures, scanning probe microscopy (SPM) provides a powerful and nondestructive imaging option. SPM is unique in visualizing intrinsically disordered biomolecules at the nanometer scale (e.g., glycans). This review highlights recent achievements in studying biomolecules using SPM technique, focusing on DNA bases, amino acids, proteins, and glycans. The atomic‐level analysis of biomolecules made possible by SPM allows for a more accurate definition of the local structure–property relationship. High‐resolution SPM imaging of single biomolecules offers a new way to study basic processes of life at the molecular level.

Probe microscopy is all you need * * Notice: This manuscript has been authored by UT-Battelle, LLC, under Contract No. DE-AC0500OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published

We pose that microscopy offers an ideal real-world experimental environment for the development and deployment of active Bayesian and reinforcement learning methods. Indeed, the tremendous progress achieved by machine learning (ML) and artificial intelligence over the last decade has been largely achieved via the utilization of static data sets, from the paradigmatic MNIST to the bespoke corpora of text and image data used to train large models such as GPT3, DALL·E and others. However, it is now recognized that continuous, minute improvements to state-of-the-art do not necessarily translate to advances in real-world applications. We argue that a promising pathway for the development of ML methods is via the route of domain-specific deployable algorithms in areas such as electron and scanning probe microscopy and chemical imaging. This will benefit both fundamental physical studies and serve as a test bed for more complex autonomous systems such as robotics and manufacturing. Favorable environment characteristics of scanning and electron microscopy include low risk, extensive availability of domain-specific priors and rewards, relatively small effects of exogenous variables, and often the presence of both upstream first principles as well as downstream learnable physical models for both statics and dynamics. Recent developments in programmable interfaces, edge computing, and access to application programming interfaces (APIs) facilitating microscope control, all render the deployment of ML codes on operational microscopes straightforward. We discuss these considerations and hope that these arguments will lead to create novel set of development targets for the ML community by accelerating both real world ML applications and scientific progress.

Microscopic evidences of nanocomposite structure in hard and optically transparent ternary AlSiN coating

In this work AlSiN ternary coatings were deposited by radio frequency magnetron sputtering in Ar/N2 reactive atmosphere. AlSi alloy target of composition 86:14 wt% has been used to deposit the coatings on float glass substrate by varying the Ar:N2 ratio i.e., 20:4, 20:6, 20:8, 20:13 and 20:15. The effect of different Ar:N2 ratio on microstructure, mechanical and optical property were studied using x-ray diffraction (XRD), stylus profilometry, Field Emission Scanning Electron Microscopy (FESEM), Energy Dispersive X-ray Spectroscopy (EDS), High Resolution Transmission Electron Microscopy (HRTEM), UV–visible spectrometry and manoindentation. The XRD measurements show the formation h-AlN phase for coating deposited for 20:6 only and confirm the crystalline nature of the coating whereas at higher and lower Ar: N2 ratio, the measurements show the amorphous nature of the coatings. 20:6 deposited coating developed a wurtzite-AlN nanocrystalline structure. The thickness of the coatings decreased with respect to the increasing Ar: N2 ratio. The FESEM shows uneven and dense microstructure of the coatings. HRTEM study confirms the amorphous nature of 20:4 and 20:13 Ar: N2 ratio, and the polycrystalline nature of 20:6 coating. The elemental compositions were confirmed by EDS. The optical transparency of the coating was more than 95% for all the coatings in the visible range. The roughness of the samples was also measured in scanning probe microscopy imaging that showed an average roughness value Ra of ∼3 nm. The maximum hardness of 31 GPa was observed for the coating prepared with an Ar: N2 ratio of 20:6.

Exploring leakage in dielectric films via automated experiments in scanning probe microscopy

Electronic conduction pathways in dielectric thin films are explored using automated experiments in scanning probe microscopy (SPM). Here, we use large field of view scanning to identify the position of localized conductive spots and develop an SPM workflow to probe their dynamic behavior at higher spatial resolution as a function of time, voltage, and scanning process in an automated fashion. Using this approach, we observe the variable behaviors of the conductive spots in a 20-nm-thick ferroelectric Hf0.54Zr0.48O2 film, where conductive spots disappear and reappear during continuous scanning. There are also fresh conductive spots that develop during scanning. The automated workflow is universal and can be integrated into a wide range of microscopy techniques, including SPM, electron microscopy, optical microscopy, and chemical imaging.

