Tip Sample Research Articles

Scanning Probe Nano‐Infrared Imaging and Spectroscopy of Biochemical and Natural Materials

The mid‐infrared with a characteristic wavelength of 3–20 μm is important for a wealth of technologies. In particular, mid‐infrared spectroscopy can reveal material composition and structure information by fingerprinting chemical bonds’ infrared resonances. Despite these merits, state‐of‐the‐art mid‐infrared techniques are spatially limited above tens of micrometers due to the fundamental diffraction law. Herein, recent progress in the scanning probe nanoscale infrared characterization of biochemical materials and natural specimens beyond this spatial limitation is reviewed. By leveraging the strong tip–sample local interactions, scanning probe nano‐infrared methods probe nanoscale optical and mechanical responses to disclose material composition, heterogeneity, orientation, fine structure, and phase transitions at unprecedented length scales. These advances, therefore, revolutionize the understanding of a broad range of biochemical and natural materials and offer new material manipulation and engineering opportunities close to the ultimate length scales of fundamental physical, chemical, and biological processes.

Tip‐Enhanced Raman Spectroscopy Coherence Length of 2D Materials: An Application to Graphene

Herein, a protocol is presented for determining the tip‐enhanced Raman spectroscopy (TERS) coherence length (Lc) of the two main Raman bands of graphene. This method involves performing approach curve experiments and plotting the normalized areas of the G and 2D bands as a function of tip–sample distance. The resultant data are fitted using a specific TERS formula to extract Lc. The results indicate different coherence lengths for the G and 2D bands in graphene as and nm. While this protocol is specifically done for graphene, the underlying theoretical framework, based on mode symmetry, can be extended to other 2D materials, such as transition metal dichalcogenides. This demonstrates the versatility and potential of TERS in exploring the coherence properties of various 2D materials.

Effects of air damping on quality factors of different probes in tapping mode atomic force microscopy

Abstract The AFM probe in tapping mode is a continuous process of energy dissipation, from moving away from to intermittent contact with the sample surfaces. At present, studies regarding the energy dissipation mechanism of this continuous process have only been reported sporadically, and there are no systematic explanations or experimental verifications of the energy dissipation mechanism in each stage of the continuous process. The quality factors can be used to characterize the energy dissipation in TM-AFM systems. In this study, the vibration model of the microcantilever beam was established, coupling the vibration and damping effects of the microcantilever beam. The quality factor of the vibrating microcantilever beam under damping was derived, and the air viscous damping when the probe is away from the sample and the air squeeze film damping when the probe is close to the sample were calculated. In addition, the mechanism of the damping effects of different shapes of probes at different tip–sample distances was analyzed. The accuracy of the theoretical simplified model was verified using both experimental and simulation methods. A clearer understanding of the kinetic characteristics and damping mechanism of the TM-AFM was achieved by examining the air damping dissipation mechanism of AFM probes in the tapping mode, which was very important for improving both the quality factor and the imaging quality of the TM-AFM system. This study’s research findings also provided theoretical references and experimental methods for the future study of the energy dissipation mechanism of micro-nano-electromechanical systems.

Bayesian Inference Under the Multispecies Coalescent with Ancient DNA Sequences.

Ancient DNA (aDNA) is increasingly being used to investigate questions such as the phylogenetic relationships and divergence times of extant and extinct species. If aDNA samples are sufficiently old, expected branch lengths (in units of nucleotide substitutions) are reduced relative to contemporary samples. This can be accounted for by incorporating sample ages into phylogenetic analyses. Existing methods that use tip (sample) dates infer gene trees rather than species trees, which can lead to incorrect or biased inferences of the species tree. Methods using a multispecies coalescent (MSC) model overcome these issues. We developed an MSC model with tip dates and implemented it in the program bpp. The method performed well for a range of biologically realistic scenarios, estimating calibrated divergence times and mutation rates precisely. Simulations suggest that estimation precision can be best improved by prioritizing sampling of many loci and more ancient samples. Incorrectly treating ancient samples as contemporary in analyzing simulated data, mimicking a common practice of empirical analyses, led to large systematic biases in model parameters, including divergence times. Two genomic datasets of mammoths and elephants were analyzed, demonstrating the method's empirical utility.

