Tip Calibration Research Articles

The red giant branch tip in the SDSS, PS1, JWST, NGRST, and Euclid photometric systems

We used synthetic photometry from Gaia DR3 BP and RP spectra for a large selected sample of stars in the Large Magellanic Cloud (LMC) and Small Magellanic Cloud (SMC) to derive the magnitude of the red giant branch (RGB) tip for these two galaxies in several passbands across a range of widely used optical photometric systems, including those of space missions that have not yet started their operations. The RGB tip is estimated by fitting a well motivated model to the RGB luminosity function (LF) within a fully Bayesian framework, allowing for a proper representation of the uncertainties of all the involved parameters and their correlations. By adopting the best available distance and interstellar extinction estimates, we provide a calibration of the RGB tip as a standard candle for the following passbands: Johnson-Kron-Cousins I (mainly used for validation purposes), Hubble Space Telescope F814W, Sloan Digital Sky Survey i and z, PanSTARRS 1 y, James Webb Space Telescope F090W, Nancy Grace Roman Space Telescope Z087, and Euclid IE, with an accuracy within a few per cent, depending on the case. We used theoretical models to explore the trend of the absolute magnitude of the tip as a function of colour in the different passbands (beyond the range spanned by the LMC and SMC), as well as its dependency on age. These calibrations can be very helpful to obtain state-of-the-art RGB tip distance estimates to stellar systems in a very large range of distances directly from data in the natural photometric system of these surveys and/or missions, without recurring to photometric transformations. We have made the photometric catalogues publicly available for calibrations in additional passbands or for different approaches in the estimate of the tip, as well as for stellar populations and stellar astrophysics studies that may take advantage of large and homogeneous datasets of stars with magnitudes in 22 different passbands.

Application of the nuclear tracks methodology for the validation of atomic force microscope probe tips

Atomic force microscopy (AFM) is a well-established technique for studying materials at nanoscale dimensions. The resolution of this instrument strongly relies on the sharpness of its tip, which can become compromised through wear and breakage, often due to contamination at the AFM tip apex. To evaluate the condition of both new and used tips, scanning electron microscopy (SEM) inspection is commonly employed. However, SEM services may not always be readily available or in high demand. In this study, we present an AFM tip calibration device that utilizes a pattern of etched tracks on CR-39 material. To construct this device, you will require a radioactive alpha particle source, typically Americium-241, as well as a controlled temperature bath set at 60 degrees Celsius, which contains a 6.25 M KOH solution. This endeavor serves as another intriguing and practical application of the nuclear tracks methodology.

Calibration and data-analysis routines for nanoindentation with spherical tips

Instrumented spherical nanoindentation with a continuous stiffness measurement has gained increased popularity in microphysical investigations of grain boundaries, twins, dislocation densities, ion-induced damage, and more. These studies rely on different methodologies for instrument and tip calibration. Here, we test, integrate, and re-adapt published strategies for tip and machine-stiffness calibration for spherical tips. We propose a routine for independently calibrating the effective tip radius and the machine stiffness using standard reference materials, which requires the parametrization of the effective radius as a function of load. We validate our proposed workflow against key benchmarks and apply the resulting calibrations to data collected in materials with varying ductility to extract indentation stress–strain curves. We also test the impact of the machine stiffness on recently proposed methods for identification of yield stress. Finally, we synthesize these analyses in a single workflow for use in future studies aiming to extract and process data from spherical nanoindentation.Graphic abstract

Ancient mitogenomes from the Southern Pampas of Argentina reflect local differentiation and limited extra-regional linkages after rapid initial colonization.

This study aims to contribute to the recovery of Indigenous evolutionary history in the Southern Pampas region of Argentina through an analysis of ancient complete mitochondrial genomes. We generated DNA data for nine complete mitogenomes from the Southern Pampas, dated to between 2531 and 723 cal BP. In combination with previously published ancient mitogenomes from the region and from throughout South America, we documented instances of extra-regional lineage-sharing, and estimated coalescent ages for local lineages using a Bayesian method with tip calibrations in a phylogenetic analysis. We identified a novel mitochondrial haplogroup, B2b16, and two recently defined haplogroups, A2ay and B2ak1, as well as three local haplotypes within founder haplogroups C1b and C1d. We detected lineage-sharing with ancient and contemporary individuals from Central Argentina, but not with ancient or contemporary samples from North Patagonian or Littoral regions of Argentina, despite archeological evidence of cultural interactions with the latter regions. The estimated coalescent age of these shared lineages is ~10,000 years BP. The history of the human populations in the Southern Pampas is temporally deep, exhibiting long-term continuity of mitogenome lineages. Additionally, the identification of highly localized mtDNA clades accords with a model of relatively rapid initial colonization of South America by Indigenous communities, followed by more local patterns of limited gene flow and genetic drift in various South American regions, including the Pampas.

