Browse
Submit Data
Databases
API
Help

Dataset Information

35 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ultrahigh-resolution imaging of water networks by atomic force microscopy.

ABSTRACT: Local defects in water layers growing on metal surfaces have a key influence on the wetting process at the surfaces; however, such minor structures are undetectable by macroscopic methods. Here, we demonstrate ultrahigh-resolution imaging of single water layers on a copper(110) surface by using non-contact atomic force microscopy (AFM) with molecular functionalized tips at 4.8?K. AFM with a probe tip terminated by carbon monoxide predominantly images oxygen atoms, whereas the contribution of hydrogen atoms is modest. Oxygen skeletons in the AFM images reveal that the water networks containing local defects and edges are composed of pentagonal and hexagonal rings. The results reinforce the applicability of AFM to characterize atomic structures of weakly bonded molecular assemblies.

SUBMITTER: Shiotari A

PROVIDER: S-EPMC5296746 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Ultrahigh-resolution imaging of water networks by atomic force microscopy.

Shiotari Akitoshi A Sugimoto Yoshiaki Y

Nature communications 20170203

Local defects in water layers growing on metal surfaces have a key influence on the wetting process at the surfaces; however, such minor structures are undetectable by macroscopic methods. Here, we demonstrate ultrahigh-resolution imaging of single water layers on a copper(110) surface by using non-contact atomic force microscopy (AFM) with molecular functionalized tips at 4.8 K. AFM with a probe tip terminated by carbon monoxide predominantly images oxygen atoms, whereas the contribution of hyd ...[more]

PMID: 28155856

Similar Datasets

Weakly perturbative imaging of interfacial water with submolecular resolution by atomic force microscopy.

Project description:Scanning probe microscopy has been extensively applied to probe interfacial water in many interdisciplinary fields but the disturbance of the probes on the hydrogen-bonding structure of water has remained an intractable problem. Here, we report submolecular-resolution imaging of the water clusters on a NaCl(001) surface within the nearly noninvasive region by a qPlus-based noncontact atomic force microscopy. Comparison with theoretical simulations reveals that the key lies in probing the weak high-order electrostatic force between the quadrupole-like CO-terminated tip and the polar water molecules at large tip-water distances. This interaction allows the imaging and structural determination of the weakly bonded water clusters and even of their metastable states with negligible disturbance. This work may open an avenue for studying the intrinsic structure and dynamics of ice or water on surfaces, ion hydration, and biological water with atomic precision.

| S-EPMC5760619 | biostudies-other

Super-resolution visible photoactivated atomic force microscopy.

Project description:Imaging the intrinsic optical absorption properties of nanomaterials with optical microscopy (OM) is hindered by the optical diffraction limit and intrinsically poor sensitivity. Thus, expensive and destructive electron microscopy (EM) has been commonly used to examine the morphologies of nanostructures. Further, while nanoscale fluorescence OM has become crucial for investigating the morphologies and functions of intracellular specimens, this modality is not suitable for imaging optical absorption and requires the use of possibly undesirable exogenous fluorescent molecules for biological samples. Here we demonstrate super-resolution visible photoactivated atomic force microscopy (pAFM), which can sense intrinsic optical absorption with ~8 nm resolution. Thus, the resolution can be improved down to ~8 nm. This system can detect not only the first harmonic response, but also the higher harmonic response using the nonlinear effect. The thermoelastic effects induced by pulsed laser irradiation allow us to obtain visible pAFM images of single gold nanospheres, various nanowires, and biological cells, all with nanoscale resolution. Unlike expensive EM, the visible pAFM system can be simply implemented by adding an optical excitation sub-system to a commercial atomic force microscope.

| S-EPMC6062039 | biostudies-literature

Imaging Water Thin Films in Ambient Conditions Using Atomic Force Microscopy.

