A scanning tunneling microscope capable of electron spin resonance and pump-probe spectroscopy at mK temperature and in vector magnetic field.

In the last decade, detecting spin dynamics at the atomic scale has been enabled by combining techniques such as electron spin resonance (ESR) or pump-probe spectroscopy with scanning tunneling microscopy (STM). Here, we demonstrate an ultra-high vacuum STM operational at milliKelvin (mK) temperatures and in a vector magnetic field capable of both ESR and pump-probe spectroscopy. By implementing GHz compatible cabling, we achieve appreciable RF amplitudes at the junction while maintaining the mK base temperature and high energy resolution. We demonstrate the successful operation of our setup by utilizing two experimental ESR modes (frequency sweep and magnetic field sweep) on an individual TiH molecule on MgO/Ag(100) and extract the effective g-factor. We trace the ESR transitions down to MHz into an unprecedented low frequency band enabled by the mK base temperature. We also implement an all-electrical pump-probe scheme based on waveform sequencing suited for studying dynamics down to the nanoseconds range. We benchmark our system by detecting the spin relaxation time T1 of individual Fe atoms on MgO/Ag(100) and note a field strength and orientation dependent relaxation time.

Improving lung cancer diagnosis by combining exhaled-breath data and clinical parameters.

INTRODUCTION: Exhaled-breath analysis of volatile organic compounds could detect lung cancer earlier, possibly leading to improved outcomes. Combining exhaled-breath data with clinical parameters may improve lung cancer diagnosis. METHODS: Based on data from a previous multi-centre study, this article reports additional analyses. 138 subjects with non-small cell lung cancer (NSCLC) and 143 controls without NSCLC breathed into the Aeonose. The diagnostic accuracy, presented as area under the receiver operating characteristic curve (AUC-ROC), of the Aeonose itself was compared with 1) performing a multivariate logistic regression analysis of the distinct clinical parameters obtained, and 2) using this clinical information beforehand in the training process of the artificial neural network (ANN) for the breath analysis. RESULTS: NSCLC patients (mean±sd age 67.1±9.1 years, 58% male) were compared with controls (62.1±7.0 years, 40.6% male). The AUC-ROC of the classification value of the Aeonose itself was 0.75 (95% CI 0.69-0.81). Adding age, number of pack-years and presence of COPD to this value in a multivariate regression analysis resulted in an improved performance with an AUC-ROC of 0.86 (95% CI 0.81-0.90). Adding these clinical variables beforehand to the ANN for classifying the breath print also led to an improved performance with an AUC-ROC of 0.84 (95% CI 0.79-0.89). CONCLUSIONS: Adding readily available clinical information to the classification value of exhaled-breath analysis with the Aeonose, either post hoc in a multivariate regression analysis or a priori to the ANN, significantly improves the diagnostic accuracy to detect the presence or absence of lung cancer.

Sensitivity and specificity of an electronic nose in diagnosing pulmonary tuberculosis among patients with suspected tuberculosis.

OBJECTIVE: To investigate the potency of a hand-held point-of-care electronic-nose to diagnose pulmonary tuberculosis (PTB) among those suspected of PTB. METHODS: Setting: Lung clinics and Dr. Sardjito Hospital, Yogyakarta, Indonesia. Participants: patients with suspected PTB and healthy controls. Sampling: 5 minutes exhaled breath. Sputum-smear-microscopy, culture, chest-radiography, and follow-up for 1.5-2.5 years, were used to classify patients with suspected PTB as active PTB, probably active PTB, probably no PTB, and no PTB. After building a breath model based on active PTB, no PTB, and healthy controls (Calibration phase), we validated the model in all patients with suspected PTB (Validation phase). In each variable (sex, age, Body Mass Index, co-morbidities, smoking status, consumption of alcohol, use of antibiotics, flu symptoms, stress, food and drink intake), one stratum's Receiver Operating Characteristic (ROC)-curve indicating sensitivity and specificity of the breath test was compared with another stratum's ROC-curve. Differences between Area-under-the-Curve between strata (p<0.05) indicated an association between the variable and sensitivity-specificity of the breath test. Statistical analysis was performed using STATA/SE 15. RESULTS: Of 400 enrolled participants, 73 were excluded due to extra-pulmonary TB, incomplete data, previous TB, and cancer. Calibration phase involved 182 subjects, and the result was validated in 287 subjects. Sensitivity was 85% (95%CI: 75-92%) and 78% (95%CI: 70-85%), specificity was 55% (95%CI: 44-65%) and 42% (95%CI: 34-50%), in calibration and validation phases, respectively. Test sensitivity and specificity were lower in men. CONCLUSION: The electronic-nose showed modest sensitivity and low specificity among patients with suspected PTB. To improve the sensitivity, a larger calibration group needs to be involved. With its portable form, it could be used for TB screening in remote rural areas and health care settings.