Relative performance of Bayesian morphological clock and parsimony methods for phylogenetic reconstructions: Insights from the case of Myomiminae and Dryomyinae glirid rodents.

Extinct organisms provide crucial information about the origin and time of origination of extant groups. The importance of morphological phylogenetics for rigorously dating the tree of life is now widely recognized and has been revitalized by methodological developments such as the application of tip-dating Bayesian approaches. Traditionally, molecular clocks have been node calibrated. However, node calibrations are often unsatisfactory because they do not allow the fossil age to inform about phylogenetic hypothesis. The introduction of tip calibrations allow fossil species to be included alongside their living relatives, and the absence of molecular sequence data for these taxa to be remedied by supplementing the sequence alignments for living taxa with phenotype character matrices for both living and fossil taxa. Therefore, only phylogenetic analyses that take into account morphological characters can incorporate both fossil and extant species. Herein we present an unprecedented morphological dataset for a vast group of glirid rodents, to which different phylogenetic methodologies have been applied. We have compared the tree topologies resulting from traditional parsimony and Bayesian phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip-dated clock methods seem to outperform parsimony with our dataset. The strict consensus tree recovered by tip dating invalidates the classic classification and allows dates to be proposed for the divergence and origin of the different clades.

Performance test of cantilever transfer standard used for afm tip calibration based on electromagnetic compensation

This paper describes stiffness measurement of cantilever transfer standards used for Atomic Force Microscopy (AFM) tip calibration based on electromagnetic compensation. The transfer standard of cantilever is designed and manufactured based on the bulk fabrication of SOI wafers. The measure range of the transfer standard covers from 0.04 N/m to 16 N/m. The series of transfer standard is designed for the calibration test of the cantilever used in AFM, along with the test apparatus specifically designed. The relative uncertainty of the stiffness is smaller than 2.4 % (<em>k</em> = 2).

Raising names from the dead: A time-calibrated phylogeny of frog shells (Bursidae, Tonnoidea, Gastropoda) using mitogenomic data

With 59 Recent species, Bursidae, known as «frog shells», are a small but widely distributed group of tropical and subtropical gastropods that are most diverse in the Indo-West Pacific. The present study is aimed at reconstructing phylogenetic relationships of bursid gastropods based on extensive and representative taxon sampling. Five genetic markers (cytochrome c oxidase subunit I (cox1), 16 s and 12 s rRNA mitochondrial genes, 28 s rRNA and Histone H3 nuclear gene) were sequenced for over 30 species in every known genus but Crossata. Furthermore, we sequenced the complete mt-genome of 9 species (10 specimens) (Aspa marginata, Marsupina bufo, Korrigania quirihorai, Korrigania fijiensis, Tutufa rubeta, Bursa lamarckii, Lampasopsis rhodostoma (twice), Bufonaria perelegans and Bursa aff. tuberosissima). Our analysis recovered Bursidae as a monophyletic group, whereas the genus Bursa was found to be polyphyletic. The genera Talisman and Dulcerana are resurrected and the genera Alanbeuella gen. nov. and Korrigania gen. nov. are described. Dating analysis using 21 extinct taxa for node and simplified tip calibrations was performed, showing a diversification of the group in two phases. Diversification may be linked to tectonic events leading to biodiversity relocation from the western Tethys toward the Indo-Pacific.

Ultrasound calibration with ladder phantom at multiple depths for breast biopsy navigation system

Ultrasound guided breast biopsy navigation system with a graphical user interface and a passive robotic needle holder is developed to increase the performance and reliability of the radiologist. Ultrasound calibration and tool tip calibration are required before using the system. A ladder phantom is developed to be used for ultrasound calibration in real time system with only one ultrasound image required. The passive robotic needle holder structure results in an identity matrix for the makes the rotation matrix; therefore, only translation and scaling are required in the system. This method can be applied to multiple ultrasound depths, which has a relationship at each depth and a relationship to the ultrasound image on the display. The results show high accuracy (<1 mm.) and rapid calibration (5–10 minutes) which is suitable for a real time system like a breast biopsy navigation system based on tests with a breast phantom.