Project description:All surfaces exposed to ambient conditions are covered by a thin film of water. Other than at high humidity conditions, i.e., relative humidity higher than 80%, those water films have nanoscale thickness. Nevertheless, even the thinnest film can profoundly affect the physical and chemical properties of the substrate. Information on the structure of these water films can be obtained from spectroscopic techniques based on photons, but these usually have poor lateral resolution. When information with nanometer resolution in the three dimensions is needed, for example for surfaces showing heterogeneity in water affinity at the nanoscale, Atomic Force Microscopy (AFM) is the preferred tool since it can provide such resolution while being operated in ambient conditions. A complication in the interpretation of the data arises when using AFM, however, since, in most cases, direct interaction between a solid probe and a solid surface occurs. This induces strong perturbations of the liquid by the probe that should be controlled or avoided. The aim of this review is to provide an overview of different AFM methods developed to overcome this problem, measuring different interactions between the AFM probe and the water films, and to discuss the type of information about the water film that can be obtained from these interactions.

| S-EPMC5456730 | biostudies-other

Atomic-resolution imaging of rutile TiO2(110)-(1 × 2) reconstructed surface by non-contact atomic force microscopy.

Project description:The structure of the rutile TiO2(110)-(1 × 2) reconstructed surface is a phase induced by oxygen reduction. There is ongoing debate about the (1 × 2) reconstruction, because it cannot be clarified whether the (1 × 2) structure is formed over a wide area or only locally using macroscopic analysis methods such as diffraction. We used non-contact atomic force microscopy, scanning tunneling microscopy, and low-energy electron diffraction at room temperature to characterize the surface. Ti2O3 rows appeared as bright spots in both NC-AFM and STM images observed in the same area. High-resolution NC-AFM images revealed that the rutile TiO2(110)-(1 × 2) reconstructed surface is composed of two domains with different types of asymmetric rows.

| S-EPMC7082707 | biostudies-literature

Stochastic excitation for high-resolution atomic force acoustic microscopy imaging: a system theory approach.

Project description:In this work, a high-resolution atomic force acoustic microscopy imaging technique is developed in order to obtain the local indentation modulus at the nanoscale level. The technique uses a model that gives a qualitative relationship between a set of contact resonance frequencies and the indentation modulus. It is based on white-noise excitation of the tip-sample interaction and uses system theory for the extraction of the resonance modes. During conventional scanning, for each pixel, the tip-sample interaction is excited with a white-noise signal. Then, a fast Fourier transform is applied to the deflection signal that comes from the photodiodes of the atomic force microscopy (AFM) equipment. This approach allows for the measurement of several vibrational modes in a single step with high frequency resolution, with less computational cost and at a faster speed than other similar techniques. This technique is referred to as stochastic atomic force acoustic microscopy (S-AFAM), and the frequency shifts of the free resonance frequencies of an AFM cantilever are used to determine the mechanical properties of a material. S-AFAM is implemented and compared with a conventional technique (resonance tracking-atomic force acoustic microscopy, RT-AFAM). A sample of a graphite film on a glass substrate is analyzed. S-AFAM can be implemented in any AFM system due to its reduced instrumentation requirements compared to conventional techniques.

| S-EPMC7214876 | biostudies-literature

Structural information, resolution, and noise in high-resolution atomic force microscopy topographs.

Project description:AFM has developed into a powerful tool in structural biology, providing topographs of proteins under close-to-native conditions and featuring an outstanding signal/noise ratio. However, the imaging mechanism exhibits particularities: fast and slow scan axis represent two independent image acquisition axes. Additionally, unknown tip geometry and tip-sample interaction render the contrast transfer function nondefinable. Hence, the interpretation of AFM topographs remained difficult. How can noise and distortions present in AFM images be quantified? How does the number of molecule topographs merged influence the structural information provided by averages? What is the resolution of topographs? Here, we find that in high-resolution AFM topographs, many molecule images are only slightly disturbed by noise, distortions, and tip-sample interactions. To identify these high-quality particles, we propose a selection criterion based on the internal symmetry of the imaged protein. We introduce a novel feature-based resolution analysis and show that AFM topographs of different proteins contain structural information beginning at different resolution thresholds: 10 A (AqpZ), 12 A (AQP0), 13 A (AQP2), and 20 A (light-harvesting-complex-2). Importantly, we highlight that the best single-molecule images are more accurate molecular representations than ensemble averages, because averaging downsizes the z-dimension and "blurs" structural details.

| S-EPMC2711429 | biostudies-literature

Ultra-high resolution imaging of thin films and single strands of polythiophene using atomic force microscopy.