Synthesis of Giant Dendritic Polyphenylenes with 366 and 546 Carbon Atoms and Their High-vacuum Electrospray Deposition.

Dendritic polyphenylenes (PPs) can serve as precursors of nanographenes (NGs) if their structures represent 2D projections without overlapping benzene rings. Here, we report the synthesis of two giant dendritic PPs fulfilling this criteria with 366 and 546 carbon atoms by applying a “layer‐by‐layer” extension strategy. Although our initial attempts on their cyclodehydrogenation toward the corresponding NGs in solution were unsuccessful, we achieved their deposition on metal substrates under ultrahigh vacuum through the electrospray technique. Scanning probe microscopy imaging provides valuable information on the possible thermally induced partial planarization of such giant dendritic PPs on a metal surface.

Deep Bayesian local crystallography

The advent of high-resolution electron and scanning probe microscopy imaging has opened the floodgates for acquiring atomically resolved images of bulk materials, 2D materials, and surfaces. This plethora of data contains an immense volume of information on materials structures, structural distortions, and physical functionalities. Harnessing this knowledge regarding local physical phenomena necessitates the development of the mathematical frameworks for extraction of relevant information. However, the analysis of atomically resolved images is often based on the adaptation of concepts from macroscopic physics, notably translational and point group symmetries and symmetry lowering phenomena. Here, we explore the bottom-up definition of structural units and symmetry in atomically resolved data using a Bayesian framework. We demonstrate the need for a Bayesian definition of symmetry using a simple toy model and demonstrate how this definition can be extended to the experimental data using deep learning networks in a Bayesian setting, namely rotationally invariant variational autoencoders.

Enabling autonomous scanning probe microscopy imaging of single molecules with deep learning.

Scanning probe microscopies allow investigating surfaces at the nanoscale, in real space and with unparalleled signal-to-noise ratio. However, these microscopies are not used as much as it would be expected considering their potential. The main limitations preventing a broader use are the need of experienced users, the difficulty in data analysis and the time-consuming nature of experiments that require continuous user supervision. In this work, we addressed the latter and developed an algorithm that controlled the operation of an Atomic Force Microscope (AFM) that, without the need of user intervention, allowed acquiring multiple high-resolution images of different molecules. We used DNA on mica as a model sample to test our control algorithm, which made use of two deep learning techniques that so far have not been used for real time SPM automation. One was an object detector, YOLOv3, which provided the location of molecules in the captured images. The second was a Siamese network that could identify the same molecule in different images. This allowed both performing a series of images on selected molecules while incrementing the resolution, as well as keeping track of molecules already imaged at high resolution, avoiding loops where the same molecule would be imaged an unlimited number of times. Overall, our implementation of deep learning techniques brings SPM a step closer to full autonomous operation.

SECM Investigation of Carbon Composite Thermoplastic Electrodes.

Thermoplastic electrodes (TPEs) are carbon composite electrodes consisting of graphite and thermoplastic polymer binder. TPE production is a solvent-based method, which makes it easy to fabricate and pattern into complex geometries, contrary to classical carbon composite electrodes. Depending on the composition (carbon type, binder, and composition ratio), TPEs can give excellent electrochemical performance and high conductivity. However, these TPEs are relatively new electrode materials, and thorough electrochemical characterization is still missing to understand and predict why large differences between TPEs exist. We used scanning electrochemical microscopy (SECM) as a screening tool to characterize TPEs. SECM data treatment based on scanning probe microscopy imaging allows a fast and easy comparison of the numerous images, as well as the optimization of the preparation. Experiments suggest that TPEs behave as a network of interacting microelectrodes made by electrochemically active islands isolated between less active areas. Higher carbon content in TPEs is not always indicative of more uniform electrodes with better electrochemical performances. Using various SECM redox probes, it is possible to select a specific graphite or polymer type for the analyte of interest. For example, TPEs made with COC:3569 are the best compromise for general detection, whereas PMMA:11 μm is better suited for catechol-like polyphenol analysis.

