Atom probe tomography of apatites and bone-type mineralized tissues

Bone hierarchical organization through the lens of materials science: Present opportunities and future challenges

Multiscale characterization is essential to better understand the hierarchical architecture of bone and an array of analytical methods contributes to exploring the various structural and compositional aspects. Incorporating X-ray tomography, X-ray scattering, vibrational spectroscopy, and atom probe tomography alongside electron microscopy provides a comprehensive approach, offering insights into the diverse levels of organization within bone. X-ray scattering techniques reveal information about collagen-mineral spatial relationships, while X-ray tomography captures 3D structural details, especially at the microscale. Electron microscopy, such as scanning and transmission electron microscopy, extends resolution to the nanoscale, showcasing intricate features such as collagen fibril organization. Additionally, atom probe tomography achieves sub-nanoscale resolution and high chemical sensitivity, enabling detailed examination of bone composition. Despite various technical challenges, a correlative approach allows for a comprehensive understanding of bone material properties. Real-time investigations through in situ and in operando approaches shed light on the dynamic processes in bone. Recently developed techniques such as liquid, in situ transmission electron microscopy provide insights into calcium phosphate formation and collagen mineralization. Mechanical models developed in the effort to link structure, composition, and function currently remain oversimplified but can be improved. In conclusion, correlative analytical platforms provide a holistic perspective of bone extracellular matrix and are essential for unraveling the intricate interplay between structure and composition within bone.

In Situ Metallic Coating of Atom Probe Specimen for Enhanced Yield, Performance, and Increased Field-of-View

Atom probe tomography requires needle-shaped specimens with a diameter typically below 100 nm, making them both very fragile and reactive, and defects (notches at grain boundaries or precipitates) are known to affect the yield and data quality. The use of a conformal coating directly on the sharpened specimen has been proposed to increase yield and reduce background. However, to date, these coatings have been applied ex situ and mostly are not uniform. Here, we report on the controlled focused-ion beam in situ deposition of a thin metal film on specimens immediately after specimen preparation. Different metallic targets e.g. Cr were attached to a micromanipulator via a conventional lift-out method and sputtered using Ga or Xe ions. We showcase the many advantages of coating specimens from metallic to nonmetallic materials. We have identified an increase in data quality and yield, an improvement of the mass resolution, as well as an increase in the effective field-of-view. This wider field-of-view enables visualization of the entire original specimen, allowing to detect the complete surface oxide layer around the specimen. The ease of implementation of the approach makes it very attractive for generalizing its use across a very wide range of atom probe analyses.

Ultrastructure and Nanoporosity of Human Bone Shown with Correlative On-Axis Electron and Spectroscopic Tomographies

Mineralized collagen fibrils are the building block units of bone at the nanoscale. While it is known that collagen fibrils are mineralized both inside their gap zones (intra-fibrillar mineralization) and on their outer surfaces (extra-fibrillar mineralization), a clear visualization of this architecture in three dimensions (3D), combining structural and compositional information over large volumes, but without compromising the resolution, remains challenging. In this study, we demonstrate the use of on-axis Z-contrast electron tomography (ET) with correlative energy-dispersive X-ray spectroscopy (EDX) tomography to examine rod-shaped samples with diameters up to 700 nm prepared from individual osteonal lamellae in the human femur. Our work mainly focuses on two aspects: (i) low-contrast nanosized circular spaces ("holes") observed in sections of bone oriented perpendicular to the long axis of a long bone, and (ii) extra-fibrillar mineral, especially in terms of morphology and spatial relationship with respect to intra-fibrillar mineral and collagen fibrils. From our analyses, it emerges quite clearly that most "holes" are cross-sectional views of collagen fibrils. While this had been postulated before, our 3D reconstructions and reslicing along meaningful two-dimensional (2D) cross-sections provide a direct visual confirmation. Extra-fibrillar mineral appears to be composed of thin plates that are interconnected and span over several collagen fibrils, confirming that mineralization is cross-fibrillar, at least for the extra-fibrillar phase. EDX tomography shows mineral signatures (Ca and P) within the gap zones, but the signal appears weaker than that associated with the extra-fibrillar mineral, pointing toward the existence of dissimilarities between the two types of mineralization.

Challenging Prevalent Solid Electrolyte Interphase (SEI) Models: An Atom Probe Tomography Study on a Commercial Graphite Electrode

Lithium-ion batteries (LIBs) are the dominating energy storage technology for electric vehicles and portable electronic devices. Since the resources of raw materials for LIBs are limited and recycling technologies for LIBs are still under development, improvements in the long-term stability of LIBs are of paramount importance and, in addition, would lead to a reduction in the levelized cost of storage (LCOS). A crucial limiting factor is the aging of the solid electrolyte interphase (SEI) on the active material particles in the anode. Here, we demonstrate the potential of atom probe tomography for elucidating the complex mosaic-type structure of the SEI in a graphite composite anode. Our 3D reconstruction shows unseen details and reveals the existence of an apolar organic microphase pervading the SEI over its entire thickness. This finding is in stark contrast to the prevalent two-layer SEI model, in which organic compounds are the dominating species only in the outer SEI layer being in contact with the liquid electrolyte. The observed spatial arrangement of the apolar organic microphase promises a better understanding of the passivation capability of the SEI, which is necessary to expand the battery lifetime.

Elucidating the Structure and Composition of Individual Bimetallic Nanoparticles in Supported Catalysts by Atom Probe Tomography

Understanding and controlling the structure and composition of nanoparticles in supported metal catalysts are crucial to improve chemical processes. For this, atom probe tomography (APT) is a unique tool, as it allows for spatially resolved three-dimensional chemical imaging of materials with sub-nanometer resolution. However, thus far APT has not been applied for mesoporous oxide-supported metal catalyst materials, due to the size and number of pores resulting in sample fracture during experiments. To overcome these issues, we developed a high-pressure resin impregnation strategy and showcased the applicability to high-porous supported Pd-Ni-based catalyst materials, which are active in CO2 hydrogenation. Within the reconstructed volume of 3 × 105 nm3, we identified over 400 Pd-Ni clusters, with compositions ranging from 0 to 16 atom % Pd and a size distribution of 2.6 ± 1.6 nm. These results illustrate that APT is capable of quantitatively assessing the size, composition, and metal distribution for a large number of nanoparticles at the sub-nm scale in industrial catalysts. Furthermore, we showcase that metal segregation occurred predominately between nanoparticles, shedding light on the mechanism of metal segregation. We envision that the presented methodology expands the capabilities of APT to investigate porous functional nanomaterials, including but not limited to solid catalysts.