Enhancing ferroelectric characterization at nanoscale: A comprehensive approach for data processing in spectroscopic piezoresponse force microscopy

Switching Spectroscopy Piezoresponse Force Microscopy (SSPFM) stands out as a powerful method for probing ferroelectric properties within materials subjected to incremental polarization induced by an external electric field. However, the dense data processing linked to this technique is a critical factor influencing the quality of obtained results. Furthermore, meticulous exploration of various artifacts, such as electrostatics, which may considerably influence the signal, is a key factor in obtaining quantitative results. In this paper, we present a global methodology for SSPFM data processing, accessible in open-source with a user-friendly Python application called PySSPFM. A ferroelectric thin film sample of potassium sodium niobate has been probed to illustrate the different aspects of our methodology. Our approach enables the reconstruction of hysteresis nano-loops by determining the PR as a function of applied electric field. These hysteresis loops are then fitted to extract characteristic parameters that serve as measures of the ferroelectric properties of the sample. Various artifact decorrelation methods are employed to enhance measurement accuracy, and additional material properties can be assessed. Performing this procedure on a grid of points across the surface of the sample enables the creation of spatial maps. Furthermore, different techniques have been proposed to facilitate post-treatment analysis, incorporating algorithms for machine learning (K-means), phase separation, and mapping cross correlation, among others. Additionally, PySSPFM enables a more in-depth investigation of the material by studying the nanomechanical properties during poling, through the measurement of the resonance properties of the cantilever–tip–sample surface system.

Modification of transition pathways in polarized resonance Raman spectroscopy for carbon nanotubes by highly confined near-field light

We observed a modification of transition pathways in polarized resonance Raman spectroscopy during tip-enhanced Raman spectroscopy (TERS) analysis of metallic carbon nanotubes (CNTs). At a spatial resolution reaching up to the sub-nanometer regime, the signal intensity of the typical D-band is observed to be even higher than the intensity of the G-band all over the probed CNTs in TERS imaging. The measured D-band is attributed to the non-vertical transitions of electrons in k-space that are facilitated by highly confined near-field light at the tip–sample junction of our scanning tunneling microscope based TERS system. The D-band signal was observed even when the CNTs were excited by light polarized perpendicular to the tube axis that corresponds to electronic excitations between different cutting line numbers of a CNT. By combining the electron pathways brought about by both the near-field light and its polarization, we found a unique optical transition of electrons of CNTs in near-field Raman spectroscopy.

Probe chip nanofabrication enabled reverse tip sample scanning probe microscopy concept and measurements

We introduce a new scanning probe microscopy (SPM) concept called reverse tip sample scanning probe microscopy (RTS SPM), where the tip and sample positions are reversed as compared to traditional SPM. The main benefit of RTS SPM over the standard SPM configuration is that it allows for simple and fast tip changes. This overcomes two major limitations of SPM which are slow data acquisition and a strong dependency of the data on the tip condition. A probe chip with thousands of sharp integrated tips is the basis of our concept. We have developed a nanofabrication protocol for Si based probe chips and their functionalization with metal and diamond coatings, evaluated our probe chips for various RTS SPM applications (multi-tip imaging, SPM tomography, and correlative SPM), and showed the high potential of the RTS SPM concept.

Enabling focused ion beam sample preparation for application in reverse tip sample scanning probe microscopy

Focused ion beam (FIB) has become a powerful tool for transmission electron microscopy sample preparation in the nanoelectronics industry and has in recent years also shown its benefits for specific preparation steps in electrical scanning probe microscopy (SPM). Most recently, a novel SPM approach – so-called reverse tip sample (RTS) SPM – has been proposed in which the position of sample and tip are switched compared to standard SPM; in RTS SPM the sample is attached to the end of a cantilever beam. To achieve this configuration, the region of interest must first be extracted from a substrate and then needs to be reliably fixed to the cantilever by FIB. Therefore, we have explored and developed dedicated FIB preparation methods for RTS SPM in this work. Our established procedures ensure a strong mechanical and good electrical connection of the sample to the cantilever for both cross-section and top view sample preparation. Furthermore, we introduce an approach for mounting samples from a full wafer size workflow. This paper presents the developed FIB procedures and discusses the quality and stability of all mounted samples and their electrical evaluation in RTS SPM.