Nanoscratch self-healing characteristics of polyvinyl polymer thin films embedded with Al2O3 nanoparticles with thermal and UV energy reactivity

Self-healing materials can partially or completely heal the damage done to them, and it is expected that their original function will be thereby restored. Herein, we report a novel self-healing polyvinyl (Sh-PV) containing functional polymer that reacts to thermal and ultraviolet (UV) energy. The structure of Sh-PV was characterized by fourier transform infrared spectroscopy (FTIR) and nuclear magnetic resonance spectroscopy (1H NMR). In addition, aluminum oxide (Al2O3) inorganic nanoparticles (NPs) were added and hybridized to improve their poor self-healing efficiency and surface hardness of the coated thin film. Mechanical nanoscratch testing and scanning probe microscopy (SPM) imaging of surface using a nanoindenter were performed to investigate the healing ability of self-healing thin films. The organic–inorganic hybrid self-healing polymer thin film exhibited a 10 % improvement in surface hardness as well as 100 % healing against nanoscale damage compared to virgin self-healing polymers. Here, we discuss and evaluate the optimized method and mechanism of the self-healing system based on the results of self-healing materials and physical recovery methods for healing surface damage.

Construction and Scanning Probe Microscopy Imaging of Two-dimensional Nanomaterials

Several fabrication technologies for molecular level ultra-thin films, from organic to organic–inorganic hybrids, are introduced using the surface imaging technology of scanning probe microscopy (SPM). Electrochemical scanning tunneling microscopy (EC-STM), atomic force microscopy (AFM) and related techniques enable the observation of the surface of 2D materials in near real-time and in real-space. The combination of 2D materials and SPM technology opens up a new avenue of surface and material science, despite its many restrictions.

New imaging modes for analyzing suspended ultra-thin membranes by double-tip scanning probe microscopy

Scanning probe microscopy (SPM) techniques are amongst the most important and versatile experimental methods in surface- and nanoscience. Although their measurement principles on rigid surfaces are well understood and steady progress on the instrumentation has been made, SPM imaging on suspended, flexible membranes remains difficult to interpret. Due to the interaction between the SPM tip and the flexible membrane, morphological changes caused by the tip can lead to deformations of the membrane during scanning and hence significantly influence measurement results. On the other hand, gaining control over such modifications can allow to explore unknown physical properties and functionalities of such membranes. Here, we demonstrate new types of measurements that become possible with two SPM instruments (atomic force microscopy, AFM, and scanning tunneling microscopy, STM) that are situated on opposite sides of a suspended two-dimensional (2D) material membrane and thus allow to bring both SPM tips arbitrarily close to each other. One of the probes is held stationary on one point of the membrane, within the scan area of the other probe, while the other probe is scanned. This way new imaging modes can be obtained by recording a signal on the stationary probe as a function of the position of the other tip. The first example, which we term electrical cross-talk imaging (ECT), shows the possibility of performing electrical measurements across the membrane, potentially in combination with control over the forces applied to the membrane. Using ECT, we measure the deformation of the 2D membrane around the indentation from the AFM tip. In the second example, which we term mechanical cross-talk imaging (MCT), we disentangle the mechanical influence of a scanning probe tip (e.g. AFM) on a freestanding membrane by means of independently recording the response of the opposing tip. In this way we are able to separate the tip-induced membrane deformation topography from the (material-dependent) force between the tip and the membrane. Overall, the results indicate that probing simultaneously both surfaces of ultra-thin membranes, such as suspended 2D materials, could provide novel insights into the electronic properties of the materials.

Physical and mechanical properties of polyvinylidene fluoride - Short sugar palm fiber nanocomposites

Abstract The characterization of natural fiber composites has become of paramount importance. The aim of this work is to prepare, produce, and investigate the mechanical, nanomechanical, and physical properties of polyvinylidene fluoride (PVDF) reinforced with short sugar palm fiber (SSPF) composites. Preparation involves successive phases: a melt-mixing approach and a hot/cold compression molding procedure. The mechanical test examines the flexural and tensile strengths. This work introduces nanomechanical testing through the quasistatic nanoindentation to measure the hardness, fracture toughness, stiffness, and Young's modulus. Physical properties are analyzed by measuring the composites' density, water absorption, moisture content, and thickness swelling. Mechanical properties displayed good flexural and tensile enhancements. The use of short fiber led to adequate interfacial bonding between the fiber and matrix. Composites exhibited high compatibility, strength, and a homogenous structure in the fiber-matrix. Nanomechanical test displayed a dynamic modulus mapping on the fiber. The scan line analysis and in-situ scanning probe microscopy (SPM) imaging presented improved hardness, Young's modulus, stiffness, and fracture phenomena. The composites exhibited outstanding physical properties and excellent resistance to water absorption, moisture content, and thickness swelling. The novel findings provide insight on how biocomposite materials can be utilized in various engineering applications. This signifies their high competency and applicability for green production.