Uncertainty Analysis of Stray Field Measurements by Quantitative Magnetic Force Microscopy

Magnetic force microscopy (MFM) measurements generally provide phase images which represent the signature of domain structures on the surface of nanomaterials. To quantitatively determine magnetic stray fields based on an MFM image requires calibrated properties of the magnetic tip. In this work, an approach is presented for calibrating a magnetic tip using a Co/Pt multilayered film as a reference sample which shows stable well-known magnetic properties and well-defined perpendicular band domains. The approach is based on a regularized deconvolution process in Fourier domain with a Wiener filter and the L-curve method for determining a suitable regularization parameter to get a physically reasonable result. The calibrated tip is applied for a traceable quantitative determination of the stray fields of a test sample which has a patial frequency spectrum covered by that of the reference sample. According to the "Guide to the expression of uncertainty in measurement", uncertainties of the processing algorithm are estimated considering the fact that the regularization influences significantly the quantitative analysis. We discuss relevant uncertainty components and their propagations between real domain and Fourier domain for both, the tip calibration procedure and the stray field calculation, and propose an uncertainty evaluation procedure for quantitative magnetic force microscopy.

The impact of fossil stratigraphic ranges on tip‐calibration, and the accuracy and precision of divergence time estimates

AbstractThe molecular clock provides the only viable means of establishing realistic evolutionary timescales but it remains unclear how best to calibrate divergence time analyses. Calibrations can be applied to the tips and/or to the nodes of a phylogeny. Tip‐calibration is an attractive approach since it allows fossil species to be included alongside extant relatives in molecular clock analyses. However, most fossil species are known from multiple stratigraphical horizons and it remains unclear how such age ranges should be interpreted to codify tip‐calibrations. We use simulations and empirical data to explore the impact on precision and accuracy of different approaches to informing tip‐calibrations. In particular, we focus on the effect of using tip‐calibrations defined using the oldest vs youngest stratigraphic occurrences, the full stratigraphical range, as well as confidence intervals on these data points. The results of our simulations show that using different calibration approaches leads to different divergence‐time estimates and demonstrate that concentrating tip‐calibrations near the root of the dated phylogeny improves both precision and accuracy of estimated divergence times. Finally, our results indicate that the highest levels of accuracy and precision are achieved when fossil tips are calibrated based on the fossil occurrence from which the morphological data were derived. These trends were corroborated by analysis of an empirical dataset for Ursidae. Overall, we conclude that tip‐dating analyses should, in particular, employ tip calibrations close to the root of the tree and they should be calibrated based on the age of the fossil used to inform the morphological data used in Total Evidence Dating.

Strain Rate Sensitivity of the Nanoindentation Creep of Ag, Cu, and Ni Thin Films

Ag, Cu, and Ni films each of 150 nm, 300 nm, 600 nm and 1000 nm thickness were deposited on Si using E-beam evaporation. The structural and surface properties were explored using FE-SEM and AFM. The crystal structure and orientation of the films were examined using x-ray diffraction. Nanocrystalline grain structure formation was observed to dominate the crystal film growth. The nanomechanical and creep properties were measured using nano-indentation. The hardness results as calculated based on tip calibration and contact stiffness for Ag differ due to excessive pile-up. Since Cu and Ni endure less pile-up, the hardness results exhibit little or no difference. For Ag films, the hardness based on tip calibration increases with the normalized depth of indentation as the film thickness decreases and remains nearly flat (no size effects). On the other hand, the hardness based on contact stiffness remains the same with the normalized depth of indentation regardless of the film thickness. For creep experiments, the strain rate sensitivity, m, of the hardness for the Ag, Cu, and Ni films is reported as 0.033 ± 0.001, 0.03 ± 0.003, and 0.04 ± 0.005 respectively. The normalized activation volume (V*/b3), when plotted versus the hardness (H), decreases with increasing hardness. V*/b3 measured at the surface of the bulk materials, i.e., shallow indents, is similar to V*/b3 measured for thin films when tested at 10–20% of the film thickness to circumvent substrate effects. V*/b3 coalesces with the literature data from conventional uniaxial testing and nano-indentation data for bulk Ag, Cu, and Ni samples. Although m is different from bulk to thin films due to the differences in grain sizes, the activation volume results for thin films extrapolate substantially to the bulk material except for Ni as the results experience a slight deviation.