Endoscopic Ventricular Lavage in Pediatric Pyogenic Cerebral Ventriculitis Associated with Shunt: Outcomes and Technical Notes

Pyogenic cerebral ventriculitis (PCV) is a rare infectious entity characterized by a potent inflammatory reaction of the ventricular ependyma, which in most cases leads to death. We aim to present the technical note and protocol, based on our center's 10-year experience of the use of endoscopic ventricular lavage in pediatric patients with PCV and ventriculoperitoneal shunt (VPS). For this study, all pediatric patients (<16 years) with VP shunts and PCV who were treated with endoscopic ventricular lavage between January 2012 and January 2022 were included. 34 pediatric patients with ventriculitis were analyzed. The median age was 6 years, with 61.7% being male. Most consultations occurred on Day 2 of symptoms. Fever (38.2%) and altered consciousness (26.5%) were the most common initial symptoms. Early ventriculitis was observed in 67.7% of patients. Pathogen identification in the initial cerebrospinal fluid (CSF) sample was 70.6%, while samples from ventricular peritoneal shunt (VPS) yielded 23.53% and catheter culture 79.4%. Gram-positive bacteria, mainly S.epidermidis (44.1%), was the most commonly isolated agent. Endoscopic ventricular lavage was performed in 73.5% on the second or third day. Reinfection occurred in 23.5%, and 26.5% of patients died. Concordance analysis showed 85.3% agreement between LP and catheter tip samples. Functionality improved, with 55.88% achieving a Lansky score of 90. Early ventriculitis was associated with better Lansky scores. Endoscopic ventricular lavage can be a useful tool in the management of PCV in cases with VP shunts. Our study suggests a higher chance of isolating an infection-causing germ in the catheter tip culture specimen compared to the cerebrospinal fluid (CSF) culture. However, future studies with a larger number of patients, or multicentric studies are required for further analysis.

Thermal noise calibration of functionalized cantilevers for force microscopy: Effects of the colloidal probe position

Colloidal probes are often used in force microscopy when the geometry of the tip–sample interaction should be well controlled. Their calibration requires an understanding of their mechanical response, which is very sensitive to the details of the force sensor consisting of a cantilever and the attached colloid. We present some analytical models to describe the dynamics of the cantilever and its load positioned anywhere along its length. The thermal noise calibration of such probes is then studied from a practical point of view, leading to correction coefficients that can be applied in standard force microscope calibration routines. Experimental measurements of resonance frequencies and thermal noise profiles of raw and loaded cantilevers demonstrate the validity of the approach.

Design, Fabrication and Evaluation of Diamond Tip Chips for Reverse Tip Sample Scanning Probe Microscope Applications

Design, Fabrication and Evaluation of Diamond Tip Chips for Reverse Tip Sample Scanning Probe Microscope Applications

Nano-positive up negative down in binary oxide ferroelectrics

Ferroelectric HfO2 and ZrO2-based materials are promising candidates for next-generation ferroelectric devices, but their characterization is challenging due to complex factors such as crystal phases, degradation mechanisms, and local inhomogeneities. In this work, we propose a novel nanosized positive-up-negative-down (PUND) method to assess the ferroelectric response of doped-HfO2. This method is based on actual current probing and is immune to most electrostatic artifacts that plague other electrical atomic force microscopy (AFM) techniques. We demonstrate the PUND method’s ability to induce ferroelectric switching in Si-doped HfO2 and investigate the distinctive PUND response obtained for individual grains. We also extract the polarization charge based on a direct estimate of the tip–sample contact area. The proposed PUND method is a significant innovation as it is a method to combine the high spatial resolution of AFM with the immunity to electrostatic artifacts of current probing. This makes it a powerful tool for studying ferroelectric materials at the nanoscale, where local inhomogeneities and other effects can have a significant impact on their behavior. The PUND method is also notable for its ability to extract polarization charge based on a direct estimate of the tip–sample contact area. This is a significant improvement over previous methods, which often relied on indirect or approximate estimates of the contact area. Overall, the PUND method is a novel and innovative technique that offers significant advantages for the characterization of ferroelectric materials at the nanoscale. It is expected to have a major impact on the research and development of next-generation ferroelectric devices.

Sex Genotyping Mice by Polymerase Chain Reaction.

A simple method to determine the genetic sex of a mouse is to amplify DNA from a male-specific gene by polymerase chain reaction (PCR). This protocol is used to detect the Y-chromosome-specific gene Sry in tissue lysates of tail tip or ear punch samples.

Investigating the Microbial Contamination of Hookah Mouth Tips in Bandar Abbas City, Iran