Scanning Line Probe Microscopy: Beyond the Point Probe.

Scanning probe microscopy (SPM) techniques have become indispensable tools for studying nano- and microscale materials and processes but suffer from a trade-off between resolution and areal scan rate that limits their utility for a number of applications and sample types. Here, we present a novel approach to SPM imaging based on combining nonlocal scanning line probes with compressed sensing (CS) signal analysis methods. Using scanning electrochemical microscopy (SECM) as an exemplar SPM technique, we demonstrate this approach using continuous microband electrodes, or line probes, which are used to perform chemical imaging of electrocatalytic Pt discs deposited on an inert substrate. These results demonstrate the potential to achieve high areal SPM imaging rates using nonlocal scanning probes and CS image reconstruction.

SPM Imaging of DNA, Redox Proteins and Bacteria Spores Under in-Situ Conditions

Scanning probe microscopy (SPM) can be successfully used in biological investigations1. Scanning tunnelling microscopy (STM) and atomic force microscopy (AFM) are two main SPM techniques and they are capable of imaging biological objects at molecular level under in situ conditions. With this advantage, STM and AFM are applied to study not only the topographical structures of bio-samples in their natural environment, but also their electrochemical properties at liquid-solid interfaces. The electrochemical properties of biomolecules are usually studied by integral electrochemical methods, like cyclic voltammetry. The degree of surface coverage, the surface orientation of enzymes and the activity of a single enzyme remain a question of dispute, however, electrochemical SPM techniques can bring clarification. Electrochemical scanning tunnelling microscopy (EC-STM) and electrochemical atomic force microscopy (EC-AFM) provide visual topological information of biomolecules adsorbed on the electrode surface at single-molecular level. Some experimental issues, such as the requirement of the sample being conductive, potential damage to samples caused by the tunnelling current or tip-sample force, may limit their application. Scanning electrochemical potential microscopy (SECPM), a technique that measures the surface potential distribution at zero current, can be a promising alternative. SECPM shares most of the hardware setup with EC-STM except for the current amplifier being substituted by a potentiometer. It is easy to switch between SECPM and EC-STM to compare the topographical profile of the same area by mapping electron density and surface potential2. In our study, SPM techniques are used to study various biological objects, from nanometer-sized DNA and redox proteins to micrometer-sized bacteria spores. Since high-resolution images of DNA origami nanostructures can be achieved by using AFM3, we use both EC-AFM and SECPM techniques to investigate the morphology and potential-dependent adsorption behaviour of DNA scaffold and origamis4 on the modified HOPG surface. We found DNA scaffold can adsorb on HOPG in a certain potential range, and the adsorption structure changes with the applied electrochemical potential. Horseradish peroxidase (HRP), a redox enzyme, was studied using both, EC-STM and SECPM under in situ conditions5. HRP molecules were adsorbed on highly oriented pyrolytic graphite (HOPG) surfaces and imaged in phosphate buffered saline. We found that SECPM shows a better resolution than EC-STM in imaging this biomolecule. SECPM is also capable of measuring the surface charge distribution of the adsorbed biomolecules at the electrochemical interfaces. AFM in liquid was used to investigate the morphology and cellular process of Streptomycetes venezuelae both the wild type and the mutant6. To immobilize the bacteria on the surface for imaging, we use SiC patterned by photolithography with hole arrays (1.5×1.5×0.6 µm) to trap the bacteria and then measure under the physiological condition. The designed hole arrays trap the bacteria without causing any denaturation and due to the high electronic conductivity, they can serve as the working electrode under electrochemical conditions for EC-AFM and SECPM studies. EC-AFM was applied to image the morphology of the bacterial spore under different potential, and we found the morphology of the spore didn’t change in the wide potential window. (1) Choi, E.; Kim, A.; Son, H.; Pyo, S. G. J. Nanosci. Nanotechnol. 2014, 14 (1), 924. (2) Herpich, M.; Friedl, J.; Stimming, U. In Surface Science Tools for Nanomaterials Characterization; Springer Berlin Heidelberg: Berlin, Heidelberg, 2015; pp 1–67. (3) Bald, I.; Keller, A. Molecules 2014, 19 (9), 13803. (4) Kozyra, J.; Ceccarelli, A.; Torelli, E.; Lopiccolo, A.; Gu, J.-Y.; Fellermann, H.; Stimming, U.; Krasnogor, N. ACS Synth. Biol. 2017, 6 (7), 1140. (5) Baier, C.; Stimming, U. Angew. Chem. Int. Ed. Engl. 2009, 48 (30), 5542. (6) Santos-Beneit, F.; Gu, J.-Y.; Stimming, U.; Errington, J. Heliyon. Accepted