Galactic calibration of the tip of the red giant branch

AbstractIndications from Gaia data release 2 are that the tip of the red giant branch (a population II standard candle related to the helium flash in low mass stars) is close to –4 in absolute I magnitude in the Cousins photometric system. Our sample is high-latitude southern stars from the thick disk and inner halo, and our result is consistent with longstanding findings from globular clusters, whose distances were calibrated with RR Lyrae stars. As the Gaia mission proceeds, there is every reason to think an accurate Galactic geometric calibration of tip of the red giant branch will be a significant outcome for the extragalactic distance scale.

Comment on van Casteren et al. (2018): softer metallic spheres do abrade harder enamel.

Comment on van Casteren et al. (2018): softer metallic spheres do abrade harder enamel.

Calibrated work function mapping by Kelvin probe force microscopy.

We propose and demonstrate the implementation of an alternative work function tip calibration procedure for Kelvin probe force microscopy under ultrahigh vacuum, using monocrystalline metallic materials with known crystallographic orientation as reference samples, instead of the often used highly oriented pyrolytic graphite calibration sample. The implementation of this protocol allows the acquisition of absolute and reproducible work function values, with an improved uncertainty with respect to unprepared highly oriented pyrolytic graphite-based protocols. The developed protocol allows the local investigation of absolute work function values over nanostructured samples and can be implemented in electronic structures and devices characterization as demonstrated over a nanostructured semiconductor sample presenting Al0.7Ga0.3As and GaAs layers with variable thickness. Additionally, using our protocol we find that the work function of annealed highly oriented pyrolytic graphite is equal to 4.6 ± 0.03 eV.

Dimensional characterization of extracellular vesicles using atomic force microscopy

Extracellular vesicles (EV) are small biological entities released from cells into body fluids. EV are recognized as mediators in intercellular communication and influence important physiological processes. It has been shown that the concentration and composition of EV in body fluids may differ from healthy subjects to patients suffering from particular disease. So, EV have gained a strong scientific and clinical interest as potential biomarkers for diagnosis and prognosis of disease. Due to their small size, accurate detection and characterization of EV remain challenging. The aim of the presented work is to propose a characterization method of erythrocyte-derived EV using atomic force microscopy (AFM). The vesicles are immobilized on anti-CD235a-modified mica and analyzed by AFM under buffer liquid and dry conditions. EV detected under both conditions show very similar sizes namely ~30 nm high and ~90 nm wide. The size of these vesicles remains stable over drying time as long as 7 d at room temperature. Since the detected vesicles are not spherical, EV are characterized by their height and diameter, and not only by the height as is usually done for spherical nanoparticles. In order to obtain an accurate measurement of EV diameters, the geometry of the AFM tip was evaluated to account for the lateral broadening artifact inherent to AFM measurements. To do so, spherical polystyrene (PS) nanobeads and EV were concomitantly deposited on the same mica substrate and simultaneously measured by AFM under dry conditions. By applying this procedure, direct calibration of the AFM tip could be performed together with EV characterization under identical experimental conditions minimizing external sources of uncertainty on the shape and size of the tip, thus allowing standardization of EV measurement.

Tips and nodes are complementary not competing approaches to the calibration of molecular clocks.

Molecular clock methodology provides the best means of establishing evolutionary timescales, the accuracy and precision of which remain reliant on calibration, traditionally based on fossil constraints on clade (node) ages. Tip calibration has been developed to obviate undesirable aspects of node calibration, including the need for maximum age constraints that are invariably very difficult to justify. Instead, tip calibration incorporates fossil species as dated tips alongside living relatives, potentially improving the accuracy and precision of divergence time estimates. We demonstrate that tip calibration yields node calibrations that violate fossil evidence, contributing to unjustifiably young and ancient age estimates, less precise and (presumably) accurate than conventional node calibration. However, we go on to show that node and tip calibrations are complementary, producing meaningful age estimates, with node minima enforcing realistic ages and fossil tips interacting with node calibrations to objectively define maximum age constraints on clade ages. Together, tip and node calibrations may yield evolutionary timescales that are better justified, more precise and accurate than either calibration strategy can achieve alone.

Dating placentalia: Morphological clocks fail to close the molecular fossil gap.

Dating the origin of Placentalia has been a contentious issue for biologists and paleontologists. Although it is likely that crown‐group placentals originated in the Late Cretaceous, nearly all molecular clock estimates point to a deeper Cretaceous origin. An approach with the potential to reconcile this discrepancy could be the application of a morphological clock. This would permit the direct incorporation of fossil data in node dating, and would break long internal branches of the tree, so leading to improved estimates of node ages. Here, we use a large morphological dataset and the tip‐calibration approach of MrBayes. We find that the estimated date for the origin of crown mammals is much older, ∼130–145 million years ago (Ma), than fossil and molecular clock data (∼80–90 Ma). Our results suggest that tip calibration may result in estimated dates that are more ancient than those obtained from other sources of data. This can be partially overcome by constraining the ages of internal nodes on the tree; however, when this was applied to our dataset, the estimated dates were still substantially more ancient than expected. We recommend that results obtained using tip calibration, and possibly morphological dating more generally, should be treated with caution.