Design and performance of an ultra-high vacuum spin-polarized scanning tunneling microscope operating at 30 mK and in a vector magnetic field.

We describe the design and performance of a scanning tunneling microscope (STM) that operates at a base temperature of 30 mK in a vector magnetic field. The cryogenics is based on an ultra-high vacuum (UHV) top-loading wet dilution refrigerator that contains a vector magnet allowing for fields up to 9 T perpendicular and 4 T parallel to the sample. The STM is placed in a multi-chamber UHV system, which allows in situ preparation and exchange of samples and tips. The entire system rests on a 150-ton concrete block suspended by pneumatic isolators, which is housed in an acoustically isolated and electromagnetically shielded laboratory optimized for extremely low noise scanning probe measurements. We demonstrate the overall performance by illustrating atomic resolution and quasiparticle interference imaging and detail the vibrational noise of both the laboratory and microscope. We also determine the electron temperature via measurement of the superconducting gap of Re(0001) and illustrate magnetic field-dependent measurements of the spin excitations of individual Fe atoms on Pt(111). Finally, we demonstrate spin resolution by imaging the magnetic structure of the Fe double layer on W(110).

Sensing Noncollinear Magnetism at the Atomic Scale Combining Magnetic Exchange and Spin-Polarized Imaging.

Storing and accessing information in atomic-scale magnets requires magnetic imaging techniques with single-atom resolution. Here, we show simultaneous detection of the spin-polarization and exchange force with or without the flow of current with a new method, which combines scanning tunneling microscopy and noncontact atomic force microscopy. To demonstrate the application of this new method, we characterize the prototypical nanoskyrmion lattice formed on a monolayer of Fe/Ir(111). We resolve the square magnetic lattice by employing magnetic exchange force microscopy, demonstrating its applicability to noncollinear magnetic structures for the first time. Utilizing distance-dependent force and current spectroscopy, we quantify the exchange forces in comparison to the spin-polarization. For strongly spin-polarized tips, we distinguish different signs of the exchange force that we suggest arises from a change in exchange mechanisms between the probe and a skyrmion. This new approach may enable both nonperturbative readout combined with writing by current-driven reversal of atomic-scale magnets.

The potential of a portable, point-of-care electronic nose to diagnose tuberculosis.

INTRODUCTION: Tuberculosis (TB) is the leading cause of death due to an infectious disease worldwide. Especially in low-income countries, new diagnostic techniques that are accessible, inexpensive and easy-to-use, are needed to shorten transmission time and initiate treatment earlier. OBJECTIVE: We conducted a study with a handheld, point-of-care electronic nose (eNose) device to diagnose TB through exhaled breath. SETTING: This study includes a total of 110 patients and visitors of an expert centre of respiratory diseases in Asunción, Paraguay. TB diagnosis was established by culture of Mycobacterium tuberculosis complex and compared with the eNose results in two phases. RESULTS: The calibration phase, including only culture confirmed TB cases versus healthy people, demonstrated a sensitivity and specificity of 91% and 93% respectively. The confirmation phase, including all participants, showed a sensitivity of 88% and a specificity of 92%. The eNose showed high acceptance rate among participants, and was easy to operate. CONCLUSION: The eNose resulted in a powerful technique to differentiate between healthy people and TB patients. Its comfort, speed and usability promise great potential in vulnerable groups, in remote areas and hospital settings to triage patients with suspicion of TB.

Data analysis of electronic nose technology in lung cancer: generating prediction models by means of Aethena.