Testing the Influence of Laser Pulse Energy and Rate in the Atom Probe Tomography Analysis of Minerals

The use of atom probe tomography (APT) for mineral analysis is contributing to fundamental studies in Earth Sciences. Meanwhile, the need for standardization of this technique is becoming evident. Pending the use of mineral standards, the optimization of analysis parameters is needed to facilitate the study of different mineral groups in terms of data collection and quality. The laser pulse rate and energy are variables that highly affect the atom evaporation process occurring during APT analysis, and their testing is important to forecast mineral behavior and obtain the best possible data. In this study, five minerals representative of major groups (albite, As-pyrite, barite, olivine, and monazite) were analyzed over a range of laser pulse energies (10-50 pJ) and rates (100-250 kHz) to assess output parameter quality and evaluate compositional estimate stoichiometry. Among the studied minerals, As-pyrite, with the higher thermal conductivity and lower band gap, was the most affected by the laser pulse variation. Chemical composition estimates equal or close to the general chemical formula were achieved for monazite and As-pyrite. The analysis of multihit events has proved to be the best strategy to verify the efficacy of the evaporation process and to evaluate the best laser pulse setting for minerals.

Resolving protein-mineral interfacial interactions during in vitro mineralization by atom probe tomography

Organic macromolecules exert remarkable control over the nucleation and growth of inorganic crystallites during (bio)mineralization, as exemplified during enamel formation where the protein amelogenin regulates the formation of hydroxyapatite (HAP). However, it is poorly understood how fundamental processes at the organic-inorganic interface, such as protein adsorption and/or incorporation into minerals, regulates nucleation and crystal growth due to technical challenges in observing and characterizing mineral-bound organics at high-resolution. Here, atom probe tomography techniques were developed and applied to characterize amelogenin-mineralized HAP particles in vitro, revealing distinct organic-inorganic interfacial structures and processes at the nanoscale. Specifically, visualization of amelogenin across the mineralized particulate demonstrates protein can become entrapped during HAP crystal aggregation and fusion. Identification of protein signatures and structural interpretations were further supported by standards analyses, i.e., defined HAP surfaces with and without amelogenin adsorbed. These findings represent a significant advance in the characterization of interfacial structures and, more so, interpretation of fundamental organic-inorganic processes and mechanisms influencing crystal growth. Ultimately, this approach can be broadly applied to inform how potentially unique and diverse organic-inorganic interactions at different stages regulates the growth and evolution of various biominerals.

Discovering an unknown territory using atom probe tomography: Elemental exchange at the bioceramic scaffold/bone tissue interface

Here we report the first atom probe study to reveal the atomic-scale composition of in vivo bone formed in a bioceramic scaffold (strontium-hardystonite-gahnite) after 12-month implantation in a large bone defect in sheep tibia. The composition of the newly formed bone tissue differs to that of mature cortical bone tissue, and elements from the degrading bioceramic implant, particularly aluminium (Al), are present in both the newly formed bone and in the original mature cortical bone tissue at the perimeter of the bioceramic implant. Atom probe tomography confirmed that the trace elements are released from the bioceramic and are actively transported into the newly formed bone. NanoSIMS mapping, as a complementary technique, confirmed the distribution of the released ions from the bioceramic into the newly formed bone tissue within the scaffold. This study demonstrated the combined benefits of atom probe and nanoSIMS in assessing nanoscopic chemical composition changes at precise locations within the tissue/biomaterial interface. Such information can assist in understanding the interaction of scaffolds with surrounding tissue, hence permitting further iterative improvements to the design and performance of biomedical implants, and ultimately reducing the risk of complications or failure while increasing the rate of tissue formation. STATEMENT OF SIGNIFICANCE: The repair of critical-sized load-bearing bone defects is a challenge, and precisely engineered bioceramic scaffold implants is an emerging potential treatment strategy. However, we still do not understand the effect of the bioceramic scaffold implants on the composition of newly formed bone in vivo and surrounding existing mature bone. This article reports an innovative route to solve this problem, the combined power of atom probe tomography and nanoSIMS is used to spatially define elemental distributions across bioceramic implant sites. We determine the nanoscopic chemical composition changes at the Sr-HT Gahnite bioceramic/bone tissue interface, and importantly, provide the first report of in vivo bone tissue chemical composition formed in a bioceramic scaffold.

Nanoscale analysis of frozen honey by atom probe tomography

Three-dimensional reconstruction of the analysed volume is one of the main goals of atom probe tomography (APT) and can deliver nearly atomic resolution (~ 0.2 nm spatial resolution) and chemical information with a mass sensitivity down to the ppm range. Extending this technique to frozen biological systems would have an enormous impact on the structural analysis of biomolecules. In previous works, we have shown that it is possible to measure frozen liquids with APT. In this paper, we demonstrate the ability of APT to trace nanoscale precipitation in frozen natural honey. While the mass signals of the common sugar fragments C_xH_y and C_xO_yH_z overlap with (H₂O)_nH from water, we achieved correct stoichiometric values via different interpretation approaches for the peaks and thus determined the water content reliably. Next, we use honey to investigate the spatial resolution capabilities as a step toward the measurement of biological molecules in solution in 3D with sub-nanometer resolution. This may take analytical techniques to a new level, since methods of chemical characterization for cryogenic samples, especially biological samples, are still limited.

Aging exacerbates the morphological and mechanical response of mineralized collagen fibrils in murine cortical bone to disuse

Mineralized collagen fibrils (MCFs) are the fundamental building blocks of bone tissue and contribute significantly to the mechanical behavior of bone. However, it is still largely unknown how the collagen network in bone responds to aging and the disuse normally accompanying it. Utilizing atomic force microscopy, nanoindentation and Raman spectroscopy, age-related alterations in the microstructure and mechanical properties of murine cortical tibia at multiple scales were investigated in this study. The potential difference in the responses of bone to disuse at different ages was studied. The results indicated that the age- and disuse-related alterations in bone initiate from MCFs in the bone matrix. The D-periodic spacing, radial elastic modulus of a single MCF and the mineral-to-matrix ratio on the cortical bone surface were larger in aged mice than in adult mice. Disuse, on the other hand, mainly has a major influence on aged mice, particularly on the morphology and mechanical properties of MCFs, but it only has modest effects on adult bone. These findings revealed insights into the morphological and mechanical adaptation of mineralized collagen fibrils in murine cortical bone to aging and disuse. STATEMENT OF SIGNIFICANCE: Bone is a complex structured composite material consisting of an interwoven framework of collagen fibrils reinforced by mineral particles and embedded in an extrafibrillar mineralized matrix. Utilizing atomic force microscopy, nanoindentation and Raman spectroscopy, this study suggests that the effects of aging, as well as the accompanying disuse, on the morphology and mechanical properties of bone initiate from the mineralized collagen fibril level. More interestingly, the MCF in the bone of aged mice seems to be more sensitive to disuse than that in adult mice. These findings significantly further the current understanding of the adaptation process of bone to aging at the mineralized collagen fibril level and provide direct insights into the physiological response of bone to aging and the abnormal mechanical environment.

Applications of scanning electron microscopy and focused ion beam milling in dental research

The abilities of scanning electron microscopy (SEM) and focused ion beam (FIB) milling for obtaining high-resolution images from top surfaces, cross-sectional surfaces, and even in three dimensions, are becoming increasingly important for imaging and analyzing tooth structures such as enamel and dentin. FIB was originally developed for material research in the semiconductor industry. However, use of SEM/FIB has been growing recently in dental research due to the versatility of dual platform instruments that can be used as a milling device to obtain low-artifact cross-sections of samples combined with high-resolution images. The advent of the SEM/FIB system and accessories may offer access to previously inaccessible length scales for characterizing tooth structures for dental research, opening exciting opportunities to address many central questions in dental research. New discoveries and fundamental breakthroughs in understanding are likely to follow. This review covers the applications, key findings, and future direction of SEM/FIB in dental research in morphology imaging, specimen preparation for transmission electron microscopy (TEM) analysis, and three-dimensional volume imaging using SEM/FIB tomography.