Process optimization for lattice-selective wet etching of crystalline silicon structures

Lattice-selective etching of silicon is used in a number of applications, but it is particularly valuable in those for which the lattice-defined sidewall angle can be beneficial to the functional goals. A relatively small but important niche application is the fabrication of tip characterization standards for critical dimension atomic force microscopes (CD-AFMs). CD-AFMs are commonly used as reference tools for linewidth metrology in semiconductor manufacturing. Accurate linewidth metrology using CD-AFM, however, is critically dependent upon calibration of the tip width. Two national metrology institutes and at least two commercial vendors have explored the development of tip calibration standards using lattice-selective etching of crystalline silicon. The National Institute of Standards and Technology standard of this type is called the single crystal critical dimension reference material. These specimens, which are fabricated using a lattice-plane-selective etch on (110) silicon, exhibit near vertical sidewalls and high uniformity and can be used to calibrate CD-AFM tip width to a standard uncertainty of less than 1 nm. During the different generations of this project, we evaluated variations of the starting material and process conditions. Some of our starting materials required a large etch bias to achieve the desired linewidths. During the optimization experiment described in this paper, we found that for potassium hydroxide etching of the silicon features, it was possible to independently tune the target linewidth and minimize the linewidth nonuniformity. Consequently, this process is particularly well suited for small-batch fabrication of CD-AFM linewidth standards.

Lateral tip control effects in critical dimension atomic force microscope metrology: the large tip limit

Sidewall sensing in critical dimension atomic force microscopes (CD-AFMs) usually involves continuous lateral dithering of the tip or the use of a control algorithm and fast response piezoactuator to position the tip in a manner that resembles touch-triggering of coordinate measuring machine probes. All methods of tip position control, however, induce an effective tip width that may deviate from the actual geometrical tip width. Understanding the influence and dependence of the effective tip width on the dither settings and lateral stiffness of the tip can improve the measurement accuracy and uncertainty estimation for CD-AFM measurements. Since CD-AFM typically uses tips that range from 15 to 850 nm in geometrical width, the behavior of effective tip width throughout this range should be understood. The National Institute of Standards and Technology (NIST) has been investigating the dependence of effective tip width on the dither settings and lateral stiffness of the tip, as well as the possibility of material effects due to sample composition. For tip widths of 130 nm and lower, which also have lower lateral stiffness, the response of the effective tip width to lateral dither is greater than for larger tips. However, we have concluded that these effects will not generally result in a residual bias, provided that the tip calibration and sample measurement are performed under the same conditions. To confirm that our prior conclusions about the dependence of effective tip width on lateral stiffness are valid for large CD tips, we recently performed experiments using a very large non-CD tip with an etched plateau of ∼2-μm width. The effective lateral stiffness of these tips is at least 20 times greater than typical CD-AFM tips, and these results supported our prior conclusions about the expected behavior for larger tips. The bottom-line importance of these latest observations is that we can now reasonably conclude that a dither slope of 3 nm/V is the baseline response due to the induced motion of the cantilever base.

Nanosurface Mechanical Properties of Polymers Based on Continuous Stiffness Indentation

A systematic experimental study of the large strain surface mechanical properties of a number of polymers {polymethylmethacrylate (PMMA), polyetheretherketone (PEEK), polystyrene (PS), polycarbonate (PC), polypropylene (PP), and ultra-high molecular weight polyethylene (UHMWPE)} at the nanometer scale is described. The polymeric surfaces were indented and the data were analyzed using a contact compliance method in conjunction with a nano-indenter system. The indentation experiments were performed using a Berkovich Tip indenter with a continuous contact compliance indentation mode. The indentations were performed using a constant loading rate (300 μN/sec) to a maximum penetration depth of 5 μm. The experimental results showed a considerable strain-rate hardening effect for the polymers and a peculiarly harder response of these surfaces at the near-to-surface (submicron) layers. PMMA was the hardest polymer of the selection, whereas UHMWPE and PP were observed to be the softest polymers. The paper includes practical consideration of a creeping effect and appropriateness of tip calibration using harder surfaces for nanoindentation experimentation of polymers.