INTRODUCTION: Only 15% of lung cancer cases present with potentially curable disease. Therefore, there is much interest in a fast, non-invasive tool to detect lung cancer earlier. Exhaled breath analysis using electronic nose technology measures volatile organic compounds (VOCs) in exhaled breath that are associated with lung cancer. METHODS: The diagnostic accuracy of the Aeonose™ is currently being studied in a multi-centre, prospective study in 210 subjects suspected for lung cancer, where approximately half will have a confirmed diagnosis and the other half will have a rejected diagnosis of lung cancer. We will also include 100-150 healthy control subjects. The eNose Company (provider of the Aeonose™) uses a software program, called Aethena, comprising pre-processing, data compression and neural networks to handle big data analyses. Each individual exhaled breath measurement comprises a data matrix with thousands of conductivity values. This is followed by data compression using a Tucker3-like algorithm, resulting in a vector. Subsequently, model selection takes place after entering vectors with different presets in an artificial neural network to train and evaluate the results. Next, a 'judge model' is formed, which is a combination of models for optimizing performance. Finally, two types of cross-validation, being 'leave-10%-out' cross-validation and 'bagging', are used when recalculating the judge models. These judge models are subsequently used to classify new, blind measurements. DISCUSSION: Data analysis in eNose technology is principally based on generating prediction models that need to be validated internally and externally for eventual use in clinical practice. This paper describes the analysis of big data, captured by eNose technology in lung cancer. This is done by means of generating prediction models with Aethena, a data analysis program specifically developed for analysing VOC data.

Interlaboratory round robin on cantilever calibration for AFM force spectroscopy.

Single-molecule force spectroscopy studies performed by Atomic Force Microscopes (AFMs) strongly rely on accurately determined cantilever spring constants. Hence, to calibrate cantilevers, a reliable calibration protocol is essential. Although the thermal noise method and the direct Sader method are frequently used for cantilever calibration, there is no consensus on the optimal calibration of soft and V-shaped cantilevers, especially those used in force spectroscopy. Therefore, in this study we aimed at establishing a commonly accepted approach to accurately calibrate compliant and V-shaped cantilevers. In a round robin experiment involving eight different laboratories we compared the thermal noise and the Sader method on ten commercial and custom-built AFMs. We found that spring constants of both rectangular and V-shaped cantilevers can accurately be determined with both methods, although the Sader method proved to be superior. Furthermore, we observed that simultaneous application of both methods on an AFM proved an accurate consistency check of the instrument and thus provides optimal and highly reproducible calibration. To illustrate the importance of optimal calibration, we show that for biological force spectroscopy studies, an erroneously calibrated cantilever can significantly affect the derived (bio)physical parameters. Taken together, our findings demonstrated that with the pre-established protocol described reliable spring constants can be obtained for different types of cantilevers.

Molecular friction as a tool to identify functionalized alkanethiols.

By using the nanografting method, well-defined nanoscale patches of alkanethiols were constructed in a self-assembled monolayer (SAM) matrix on an atomically flat gold (Au(111)) surface. A series of nanografted patches, composed of alkanethiols with different end groups (-CH(3), -CF(3), -OH, -SH, -COOH, and -NH(2)), were analyzed in detail by a combination of atomic force microscopy (AFM) height and quantitative lateral friction measurements. By constructing a series of nanografted patches of methyl-terminated thiols with various chain lengths, it was shown that the absolute friction of the nanografted patches was always smaller than that of the surrounding SAM matrix, demonstrating that, because of the spatially confined self-assembly during nanografting, SAMs show less defects. In addition, the friction gradually increased for decreasing alkane chain length as expected, although a subtle odd-even effect was observed. The study of thiols with functionalized end groups (-CF(3), -OH, -SH, -COOH, and -NH(2)) gave specific insights in orientation, packing, and structure of the molecules in the SAMs. Depending on the thiol end groups, these nanografted patches exhibited large and specific differences in lateral friction force, which offers the unique possibility to use the friction as a molecular recognition tool for thiol-based self-assembled monolayers.

The effect of underlying octadecylamine monolayer on the DNA conformation on the graphite surface.