Intermittent impact dynamics of a cantilever scanning a surface at high speed

In contact-mode scanning probe microscopy (SPM), the cantilever's dynamics are conventionally investigated by assuming the tip to be always in contact with the sample's surface. At high scanning speeds, however, the cantilever's inertia becomes dominant and the tip can therefore completely detach from the surface and start impacting upon it. Experiments at the macro-scale cannot emulate the complex micro-scale dynamics, as the system exhibits negligible effects due to meniscus forces and the surrounding medium's squeeze film damping; however, they can provide qualitative insight into the cantilever's dynamics at high frequencies, corresponding to those likely to be excited during video-rate SPM imaging. This paper investigates such intermittent impact dynamics for an upscaled cantilever, analytically, numerically, and experimentally. In contact-mode scanning, a critical scan speed exists beyond which the cantilever's tip loses contact with the sample's surface; a closed-form expression for this contact loss frequency is derived. At high scan speeds, impacts cause the cantilever to switch between different contact regimes: in-, off-, and grazing-contact; within each regime, the system's modal configuration is different. Experimentally-obtained Poincare maps indicate quasi-periodic behaviour at frequencies for which the response is repetitive, as is also predicted by the model. Intermittent impacts excite the sub- and super-harmonics of the excitation frequency, which are related to the natural frequencies of different system configurations based on the “effective” tip-end boundary conditions. The cantilever's response exhibits several phenomena, such as modal transition, beating, grazing, and possible chaotic behaviour, depending upon the relation between the excitation harmonics and the natural frequencies.

Feature extraction via similarity search: application to atom finding and denoising in electron and scanning probe microscopy imaging

We develop an algorithm for feature extraction based on structural similarity and demonstrate its application for atom and pattern finding in high-resolution electron and scanning probe microscopy images. The use of the combined local identifiers formed from an image subset and appended Fourier, or other transform, allows tuning selectivity to specific patterns based on the nature of the recognition task. The proposed algorithm is implemented in Pycroscopy, a community-driven scientific data analysis package, and is accessible through an interactive Jupyter notebook available on GitHub.

Nanometrology and super-resolution imaging with DNA.

Structural DNA nanotechnology is revolutionizing the ways researchers construct arbitrary shapes and patterns in two and three dimensions on the nanoscale. Through Watson-Crick base pairing, DNA can be programmed to form nanostructures with high predictability, addressability, and yield. The ease with which structures can be designed and created has generated great interest for using DNA for a variety of metrology applications, such as in scanning probe microscopy and super-resolution imaging. An additional advantage of the programmable nature of DNA is that mechanisms for nanoscale metrology of the structures can be integrated within the DNA objects by design. This programmable structure-property relationship provides a powerful tool for developing nanoscale materials and smart rulers.

Systematic Hysteresis Compensator Design based on Extended Unparallel Prandtl-Ishlinskii Model for SPM Imaging Rectification

Scanning probe microscopy (SPM) technology plays the irreplaceable role in investigating micro/nano world, which has been bringing tremendous development opportunities to various fields. To enhance maneuverability, SPM can be modified into a nanomanipulation system with its scanning probe as the end-effector. The probe is commonly mounted on smart material based actuators to generate precise motion with nanometer level resolution. However, instinctive hysteretic characteristics ubiquitously exist in smart material actuators, which degrade their arbitrary positioning precision. To effectively represent and further reduce complex hysteretic effects, this paper proposes to utilize the modified Prandtl-Ishlinskii (PI) model: extended unparallel PI (EUPI) model, which possesses advantages such as the flexible modeling capability (compared to the prevalently implemented modified PI models) and the easy-to-use property for construction and identification (compared to the well known Preisach model and the Generalized PI (GPI) model). To effectively reduce complex hysteresis, the EUPI model based compensator (IMUPI compensator) is required to be flexible and precise. To efficiently design such a compensator satisfying stability requirement, this study proposes a systematic approach, including stabilizing gain selection and analytical calculation of boundary gains of the EUPI irreversible component. As a demonstration, satisfactorily precise IMUPI compensator was established according to this systematic design approach and tested through simulations on rectifying Atomic Force Microscopy (AFM, one special SPM) imaging process distorted by complex hysteresis.