Background: Hookah smoking is now increasing and has become a serious public health warning worldwide. Hookah smoking has led to the transmission of infectious diseases. This study investigates the microbial contamination of hookah mouth tips in Bandar Abbas City, Iran. Materials and Methods: This descriptive study was conducted in Bandar Abbas City, Iran. The hookah mouth tip samples were obtained from various hookah supply centers and the Ultersnap U device measured the microbial load of hookah mouth tips. The microbial load ranks were divided into three categories. Meanwhile, data analysis was done using the SPSS software, version 26. Results: The highest contamination tips were observed in the beach boulevard (Saheli-Blv), where vendors operate. In three parks, namely Park-e-Ghadir, Park-e-Dowlat, and 13-Hektar, one contaminated hookah mouth tip was observed in each station. A significant difference was observed between the stations in both clean and warning levels; however, this difference was not significant in the contaminated level (P˃0.05). The highest level of contamination was observed in the guild of peddlers. A significant difference was also observed between the guilds in both clean and warning levels, but this difference was not significant in the contaminated level (P˃0.05). Conclusion: Our results showed that a significant number of hookah mouth tips were in warning and contaminated levels. The highest number of contaminated hookah mouth tips were observed in the peddlers guild, which is strongly recommended to collect and prevent their inactivity, especially in public places. In addition, health warnings should be posted on all tobacco products and the environment of smoking and or cafes.

BIOTESTING OF SOIL CONDITIONS AT THE TERRITORIES ADJACENT TO AIRPORTS

The development of civil aviation is accompanied by a constant increase in man-made load on the environment. The application of methods of bioindication and biotesting of anthropogenic and technogenic influences on the ecosystem components is one of the possible options for monitoring the state of the environment at territories subject to technogenic stress due to the activities of environmentally hazardous enterprises. To study the level of man-made impact of airport activities on the state of the soil (namely, phytotoxicity), at the territory adjacent to the airport "Kyiv" named after I. Sikorskyi International Airport from the upper and lower levels at different distances from the airport runway (from 5 m to 2 km) soil samples were taken using the envelope method. As a control (conditionally clean soil), a soil sample collected at the territory of Holosiiv Park (soil type: dark gray forest soils) was used. In total, six soil samples were analyzed. On the third day of germination the growth characteristics of Allium cepa seedlings were determined. Test parameters that were used to determine the phytotoxic effect: the percentage of seed germination, namely the energy of its germination, the length of the root and the length of the stem. The analysis of the obtained data on the germination of Allium cepa seeds showed that the lowest germination was recorded for the soil samples that were taken at a distance of 5 and 1500 m from the runway, which indicates an increased level of phytotoxic impact due to the activities of the airport.&#x0D; The greatest phytotoxic effect for the stem of Allium cepa seedlings was observed for the soil sample located at a distance of 5 m from the ZPS. For soil samples taken at a distance of 5 m to 1000 m, i.e. with distance from the runway of the airport, a decrease in the level of phytotoxicity of the soil is observed. Only when approaching the highway (at a distance of 1,000 m to 2,000 m) there was observed an increase in phytotoxicity of the soil again.&#x0D; Among the investigated samples of meristem tissues, the presence of mitotic activity of cells was observed in the meristems of root tip samples of onion seedlings germinated on soil samples that were taken at a distance of 5 m, 1500 m and 2000 m from the airport. The determined mitotic indices (MI) for these soil samples are as following: for a soil sample taken at a distance of 5 m, it was 2.9 %; for a soil sample taken at a distance of 1500 m was 2.6 %; for a soil sample taken at a distance of 2000 m was 2.6 %. The research results confirm the need for constant monitoring of the soil condition at these technogenically loaded territories, in order to increase the level of environmental safety of these territories.

Template-Free Synthesis of Phosphorus/Nitrogen-Doped Mesoporous Titania Materials with Excellent Adsorption for Lysozymes.

Element-doped mesoporous titanium oxide has significant advantages in substance separation and adsorption due to its larger specific surface area and stronger hydrophobicity. However, its current synthesis methods have limitations such as complicated preparation process, high production cost, or not being environmentally friendly, and the synthesis of elementally doped titanium oxide materials by simple, low-cost, and green means is the research goal of this study. In this study, phosphorus-doped mesoporous titanium oxides (TiP) materials have been synthesized through a facile template-free method in an ethanol system, which were further modified by nitrogen doping with the use of urea as the nitrogen source. Both the synthesized TiP and P-N codoped sample (N-TiP) are amorphous with mesopores. It was revealed by FTIR and XPS spectra that the formation of Ti-O-P and -O-Ti-N bonds in the synthesized samples was due to the partial substitution of phosphorus for titanium in Ti-O-Ti bonds in mesoporous titanium oxide, while nitrogen replaced some oxygen in the -O-Ti-O bonds in the form of anions. The TiP sample was estimated by the BET method to have a relatively large surface area, up to 317 m2/g. The adsorption of TiP and N-TiP materials to lysozyme protein in a buffer solution at different pH values showed that the adsorption of TiP to lysozyme protein was larger, which was 32.68 μmol/g. It shows that TiP has potential as a multifunctional adsorbent.