DNA was immobilized on highly oriented pyrolytic graphite (HOPG) surfaces modified in octadecylamine (ODA) vapor. ODA molecules, deposited from the vapor phase onto HOPG form a nanostructured surface, which was utilized as a template for DNA adsorption. Peculiarities of double- and single-stranded DNA adsorption on these surfaces were investigated with atomic force microscopy (AFM) both in air, liquid and under different salt conditions. AFM images of DNA molecules immobilized on octadecylamine modified HOPG reveal a segmented shape of biopolymers: it constitutes straight segments with sharp turns at angles 120 degrees or 60 degrees between them, reflecting the symmetry of the underlying pattern. The analysis of DNA conformations on ODA modified HOPG surface has shown that under certain conditions DNA equilibrates on the surface on the scale of the whole molecule. A persistence length estimate of 97nm was determined for those molecules. Participation of different forces in the ODA pattern driven DNA assembly is discussed.

Scanning tunnelling spectroscopy on arrays of CdSe quantum dots: response of wave functions to local electric fields.

We use scanning tunnelling microscopy (STM) to controllably contact individual CdSe quantum dots (QDs) in a multilayer array to study electrical contacts to a model QD solid. The probability of electron injection into the QD array depends strongly on the symmetry of the QD wave functions and their response to the local electric field. Quantitative spectroscopy of the QD energy levels is possible if the potential distribution in the STM tip-QD array-substrate system is taken into account.

Giant porphyrin disks: control of their self-assembly at liquid-solid interfaces through metal-ligand interactions.

The synthesis and self-assembly behaviour of porphyrin dodecamers 1H(2) and Zn-1, which consist of twelve porphyrins that are covalently attached to a central aromatic core, is described. According to STM, 1D and 2D NMR studies, and molecular modelling calculations, the porphyrin dodecamers have a yo-yo-shaped structure. Their large pi surface, in combination with their disk-like shape, allows them to form self-assembled structures, which in the case of Zn-1 can be tuned by adding bidentate ligands. The self-assembly of the molecules at the liquid-solid interface of 1-phenyloctane with highly oriented pyrolytic graphite or Au(111) was imaged by using STM. The porphyrin disks in the self-assembled arrays have an edge-on orientation on the surface. The addition of bidentate axial ligands to the Zn-1 molecules in the arrays allows their intermolecular distance to be precisely controlled.

Real-time single-molecule imaging of oxidation catalysis at a liquid-solid interface.

Many chemical reactions are catalysed by metal complexes, and insight into their mechanisms is essential for the design of future catalysts. A variety of conventional spectroscopic techniques are available for the study of reaction mechanisms at the ensemble level, and, only recently, fluorescence microscopy techniques have been applied to monitor single chemical reactions carried out on crystal faces and by enzymes. With scanning tunnelling microscopy (STM) it has become possible to obtain, during chemical reactions, spatial information at the atomic level. The majority of these STM studies have been carried out under ultrahigh vacuum, far removed from conditions encountered in laboratory processes. Here we report the single-molecule imaging of oxidation catalysis by monitoring, with STM, individual manganese porphyrin catalysts, in real time, at a liquid-solid interface. It is found that the oxygen atoms from an O2 molecule are bound to adjacent porphyrin catalysts on the surface before their incorporation into an alkene substrate.

Macroscopic hierarchical surface patterning of porphyrin trimers via self-assembly and dewetting.

The use of bottom-up approaches to construct patterned surfaces for technological applications is appealing, but to date is applicable to only relatively small areas (approximately 10 square micrometers). We constructed highly periodic patterns at macroscopic length scales, in the range of square millimeters, by combining self-assembly of disk-like porphyrin dyes with physical dewetting phenomena. The patterns consisted of equidistant 5-nanometer-wide lines spaced 0.5 to 1 micrometers apart, forming single porphyrin stacks containing millions of molecules, and were formed spontaneously upon drop-casting a solution of the molecules onto a mica surface. On glass, thicker lines are formed, which can be used to align liquid crystals in large domains of square millimeter size.

Dynamic combinatorial olefin metathesis: templated synthesis of porphyrin boxes.

A porphyrin macrocyclic square is efficiently prepared by a dynamic combinatorial approach to olefin metathesis and shown by scanning tunneling microscopy (STM) to self-assemble into highly ordered arrays on a graphite surface.

Synthesis and self-assembly of giant porphyrin discs.

A giant porphyrin disc (M(w)= 15 kDa) has been synthesized and its self-assembly behaviour at an interface studied by liquid STM which reveals the presence of huge domains (>400 x 400 nm2) of very well ordered and molecularly resolved columnar stacks.