Atom Probe Tomography Analysis of Mica

Laser-assisted atom probe tomography (APT) is a relatively new, powerful technique for sub-nanometric mineral and biomineral analysis. However, the laser-assisted APT analysis of highly anisotropic and chemically diverse minerals, such as phyllosilicates, may prove especially challenging due to the complex interaction between the crystal structure and the laser pulse upon applying a high electric field. Micas are a representative group of nonswelling clay minerals of relevance to a number of scientific and technological fields. In this study, a Mg-rich biotite was analyzed by APT to generate preliminary data on nonisotropic minerals and to investigate the effect of the crystallographic orientation on mica chemical composition and structure estimation. The difference in results obtained for specimens extracted from the (001) and (hk0) mica surfaces indicate the importance of both experimental parameters and the crystallography. Anisotropy of mica has a strong influence on the physicochemical properties of the mineral during field evaporation and the interpretation of APT data. The promising results obtained in the present study open the way to future innovative APT applications on mica and clay minerals and contribute to the general discussion on the challenges for the analysis of geomaterials by atom probe tomography.

The homogenous alternative to biomineralization: Zn- and Mn-rich materials enable sharp organismal "tools" that reduce force requirements

We measured hardness, modulus of elasticity, and, for the first time, loss tangent, energy of fracture, abrasion resistance, and impact resistance of zinc- and manganese-enriched materials from fangs, stings and other "tools" of an ant, spider, scorpion and nereid worm. The mechanical properties of the Zn- and Mn-materials tended to cluster together between plain and biomineralized "tool" materials, with the hardness reaching, and most abrasion resistance values exceeding, those of calcified salmon teeth and crab claws. Atom probe tomography indicated that Zn was distributed homogeneously on a nanometer scale and likely bound as individual atoms to more than ¼ of the protein residues in ant mandibular teeth. This homogeneity appears to enable sharper, more precisely sculpted "tools" than materials with biomineral inclusions do, and also eliminates interfaces with the inclusions that could be susceptible to fracture. Based on contact mechanics and simplified models, we hypothesize that, relative to plain materials, the higher elastic modulus, hardness and abrasion resistance minimize temporary or permanent tool blunting, resulting in a roughly 2/3 reduction in the force, energy, and muscle mass required to initiate puncture of stiff materials, and even greater force reductions when the cumulative effects of abrasion are considered. We suggest that the sharpness-related force reductions lead to significant energy savings, and can also enable organisms, especially smaller ones, to puncture, cut, and grasp objects that would not be accessible with plain or biomineralized "tools".

Three-Dimensional Insights into Interfacial Segregation at the Atomic Scale in a Nanocrystalline Glass-Ceramic

The distribution of dopant atoms plays a key role in the effectiveness of doping, thereby requiring delicate characterizations. In this study, we found that energy-dispersive X-ray spectroscopy (EDX) and electron energy loss spectroscopy (EELS) techniques in scanning transmission electron microscopy (STEM) were not adequate to reveal the distribution of yttrium and the chemical composition of the ZrO₂/SiO₂ heterophase interface in an yttrium-doped ZrO₂-SiO₂ nanocrystalline glass-ceramic. Atom probe tomography (APT) is rarely utilized to characterize ceramics due to some inherent difficulties. However, we successfully revealed the three-dimensional distribution of ZrO₂ nanocrystallites and SiO₂ matrix at the atomic scale with APT under optimized and well-controlled conditions. We also found that the ZrO₂ nanocrystallites had a special core-shell structure, with a thin Zr/Si interfacial layer as a shell and a ZrO₂ solid solution as a core. Yttrium dopants showed interfacial segregation at both ZrO₂ grain boundaries and the ZrO₂/SiO₂ heterophase interfaces.

Facet Selectivity Guided Assembly of Nanoarchitectures onto Two-Dimensional Metal-Organic Framework Nanosheets

Facet-selective nanostructures in living systems usually exhibit outstanding optical and enzymatic properties, playing important roles in photonics, matter exchange, and biocatalysis. Bioinspired construction of facet-selective nanostructures offers great opportunities for sophisticated nanomaterials, but remains a formidable task. We have developed a macromolecule-mediated strategy for the assembly of upconversion nanoparticles (UCNPs)/two-dimensional metal-organic frameworks (2DMOFs) heterostructures with facet selectivity. Both experimental and theoretical results demonstrate that polyvinylpyrrolidone (PVP) can be utilized as an interface-selective mediator to further promote the facet-selective assembly of MOFs onto the surface of UCNPs. The UCNPs/2DMOFs nanostructures with facet selectivity display specific optical properties and show great advantages in anti-counterfeiting. Our demonstration of UCNPs/2DMOFs provides a vivid example for the controlled fabrication of facet-selective nanostructures and can promote the development of advanced functional materials for applications in biosensing, energy conversion, and information assurance.

Visualization of Collagen-Mineral Arrangement Using Atom Probe Tomography

Bone is a functional material comprised of mainly two phases: an organic collagenous phase and an inorganic mineral phase. Collagen-mineral arrangement has implications for bone function, aging, and disease. However, theories on collagen-mineral arrangement have been confined to studies with low spatial and/or compositional resolution resulting in an extensive debate over the location of mineral with respect to collagen. Herein, a strategy is developed to extract a single mineralized collagen fibril from bone and analyze its composition and structure atom-by-atom with 3D sub-nanometer accuracy and compositional clarity using atom probe tomography (APT). It is shown for the first time a method to probe fibril-level mineralization and collagen-mineral arrangement from an in vivo system with both the spatial and compositional precision required to comment on nanoscale collagen-mineral arrangement. APT of leporine bone shows distinct and helical collagen fibrils with mineralized deposits both encapsulating and incorporated into the collagenous structures. This study demonstrates a novel fibril-level detection method that can be used to probe the composition of bone and contribute new insights to the structure and organization of mineralized materials such as bones and teeth.

Functional analyses of chitinolytic enzymes in the formation of calcite prisms in Pinctada fucata

The mollusk shells present distinctive microstructures that are formed by small amounts of organic matrices controlling the crystal growth of calcium carbonate. The shell of Pinctada fucata has the prismatic layer consisting of prisms of single calcite crystals and the nacreous layer consisting of aragonite tablets. The calcite crystal of prisms contains small angle grain boundaries caused by a dense intracrystalline organic matrix network to improve mechanical strength. Previously, we identified chitin and chitinolytic enzymes as components of this intracrystalline organic matrix. In this study, to reveal the function of those organic matrices in calcium carbonate crystallization, calcites synthesized in chitin gel with or without chitinolytic enzymes were analyzed by using transmission electron microscope (TEM) and atom probe tomography (APT), showing ion clusters derived from chitin inside of a calcite and small angle grain boundaries at optimal chitinolytic concentration. Furthermore, we performed the experiment in which chitinase inhibitor was injected into a living P. fucata. Nanoindentation and electron back scattered diffraction (EBSD) show that mechanical properties and crystal orientation were changed. These results suggested that chitinolytic enzymes work cooperatively with chitin to regulate the crystal growth and mechanical properties of the prismatic layer.