Stress distribution variations during nanoindentation failure of hard coatings on silicon substrates

Regarding quality inspection of technologically important nanocomposite hard coatings based on Ti, B, Si, C, and N and bioceramics such as hydroxyapatite that are used in small-scale high-precision devices and bio-implants, it is essential to study the failure mechanisms associated with nanoindentation, such as fracture, delamination, and chipping. The stress imposed by the indenter can affect the fracture morphology and the interfacial fracture energy, depending on indenter shape, substrate type, crystallographic properties, pre-existing flaws, internal micro-cracks, and pre-strain. Reported here are finite-element-based fracture studies that provide insights into the different cracking mechanisms related to the aforementioned failure process, showing that the fracture morphology is affected by the interaction of different cracking events. The interfacial fracture energy, toughness, and residual stress are calculated using existing models with minor adjustments, and it is found that increasing the indenter sharpness improves the shear stress distribution, making the coating more prone to separation. Depending on the prevailing type of stress, the stress distribution beneath the depression results in either crack formation or a dislocation pile-up leading to strain hardening. Different forms of resistances resulting from the indentation process are found to affect the tip–sample conduction, and because of its stronger induced plasticity than that of a Berkovich indenter tip, a sharper cube-corner tip produces more resistance.

Three-dimensional photoinduced force microscopy reveals artifacts from photothermal tip vibrations

Photoinduced force microscopy (PiFM) is a technique for nanoscale characterization of optically active materials. For correct data analysis, it is important to understand and recognize potential artifacts. In this study, we provide a Fourier-based framework for the different origins of the photoinduced force, including the photothermal motion of the atomic force microscopy (AFM) tip in PiFM measurements. We use individual gold nanoparticles as a model system to explore such tip-related phenomena and to demonstrate the benefits of three-dimensional analysis of the photoinduced force. Comparison of the in-phase heterodyne PiFM signal and the derivative of the tip–sample interaction, ∂⟨kts⟩/∂zc, directly reveals a photothermal origin for the PiFM signal in our experiments. Furthermore, we observe a lateral photothermal vibration of the tip apex induced by tip asymmetry. This lateral vibration emphasizes the importance of considering the motion of the AFM tip during data analysis. The improved lateral resolution conferred by ∂⟨kts⟩/∂zc can lead to misinterpretation. Our findings highlight that meticulous data analysis is required to ensure the correct interpretation of PiFM data.

Accurate determination of stiffness and strength of graphene via AFM-based membrane deflection

The Young’s modulus and fracture strength of single and bilayer graphene (BLGr) grown by chemical vapour deposition (CVD) were determined using atomic force microscopy-based membrane deflection experiments. The uncertainty resulting from instrument calibration and the errors due to the experimental conditions like tip wear, loading position, and sample preparation were investigated to estimate the accuracy of the method. The theoretical estimation of the uncertainty on the Young’s modulus linked to the calibration is around 16%. Finite element simulations were performed to determine the effects of membrane shape and loading position on the extraction of the Young’s modulus. Off-centre loading results in the overestimation of the Young’s modulus while deviation from the circular shape leads to an underestimation of the stiffness. The simulated results were compared with experiments. With all these sources of errors taken into account, the Young’s modulus and fracture strength of CVD-grown single layer graphene are found equal to 0.88 ± 0.14 TPa and 134 ± 16 GPa, respectively. For CVD BLGr, the mean values of the Young’s modulus and fracture strength are equal to 0.70 ± 0.11 TPa and 95 ± 11 GPa, respectively.

Identification of the potential use of sago midrib (Metroxylon sp.) as drip irrigation emitters for chili plants

Drip irrigation is an irrigation system that can save water by releasing a regulated amount of water and nutrients to the roots of plants using emitters. The use of emitters is one of the additional costs in the use of drip irrigation systems. Estimating the potential of fronds as emitters are done by measuring saturated hydraulic conductivity. The method used is falling head to determine the ability of emitter material made from sago fronds to pass water that can be used to meet the water needs of chili plants. The results showed that the average hydraulic conductivity value at the end sample was higher than the middle and base samples. The hydraulic conductivity values of the tip, middle and base are 0.0077 (m/s), 0.0022 (m/s), and 0.0020 (m/s), respectively. So that the tip-sample can be used as a drip irrigation emitter. The discharge produced by the emitters of tip samples 1 and 2 amounted to 1.252 and 1.424 l/day. Based on this discharge, the number of droppers for each phase of chili plant growth using sago frond emitters, namely at the base and center, requires two emitters in months 3 and 4. Meanwhile, the end frond emitter only requires two emitters in month three, and in other growth phases only requires one emitter.