Project description:Real-space images of polymers with sub-molecular resolution could provide valuable insights into the relationship between morphology and functionality of polymer optoelectronic devices, but their acquisition is problematic due to perceived limitations in atomic force microscopy (AFM). We show that individual thiophene units and the lattice of semicrystalline spin-coated films of polythiophenes (PTs) may be resolved using AFM under ambient conditions through the low-amplitude (≤ 1 nm) excitation of higher eigenmodes of a cantilever. PT strands are adsorbed on hexagonal boron nitride near-parallel to the surface in islands with lateral dimensions ~10 nm. On the surface of a spin-coated PT thin film, in which the thiophene groups are perpendicular to the interface, we resolve terminal CH3-groups in a square arrangement with a lattice constant 0.55 nm from which we can identify abrupt boundaries and also regions with more slowly varying disorder, which allow comparison with proposed models of PT domains.

| S-EPMC6449331 | biostudies-literature

Direct Imaging of Protein Organization in an Intact Bacterial Organelle Using High-Resolution Atomic Force Microscopy.

Project description:The function of bioenergetic membranes is strongly influenced by the spatial arrangement of their constituent membrane proteins. Atomic force microscopy (AFM) can be used to probe protein organization at high resolution, allowing individual proteins to be identified. However, previous AFM studies of biological membranes have typically required that curved membranes are ruptured and flattened during sample preparation, with the possibility of disruption of the native protein arrangement or loss of proteins. Imaging native, curved membranes requires minimal tip-sample interaction in both lateral and vertical directions. Here, long-range tip-sample interactions are reduced by optimizing the imaging buffer. Tapping mode AFM with high-resonance-frequency small and soft cantilevers, in combination with a high-speed AFM, reduces the forces due to feedback error and enables application of an average imaging force of tens of piconewtons. Using this approach, we have imaged the membrane organization of intact vesicular bacterial photosynthetic "organelles", chromatophores. Despite the highly curved nature of the chromatophore membrane and lack of direct support, the resolution was sufficient to identify the photosystem complexes and quantify their arrangement in the native state. Successive imaging showed the proteins remain surprisingly static, with minimal rotation or translation over several-minute time scales. High-order assemblies of RC-LH1-PufX complexes are observed, and intact ATPases are successfully imaged. The methods developed here are likely to be applicable to a broad range of protein-rich vesicles or curved membrane systems, which are an almost ubiquitous feature of native organelles.

| S-EPMC5269641 | biostudies-literature

Atomic Force Microscopy Imaging of Crystalline Sucrose in Alcohols.

Project description:Imaging nanometer- or molecule-scale topography has been achieved by dynamic atomic force microscopy (AFM) when a solid object of interest is damaged by vacuum exposure or electron irradiation. Imaging in a liquid offers a means to remove contaminations from the surface scanned using the microscope tip when the object is soluble to the surrounding liquid, typically water. In the present study, we attempted to take topographic images of crystalline sucrose. A problem arose due to the high solubility of this compound to water. Cantilever oscillation could not be excited in the saturated, viscous aqueous solution. By using n-hexanol instead of water, the solubility in the solvent and thus viscosity of the solution were reduced sufficiently to excite cantilever oscillation. Single-height steps and sucrose molecules were recognized in the images and thereby recorded on the (001)-oriented facets of sucrose crystals. Furthermore, two-dimensional distribution of liquid-induced force pushing or pulling the tip was mapped on planes perpendicular to the hexanol-sucrose interface. Observed uneven force distributions indicated liquid hexanol structured on the corrugated surface of sucrose. The viscosity tuning demonstrated here, which is not limited to hexanol instead of water, extends the range of liquid-solid interfaces to be probed by dynamic AFM.

| S-EPMC7033667 | biostudies-literature

Noninvasive Subcellular Imaging Using Atomic Force Acoustic Microscopy (AFAM).

Project description:We report an imaging approach applying the atomic force acoustic microscopy (AFAM), which has unique potential for nondestructive imaging of cell internal structures. To obtain high spatial resolution images, we optimized the significant imaging parameters, including scanning speeds, feedback configurations and acoustic frequencies of an AFAM system, to increase the amplitude of the acoustic signal and to stabilize the morphological signals. We also combined the acoustic amplitude and phase signals, and generated pseudo-color figures for better illustration of subcellular features such as pseudopodia, membranes and nucleus-like. The subcellular structural image atlas can describe nanoscale details of multiple samples and provide clearer images of the subcellular features compared to other conventional techniques. This study builds a strong basis of transmission AFAM for cell imaging, which can help researchers to clarify the cell structures in diverse biological fields and push the understanding of biology evolution to a new stage.

| S-EPMC6523517 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data