Mapping Bone Surface Composition Using Real-Time Surface Tracked Micro-Raman Spectroscopy

The surface of bone tells a story - one that is worth a thousand words - of how it is built and how it is repaired. Chemical (i.e., composition) and physical (i.e., morphology) characteristics of the bone surface are analogous to a historical record of osteogenesis and provide key insights into bone quality. Analysis of bone chemistry is of particular relevance to the advancement of human health, cell biology, anthropology/archaeology, and biomedical engineering. Although scanning electron microscopy remains a popular and versatile technique to image bone across multiple length scales, limited chemical information can be obtained. Micro-Raman spectroscopy is a valuable tool for nondestructive chemical/compositional analysis of bone. However, signal integrity losses occur frequently during wide-field mapping of non-planar surfaces. Samples for conventional Raman imaging are, therefore, rendered planar through polishing or sectioning to ensure uniform signal quality. Here, we demonstrate ν1 PO43- and ν1 CO32- peak intensity losses where the sample surface and the plane of focus are offset by over 1-2 μm when underfocused and 2-3 μm when overfocused at 0.5-1 s integration time (15 mW, 633 nm laser). A technique is described for mapping the composition of the inherently irregular/non-planar surface of bone. The challenge posed by the native topology characteristic of this unique biological system is circumvented via real-time focus-tracking based on laser focus optimization by continuous closed-loop feedback. At the surface of deproteinized and decellularized/defatted sheep tibial cortical bone, regions of interest up to 1 mm2 were scanned at micrometer and submicrometer resolution. Despite surface height deviations exceeding 100 μm, it is possible to seamlessly probe local gradients in organic and inorganic constituents of the extracellular matrix as markers of bone metabolism and bone turnover, blood vessels and osteocyte lacunae, and the rope-like mineralized bundles that comprise the mineral phase at the bone surface.

Atom Probe Tomography of Encapsulated Hydroxyapatite Nanoparticles

Hydroxyapatite nanoparticles (HAP NPs) are important for medicine, bioengineering, catalysis, and water treatment. However, current understanding of the nanoscale phenomena that confer HAP NPs their many useful properties is limited by a lack of information about the distribution of the atoms within the particles. Atom probe tomography (APT) has the spatial resolution and chemical sensitivity for HAP NP characterization, but difficulties in preparing the required needle-shaped samples make the design of these experiments challenging. Herein, two techniques are developed to encapsulate HAP NPs and prepare them into APT tips. By sputter-coating gold or the atomic layer deposition of alumina for encapsulation, partially fluoridated HAP NPs are successfully characterized by voltage- or laser-pulsing APT, respectively. Analyses reveal that significant tradeoffs exist between encapsulant methods/materials for HAP characterization and that selection of a more robust approach will require additional technique development. This work serves as an essential starting point for advancing knowledge about the nanoscale spatiochemistry of HAP NPs.

Machine-learning-enhanced time-of-flight mass spectrometry analysis

Mass spectrometry is a widespread approach used to work out what the constituents of a material are. Atoms and molecules are removed from the material and collected, and subsequently, a critical step is to infer their correct identities based on patterns formed in their mass-to-charge ratios and relative isotopic abundances. However, this identification step still mainly relies on individual users' expertise, making its standardization challenging, and hindering efficient data processing. Here, we introduce an approach that leverages modern machine learning technique to identify peak patterns in time-of-flight mass spectra within microseconds, outperforming human users without loss of accuracy. Our approach is cross-validated on mass spectra generated from different time-of-flight mass spectrometry (ToF-MS) techniques, offering the ToF-MS community an open-source, intelligent mass spectra analysis.

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A machine-learning method provides reliable atomic/molecular labels for ToF-MS

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No human labeling or prior information required

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The training dataset is artificially generated based on isotopic abundances

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Method validated on a variety of materials and two ToF-MS-based techniques

Time-of-flight mass spectrometry (ToF-MS) is a mainstream analytical technique widely used in biology, chemistry, and materials science. ToF-MS provides quantitative compositional analysis with high sensitivity across a wide dynamic range of mass-to-charge ratios. A critical step in ToF-MS is to infer the identity of the detected ions. Here, we introduce a machine-learning-enhanced algorithm to provide a user-independent approach to performing this identification using patterns from the natural isotopic abundances of individual atomic and molecular ions, without human labeling or prior knowledge of composition. Results from several materials and techniques are compared with those obtained by field experts. Our open-source, easy-to-implement, reliable analytic method accelerates this identification process. A wide range of ToF-MS-based applications can benefit from our approach, e.g., hunting for patterns of biomarkers or for contamination on solid surfaces in high-throughput data.

Atom probe tomography

Atom probe tomography (APT) provides three-dimensional compositional mapping with sub-nanometre resolution. The sensitivity of APT is in the range of parts per million for all elements, including light elements such as hydrogen, carbon or lithium, enabling unique insights into the composition of performance-enhancing or lifetime-limiting microstructural features and making APT ideally suited to complement electron-based or X-ray-based microscopies and spectroscopies. Here, we provide an introductory overview of APT ranging from its inception as an evolution of field ion microscopy to the most recent developments in specimen preparation, including for nanomaterials. We touch on data reconstruction, analysis and various applications, including in the geosciences and the burgeoning biological sciences. We review the underpinnings of APT performance and discuss both strengths and limitations of APT, including how the community can improve on current shortcomings. Finally, we look forwards to true atomic-scale tomography with the ability to measure the isotopic identity and spatial coordinates of every atom in an ever wider range of materials through new specimen preparation routes, novel laser pulsing and detector technologies, and full interoperability with complementary microscopy techniques.

Field evaporation and atom probe tomography of pure water tips

Measuring biological samples by atom probe tomography (APT) in their natural environment, i.e. aqueous solution, would take this analytical method, which is currently well established for metals, semi-conductive materials and non-metals, to a new level. It would give information about the 3D chemical structure of biological systems, which could enable unprecedented insights into biological systems and processes, such as virus protein interactions. For this future aim, we present as a first essential step the APT analysis of pure water (Milli-Q) which is the main component of biological systems. After Cryo-preparation, nanometric water tips are field evaporated with assistance by short laser pulses. The obtained data sets of several tens of millions of atoms reveal a complex evaporation behavior. Understanding the field evaporation process of water is fundamental for the measurement of more complex biological systems. For the identification of the individual signals in the mass spectrum, DFT calculations were performed to prove the stability of the detected molecules.

New frontiers in atom probe tomography: a review of research enabled by cryo and/or vacuum transfer systems

There has been a recent surge in the use of cryo and/or vacuum specimen preparation and transfer systems to broaden the scope of research enabled by the microscopy technique of atom probe tomography. This is driven by the fact that, as for many microscopes, the application of atom probes to air- and temperature-sensitive materials or wet biological specimens has previously been limited by transfer through air at room temperature. Here we provide an overview of areas of research that benefit from these new transfer and analysis protocols, as well as a review of current advances in transfer devices, environmental cells, and glove boxes for controlled specimen manipulation. This includes the study of catalysis and corrosion, biological samples, liquid-solid interfaces, natural aging, and the distribution of hydrogen in materials.

Mechanics of Mineralized Collagen Fibrils upon Transient Loads

Collagen is a key structural protein in the human body, which undergoes mineralization during the formation of hard tissues. Earlier studies have described the mechanical behavior of bone at different scales, highlighting material features across hierarchical structures. Here we present a study that aims to understand the mechanical properties of mineralized collagen fibrils upon tensile/compressive transient loads, investigating how the kinetic energy propagates and it is dissipated at the molecular scale, thus filling a gap of knowledge in this area. These specific features are the mechanisms that nature has developed to passively dissipate stress and prevent structural failures. In addition to the mechanical properties of the mineralized fibrils, we observe distinct nanomechanical behaviors for the two regions (i.e., overlap and gap) of the D-period to highlight the effect of the mineralization. We notice decreasing trends for both wave speeds and Young's moduli over input velocity with a marked strengthening effect in the gap region due to the accumulation of the hydroxyapatite. In contrast, the dissipative behavior is not affected by either loading conditions or the mineral percentage, showing a stronger damping effect upon faster inputs compatible to the bone behavior at the macroscale. Our results offer insights into the dissipative behavior of mineralized collagen composites to design and characterize bioinspired composites for replacement devices (e.g., prostheses for sound transmission or conduction) or optimized structures able to bear transient loads, for example, impact, fatigue, in structural applications.

Chemical gradients in human enamel crystallites

Dental enamel is a principal component of teeth1, and has evolved to bear large chewing forces, resist mechanical fatigue and withstand wear over decades2. Functional impairment and loss of dental enamel, caused by developmental defects or tooth decay (caries), affect health and quality of life, with associated costs to society3. Although the past decade has seen progress in our understanding of enamel formation (amelogenesis) and the functional properties of mature enamel, attempts to repair lesions in this material or to synthesize it in vitro have had limited success4-6. This is partly due to the highly hierarchical structure of enamel and additional complexities arising from chemical gradients7-9. Here we show, using atomic-scale quantitative imaging and correlative spectroscopies, that the nanoscale crystallites of hydroxylapatite (Ca5(PO4)3(OH)), which are the fundamental building blocks of enamel, comprise two nanometric layers enriched in magnesium flanking a core rich in sodium, fluoride and carbonate ions; this sandwich core is surrounded by a shell with lower concentration of substitutional defects. A mechanical model based on density functional theory calculations and X-ray diffraction data predicts that residual stresses arise because of the chemical gradients, in agreement with preferential dissolution of the crystallite core in acidic media. Furthermore, stresses may affect the mechanical resilience of enamel. The two additional layers of hierarchy suggest a possible new model for biological control over crystal growth during amelogenesis, and hint at implications for the preservation of biomarkers during tooth development.

Effect of crystallographic orientation on atom probe tomography geochemical data?

The recent application of atom probe tomography (APT) to minerals is becoming a powerful tool to unravel geological information from the nanoscale perspective. Yet, there are still unknown fundamental aspects of this microscopy technique for geological applications and the potential crystallographic orientation effect is a significant one. Here, the influence of the crystallographic orientation on the quality of atom probe tomography geochemical data is investigated for two minerals with the same crystal system and different morphology: spinel (isometric, hexoctahedral, octahedron morphology) and galena (isometric, hexoctahedral, cube morphology). Two separate crystals of barite (orthorhombic, dipyramidal, prism morphology) were also analyzed to test the reproducibility of APT data. Despite the general absence of expected stoichiometry, overall bulk and isotopic chemical composition are not affected by crystallographic orientation. 3D data reconstructions of the specimens showed similar spatial distribution of the ion species for each mineral and 2D density maps showed identical (barite, galena) or specular (spinel) patterns for each pair of planes analyzed. Our findings indicate a negligible effect of the crystallographic orientation in APT geochemical data for standard highly symmetric minerals but also suggest the possible influence of the crystallographic structure and composition on the mineral stoichiometry and elements spatial distribution density.

Phase Segmentation in Atom-Probe Tomography Using Deep Learning-Based Edge Detection

Atom-probe tomography (APT) facilitates nano- and atomic-scale characterization and analysis of microstructural features. Specifically, APT is well suited to study the interfacial properties of granular or heterophase systems. Traditionally, the identification of the interface between, for precipitate and matrix phases, in APT data has been obtained either by extracting iso-concentration surfaces based on a user-supplied concentration value or by manually perturbing the concentration value until the iso-concentration surface qualitatively matches the interface. These approaches are subjective, not scalable, and may lead to inconsistencies due to local composition inhomogeneities. We introduce a digital image segmentation approach based on deep neural networks that transfer learned knowledge from natural images to automatically segment the data obtained from APT into different phases. This approach not only provides an efficient way to segment the data and extract interfacial properties but does so without the need for expensive interface labeling for training the segmentation model. We consider here a system with a precipitate phase in a matrix and with three different interface modalities-layered, isolated, and interconnected-that are obtained for different relative geometries of the precipitate phase. We demonstrate the accuracy of our segmentation approach through qualitative visualization of the interfaces, as well as through quantitative comparisons with proximity histograms obtained by using more traditional approaches.

Nanoscale pathways for human tooth decay - Central planar defect, organic-rich precipitate and high-angle grain boundary

Understanding the pathways and mechanisms of human tooth decay is central to the development of both prophylaxes and treatments, but only limited information is presently available about the initiation of caries at the nanoscale. By combining atom probe tomography and high-resolution electron microscopy, we have found three distinct initial sites for human dental enamel dissolution: a) along the central dark line (CDL) within carbonated apatite nanocrystals, b) at organic-rich precipitates and c) along high-angle grain boundaries. 3D maps of the atoms within hydroxyapatite nanocrystallites in sound and naturally-decayed human dental enamel reveal a higher concentration of Mg and Na in the CDL. The CDL is therefore thought to provide a pathway for the exchange of ions during demineralization and remineralization. Mg and Na enrichment of the CDL also suggests that it is associated with the ribbon-like organic-rich precursor in amelogenesis. Organic-rich precipitates and high-angle grain boundaries were also shown to be more vulnerable to corrosion while low-angle grain boundaries remained intact. This is attributed to the lower crystallinity in these regions.

Atom Probe Tomography for 3D Structural and Chemical Analysis of Individual Proteins

Determination of the 3D structure of proteins and other biomolecules is a major goal in structural biology, to provide insights to their biological function. Such structures are historically unveiled experimentally by X-ray crystallography or NMR spectroscopy, and in recent years using cryo-electron microscopy. Here, a method for structural analysis of individual proteins on the sub-nanometer scale using atom probe tomography is described. This technique offers a combination of high-resolution analysis of biomolecules in 3D, and the chemical sensitivity of mass spectrometry. As a model protein, the well-characterized antibody IgG is used. IgG is encapsulated in an amorphous solid silica matrix via a sol-gel process to provide the requisite support for atom probe analysis. The silica synthesis is tuned to resemble physiological conditions. The 3D reconstructions show good agreement with the protein databank IgG crystal structure. This suggests that the silica-embedding strategy can open the field of atom probe tomography to the analysis of biological molecules. In addition to high-resolution structural information, the technique may potentially provide chemical information on the atomic scale using isotopic labeling. It is envisaged that this method may constitute a useful complement to existing tools in structural biology, particularly for the examination of proteins with low propensity for crystallization.

Direct Three-Dimensional Observation of Core/Shell-Structured Quantum Dots with a Composition-Competitive Gradient

Synthesizing semiconductor nanoparticles through core/shell structuring is an effective strategy to promote the functional, physical, and kinetic performance of optoelectronic materials. However, elucidating the internal structure and related atomic distribution of core/shell structured quantum dots (QDs) in three dimensions, particularly at heterostructure interfaces, has been an overarching challenge. Herein, by applying complementary analytical techniques of electron microscopy and atom probe tomography, the dimensional, structural, topological, and compositional information on commercially available 11.8 nm-sized CdSSe/ZnS QDs were obtained. Systematic experiments at high resolution reveal the presence of a 1.8 nm-thick Cd _xZn_{1 - x}S inner shell with a composition gradient between the CdSe core and the ZnS outermost shell. More strikingly, the inner shell shows compositional variation because of competitive atomic configuration between Cd and ZnS, but it structurally retains a zinc-blende crystal structure with the core. The inner shell may grow through the decreased reactivity of S with Cd, followed by atomic diffusion-related processes. The composition-competitive gradient inner shell alleviates lattice misfit strain at heterostructure interfaces, thereby enhancing the quantum yield and photostabilty to a greater extent than those of other single-shell structures. Thus, this precise measurement approach could offer a potential pathway to develop a wide variety of three-dimensional core/shell-structured materials.

A near atomic-scale view at the composition of amyloid-beta fibrils by atom probe tomography

Amyloid-beta (Ab) proteins play an important role in a number of neurodegenerative diseases. Ab is found in senile plaques in brains of Alzeimer’s disease patients. The 42 residues of the monomer form dimers which stack to fibrils gaining several micrometers in length. Using Ab fibrils with ¹³C and ¹⁵N marker substitution, we developed an innovative approach to obtain insights to structural and chemical information of the protein. We deposited the modified protein fibrils to pre-sharped aluminium needles with >100-nm apex diameters and, using the position-sensitive mass-to-charge spectrometry technique of atom probe tomography, we acquired the chemically-resolved three dimensional information for every detected ion evaporated in small fragments from the protein. We also discuss the influence of experimental parameters such as pulse energy and pulse frequency of the used Laser beam which lead to differences in the size of the gained fragments, developing the capability of localising metal atom within Ab plaques.

Atomic layout of an orthodontic titanium mini-implant in human tissue: Insights into the possible mechanisms during osseointegration

OBJECTIVES

To evaluate nanoscale molecular interactions in the interface between human bone and orthodontic titanium implants.

MATERIALS AND METHODS

An orthodontic implant (sandblasted with large grit and with an acid-etched surface treated with Ti6A14V alloy) retrieved from the mandible of human after 2 months of healing was used to analyze the molecular interactive mechanism between the implant and the surrounding bone tissue. To preserve the natural state of the sample as much as possible, cryofixation and scanning electron microscope/focused ion beam milling without any chemical treatment were used during sample preparation. Atom probe tomography was used to investigate the chemical composition and structure at the interface between the implant and human bone tissue.

RESULTS

Three-dimensional (3D) reconstruction of the whole sample revealed a 20 × 50-nm² plate-like bony element diffusion layer in the sample. The iso concentration analysis of the diffusion layer indicated that the bony element, calcium, and the implant element, titanium oxide, were interspersed with each other. Detailed ionic distribution was illustrated by 3D reconstruction with partial region of interest and one-dimensional concentration profiles of the implant-bone interface.

CONCLUSIONS

The study results advance nanoscale understanding of osseointegration and suggest a potential nanostructure for increasing bond strength of biomaterials to bone.

Biomineralization-Inspired Material Design for Bone Regeneration

Synthetic substitutes of bone grafts, such as calcium phosphate-based ceramics, have shown some good clinical successes in the regeneration of large bone defects and are currently extensively used. In the past decade, the field of biomineralization has delivered important new fundamental knowledge and techniques to better understand this fascinating phenomenon. This knowledge is also applied in the field of biomaterials, with the aim of bringing the composition and structure, and hence the performance, of synthetic bone graft substitutes even closer to those of the extracellular matrix of bone. The purpose of this progress report is to critically review advances in mimicking the extracellular matrix of bone as a strategy for development of new materials for bone regeneration. Lab-made biomimicking or bioinspired materials are discussed against the background of the natural extracellular matrix, starting from basic organic and inorganic components, and progressing into the building block of bone, the mineralized collagen fibril, and finally larger, 2D and 3D constructs. Moreover, bioactivity studies on state-of-the-art biomimicking materials are discussed. By addressing these different topics, an overview is given of how far the field has advanced toward a true bone-mimicking material, and some suggestions are offered for bridging current knowledge and technical gaps.

Atomically resolved calcium phosphate coating on a gold substrate

Some articles have revealed that the electrodeposition of calcium phosphate (CaP) coatings entails a precursor phase, similarly to biomineralization in vivo. The chemical composition of the initial layer and its thickness are, however, still arguable, to the best of our knowledge. Moreover, while CaP and electrodeposition of metal coatings have been studied utilizing atom-probe tomography (APT), the electrodeposition of CaP ceramics has not been heretofore studied. Herein, we present an investigation of the CaP deposition on a gold substrate. Using APT and transmission electron microscopy (TEM) it is found that a mixture of phases, which could serve as transient precursor phases to hydroxyapatite (HAp), can be detected. The thickness of these phases is tens of nanometers, and they consist of amorphous CaP (ACP), dibasic calcium phosphate dihydrate (DCPD), and octacalcium phosphate (OCP). This demonstrates the value of using atomic-resolved characterization techniques for identifying the precursor phases. It also indicates that the kinetics of their transformation into the more stable HAp is not too fast to enable their observation. The coating gradually displays higher Ca/P atomic ratios, a porous nature, and concomitantly a change in its density.

Fabrication and biological properties of calcium phosphate/chitosan composite coating on titanium in modified SBF

In order to increase the biocompatibility and bioactivity of chitosan, hydroxyapatite was in situ combined into the spin-coated chitosan layer on the titanium substrate by incubating in modified simulated body fluid (m-SBF). The calcium phosphate/chitosan (CaP/CS) composite prepared in m-SBF showed a homogeneous distribution of spherical nano-clusters. The hydrophilicity of the coatings was increased by performing NaOH post-treatment of CaP/CS composites, which also affected apatite formation. Biocompatibility of the coatings was assessed by investigating the cellular response of human osteoblast-like MG-63 cells with 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Cell adhesion and osteogenic properties of the mesoporous CaP/CS composite were evaluated by SEM and ALPase assay, respectively. This in vitro study showed improved cell adhesion and differentiation on nanostructured CaP/CS composites. These results indicate that this CaP/CS composite could be a promising candidate for bone tissue engineering.

The limiting layer of fish scales: Structure and properties

Fish scales serve as a flexible natural armor that have received increasing attention across the materials community. Most efforts in this area have focused on the composite structure of the predominately organic elasmodine, and limited work addresses the highly mineralized external portion known as the Limiting Layer (LL). This coating serves as the first barrier to external threats and plays an important role in resisting puncture. In this investigation the structure, composition and mechanical behavior of the LL were explored for three different fish, including the arapaima (Arapaima gigas), the tarpon (Megalops atlanticus) and the carp (Cyprinus carpio). The scales of these three fish have received the most attention within the materials community. Features of the LL were evaluated with respect to anatomical position to distinguish site-specific functional differences. Results show that there are significant differences in the surface morphology of the LL from posterior and anterior regions in the scales, and between the three fish species. The calcium to phosphorus ratio and the mineral to collagen ratios of the LL are not equivalent among the three fish. Results from nanoindentation showed that the LL of tarpon scales is the hardest, followed by the carp and the arapaima and the differences in hardness are related to the apatite structure, possibly induced by the growth rate and environment of each fish.

STATEMENT OF SIGNIFICANCE

The natural armor of fish, turtles and other animals, has become a topic of substantial scientific interest. The majority of investigations have focused on the more highly organic layer known as the elasmodine. The present study addresses the highly mineralized external portion known as the Limiting Layer (LL). Specifically, the structure, composition and mechanical behavior of the LL were explored for three different fish, including the arapaima (Arapaima gigas), the tarpon (Megalops atlanticus) and the carp (Cyprinus carpio). Results show that there are significant differences in the surface morphology of the LL from posterior and anterior regions in the scales, and between the three species. In addition, the composition of the LL is also unique among the three fish. Results from nanoindentation showed that the LL of tarpon scales is the hardest, followed by the carp and the arapaima and the differences in hardness are related to the apatite structure, possibly induced by the growth rate and environment of each fish. In addition, a new feature was indentified in the LL, which has not been discussed before. As such, we feel this work is unique and makes a significant contribution to the field.

Advances in Multiscale Characterization Techniques of Bone and Biomaterials Interfaces

The success of osseointegrated biomaterials often depends on the functional interface between the implant and mineralized bone tissue. Several parallels between natural and synthetic interfaces exist on various length scales from the microscale toward the cellular and the atomic scale structure. Interest lies in the development of more sophisticated methods to probe these hierarchical levels in tissues at both biomaterials interfaces and natural tissue interphases. This review will highlight new and emerging perspectives toward understanding mineralized tissues, particularly bone tissue, and interfaces between bone and engineered biomaterials at multilength scales and with multidimensionality. Emphasis will be placed on highlighting novel and correlative X-ray, ion, and electron beam imaging approaches, such as electron tomography, atom probe tomography, and in situ microscopies, as well as spectroscopic and mechanical characterizations. These less conventional approaches to imaging biomaterials are contributing to the evolution of the understanding of the structure and organization in bone and bone integrating materials.

Two intensified fluorescence colors' switching achieved by branched dye nanoaggregates

In this study, a variety of branched target dyes containing double internal proton transfer segments were synthesized. For comparison, some linear analogs including a single internal proton transfer part were synthesized. The corresponding reference molecules lacking proton transfer segments were also prepared. The properties and aggregation modes of these dye aggregates were investigated on the basis of scanning electron microscopy images, transmission electron microscopy images, dynamic light scattering, X-ray diffraction, UV/visible absorption spectra and fluorescence emission spectra. The results showed that molecular aggregates with the morphologies of nano-scaled rounded or cubic particles of the target branched dyes could be yielded in mixed organic solvent/H₂O solution. A remarkable emission enhancement and fluorescence switching process (from bright yellow to luminous pure blue) under 365 nm lamp irradiation was observed for these target branched dye nanoaggregates. However, no aggregates of the reference branched dyes free of hydroxyl groups were formed and no obvious spectral variations were found. In contrast, all the studied linear dyes yielded molecular nanoaggregates in mixed organic solvent/H₂O solution, and only intensified single normal blue fluorescence emission was presented. This study provided real examples of some branched organic dye aggregates which were capable of displaying naked-eye enhanced fluorescence color switching under an UV lamp.

Pulsed-voltage atom probe tomography of low conductivity and insulator materials by application of ultrathin metallic coating on nanoscale specimen geometry

We present a novel approach for analysis of low-conductivity and insulating materials with conventional pulsed-voltage atom probe tomography (APT), by incorporating an ultrathin metallic coating on focused ion beam prepared needle-shaped specimens. Finite element electrostatic simulations of coated atom probe specimens were performed, which suggest remarkable improvement in uniform voltage distribution and subsequent field evaporation of the insulated samples with a metallic coating of approximately 10nm thickness. Using design of experiment technique, an experimental investigation was performed to study physical vapor deposition coating of needle specimens with end tip radii less than 100nm. The final geometries of the coated APT specimens were characterized with high-resolution scanning electron microscopy and transmission electron microscopy, and an empirical model was proposed to determine the optimal coating thickness for a given specimen size. The optimal coating strategy was applied to APT specimens of resin embedded Au nanospheres. Results demonstrate that the optimal coating strategy allows unique pulsed-voltage atom probe analysis and 3D imaging of biological and insulated samples.

Comparing the Consistency of Atom Probe Tomography Measurements of Small-Scale Segregation and Clustering Between the LEAP 3000 and LEAP 5000 Instruments

The local electrode atom probe (LEAP) has become the primary instrument used for atom probe tomography measurements. Recent advances in detector and laser design, together with updated hit detection algorithms, have been incorporated into the latest LEAP 5000 instrument, but the implications of these changes on measurements, particularly the size and chemistry of small clusters and elemental segregations, have not been explored. In this study, we compare data sets from a variety of materials with small-scale chemical heterogeneity using both a LEAP 3000 instrument with 37% detector efficiency and a 532-nm green laser and a new LEAP 5000 instrument with a manufacturer estimated increase to 52% detector efficiency, and a 355-nm ultraviolet laser. In general, it was found that the number of atoms within small clusters or surface segregation increased in the LEAP 5000, as would be expected by the reported increase in detector efficiency from the LEAP 3000 architecture, but subtle differences in chemistry were observed which are attributed to changes in the way multiple hit detection is calculated using the LEAP 5000.

Calcium Phosphate Bioceramics: A Review of Their History, Structure, Properties, Coating Technologies and Biomedical Applications

Calcium phosphate (CaP) bioceramics are widely used in the field of bone regeneration, both in orthopedics and in dentistry, due to their good biocompatibility, osseointegration and osteoconduction. The aim of this article is to review the history, structure, properties and clinical applications of these materials, whether they are in the form of bone cements, paste, scaffolds, or coatings. Major analytical techniques for characterization of CaPs, in vitro and in vivo tests, and the requirements of the US Food and Drug Administration (FDA) and international standards from CaP coatings on orthopedic and dental endosseous implants, are also summarized, along with the possible effect of sterilization on these materials. CaP coating technologies are summarized, with a focus on electrochemical processes. Theories on the formation of transient precursor phases in biomineralization, the dissolution and reprecipitation as bone of CaPs are discussed. A wide variety of CaPs are presented, from the individual phases to nano-CaP, biphasic and triphasic CaP formulations, composite CaP coatings and cements, functionally graded materials (FGMs), and antibacterial CaPs. We conclude by foreseeing the future of CaPs.

The bone-implant interface of dental implants in humans on the atomic scale

Osseointegration of dental implants occurs on a hierarchy of length scales down to the atomic level. A deeper understanding of the complex processes that take place at the surface of an implant on the smallest scale is of interest for the development of improved biomaterials. To date, transmission electron microscopy (TEM) has been utilized for examination of the bone-implant interface, providing details on the nanometer level. In this study we show that TEM imaging can be complemented with atom probe tomography (APT) to reveal the chemical composition of a Ti-based dental implant in a human jaw on the atomic level of resolution. As the atom probe technique has equal sensitivity for all elements, it allows for 3 dimensional characterizations of osseointegrated interfaces with unprecedented resolution. The APT reconstructions reveal a Ca-enriched zone in the immediate vicinity of the implant surface. A surface oxide of some 5nm thickness was measured on the titanium implant, with a sub-stoichiometric composition with respect to TiO₂. Minor incorporation of Ca into the thin oxide film was also evident. We conclude that the APT technique is capable of revealing chemical information from the bone-implant interface in 3D with unprecedented resolution, thus providing important insights into the mechanisms behind osseointegration.

STATEMENT OF SIGNIFICANCE

Osseointegration of dental implants occurs on a hierarchy of length scales down to the atomic level. A deeper understanding of the complex processes that take place at the surface of an implant on the smallest scale is of interest for the development of improved biomaterials. To date, transmission electron microscopy (TEM) has been utilized for examination of the bone-implant interface, providing details on the nanometer level. In this study we show that TEM imaging can be complemented with atom probe tomography (APT) to reveal the chemical composition of a Ti-based dental implant in a human jaw on the atomic level of resolution. Correlative microscopy ensures the accuracy of APT reconstructions and helps provide both chemical and structural information of the bone-implant interface on the smallest of length scales.

Atomic scale chemical tomography of human bone

Human bone is a complex hierarchical material. Understanding bone structure and its corresponding composition at the nanometer scale is critical for elucidating mechanisms of biomineralization under healthy and pathological states. However, the three-dimensional structure and chemical nature of bone remains largely unexplored at the nanometer scale due to the challenges associated with characterizing both the structural and chemical integrity of bone simultaneously. Here, we use correlative transmission electron microscopy and atom probe tomography for the first time, to our knowledge, to reveal structures in human bone at the atomic level. This approach provides an overlaying chemical map of the organic and inorganic constituents of bone on its structure. This first use of atom probe tomography on human bone reveals local gradients, trace element detection of Mg, and the co-localization of Na with the inorganic-organic interface of bone mineral and collagen fibrils, suggesting the important role of Na-rich organics in the structural connection between mineral and collagen. Our findings provide the first insights into the hierarchical organization and chemical heterogeneity in human bone in three-dimensions at its smallest length scale – the atomic level. We demonstrate that atom probe tomography shows potential for new insights in biomineralization research on bone.

Nanogeochronology of discordant zircon measured by atom probe microscopy of Pb-enriched dislocation loops

Isotopic discordance is a common feature in zircon that can lead to an erroneous age determination, and it is attributed to the mobilization and escape of radiogenic Pb during its post-crystallization geological evolution. The degree of isotopic discordance measured at analytical scales of ~10 μm often differs among adjacent analysis locations, indicating heterogeneous distributions of Pb at shorter length scales. We use atom probe microscopy to establish the nature of these sites and the mechanisms by which they form. We show that the nanoscale distribution of Pb in a ~2.1 billion year old discordant zircon that was metamorphosed c. 150 million years ago is defined by two distinct Pb reservoirs. Despite overall Pb loss during peak metamorphic conditions, the atom probe data indicate that a component of radiogenic Pb was trapped in 10-nm dislocation loops that formed during the annealing of radiation damage associated with the metamorphic event. A second Pb component, found outside the dislocation loops, represents homogeneous accumulation of radiogenic Pb in the zircon matrix after metamorphism. The (207)Pb/(206)Pb ratios measured from eight dislocation loops are equivalent within uncertainty and yield an age consistent with the original crystallization age of the zircon, as determined by laser ablation spot analysis. Our results provide a specific mechanism for the trapping and retention of radiogenic Pb during metamorphism and confirm that isotopic discordance in this zircon is characterized by discrete nanoscale reservoirs of Pb that record different isotopic compositions and yield age data consistent with distinct geological events. These data may provide a framework for interpreting discordance in zircon as the heterogeneous distribution of discrete radiogenic Pb populations, each yielding geologically meaningful ages.

Atomic-scale compositional mapping reveals Mg-rich amorphous calcium phosphate in human dental enamel

Human dental enamel, the hardest tissue in the body, plays a vital role in protecting teeth from wear as a result of daily grinding and chewing as well as from chemical attack. It is well established that the mechanical strength and fatigue resistance of dental enamel are derived from its hierarchical structure, which consists of periodically arranged bundles of hydroxyapatite (HAP) nanowires. However, we do not yet have a full understanding of the in vivo HAP crystallization process that leads to this structure. Mg(2+) ions, which are present in many biological systems, regulate HAP crystallization by stabilizing its precursor, amorphous calcium phosphate (ACP), but their atomic-scale distribution within HAP is unknown. We use atom probe tomography to provide the first direct observations of an intergranular Mg-rich ACP phase between the HAP nanowires in mature human dental enamel. We also observe Mg-rich elongated precipitates and pockets of organic material among the HAP nanowires. These observations support the postclassical theory of amelogenesis (that is, enamel formation) and suggest that decay occurs via dissolution of the intergranular phase. This information is also useful for the development of more accurate models to describe the mechanical behavior of teeth.

Atom Probe Tomographic Mapping Directly Reveals the Atomic Distribution of Phosphorus in Resin Embedded Ferritin

Here we report the atomic-scale analysis of biological interfaces within the ferritin protein using atom probe tomography that is facilitated by an advanced specimen preparation approach. Embedding ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualise atomic distributions and distinguish the inorganic-organic interface of the ferrihydrite mineral core and protein shell, as well as the organic-organic interface between the ferritin protein shell and embedding resin. In addition, we definitively show the atomic-scale distribution of phosphorus as being at the surface of the ferrihydrite mineral with the distribution of sodium mapped within the protein shell environment with an enhanced distribution at the mineral/protein interface. The sample preparation method is robust and can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment.