On-surface synthesis and characterization of teranthene and hexanthene: ultrashort graphene nanoribbons with mixed armchair and zigzag edges.

Graphene nanoribbons (GNRs) exhibit a broad range of physicochemical properties that critically depend on their width and edge topology. GNRs with armchair edges (AGNRs) are usually more stable than their counterparts with zigzag edges (ZGNRs) where the low-energy spin-polarized edge states render the ribbons prone to being altered by undesired chemical reactions. On the other hand, such edge-localized states make ZGNRs highly appealing for applications in spintronic and quantum technologies. For GNRs fabricated via on-surface synthesis under ultrahigh vacuum conditions on metal substrates, the expected reactivity of zigzag edges is a serious concern in view of substrate transfer and device integration under ambient conditions, but corresponding investigations are scarce. Using 10-bromo-9,9':10',9''-teranthracene as a precursor, we have thus synthesized hexanthene (HA) and teranthene (TA) as model compounds for ultrashort GNRs with mixed armchair and zigzag edges, characterized their chemical and electronic structure by means of scanning probe methods, and studied their chemical reactivity upon air exposure by Raman spectroscopy. We present a detailed identification of molecular orbitals and vibrational modes, assign their origin to armchair or zigzag edges, and discuss the chemical reactivity of these edges based on characteristic Raman spectral features.

Multi-Site Conformational Exchange in the Synthetic Neomycin-Sensing Riboswitch Studied by 19 F NMR.

The synthetic neomycin-sensing riboswitch interacts with its cognate ligand neomycin as well as with the related antibiotics ribostamycin and paromomycin. Binding of these aminoglycosides induces a very similar ground state structure in the RNA, however, only neomycin can efficiently repress translation initiation. The molecular origin of these differences has been traced back to differences in the dynamics of the ligand:riboswitch complexes. Here, we combine five complementary fluorine based NMR methods to accurately quantify seconds to microseconds dynamics in the three riboswitch complexes. Our data reveal complex exchange processes with up to four structurally different states. We interpret our findings in a model that shows an interplay between different chemical groups in the antibiotics and specific bases in the riboswitch. More generally, our data underscore the potential of 19 F NMR methods to characterize complex exchange processes with multiple excited states.

Observation of conformational changes that underlie the catalytic cycle of Xrn2.

Nuclear magnetic resonance (NMR) methods that quantitatively probe motions on molecular and atomic levels have propelled the understanding of biomolecular processes for which static structures cannot provide a satisfactory description. In this work, we studied the structure and dynamics of the essential 100-kDa eukaryotic 5'→3' exoribonuclease Xrn2. A combination of complementary fluorine and methyl-TROSY NMR spectroscopy reveals that the apo enzyme is highly dynamic around the catalytic center. These observed dynamics are in agreement with a transition of the enzyme from the ground state into a catalytically competent state. We show that the conformational equilibrium in Xrn2 shifts substantially toward the active state in the presence of substrate and magnesium. Finally, our data reveal that the dynamics in Xrn2 correlate with the RNA degradation rate, as a mutation that attenuates motions also affects catalytic activity. In that light, our results stress the importance of studies that go beyond static structural information.

Growth Optimization and Device Integration of Narrow-Bandgap Graphene Nanoribbons.

The electronic, optical, and magnetic properties of graphene nanoribbons (GNRs) can be engineered by controlling their edge structure and width with atomic precision through bottom-up fabrication based on molecular precursors. This approach offers a unique platform for all-carbon electronic devices but requires careful optimization of the growth conditions to match structural requirements for successful device integration, with GNR length being the most critical parameter. In this work, the growth, characterization, and device integration of 5-atom wide armchair GNRs (5-AGNRs) are studied, which are expected to have an optimal bandgap as active material in switching devices. 5-AGNRs are obtained via on-surface synthesis under ultrahigh vacuum conditions from Br- and I-substituted precursors. It is shown that the use of I-substituted precursors and the optimization of the initial precursor coverage quintupled the average 5-AGNR length. This significant length increase allowed the integration of 5-AGNRs into devices and the realization of the first field-effect transistor based on narrow bandgap AGNRs that shows switching behavior at room temperature. The study highlights that the optimized growth protocols can successfully bridge between the sub-nanometer scale, where atomic precision is needed to control the electronic properties, and the scale of tens of nanometers relevant for successful device integration of GNRs.

COVID salivary diagnostics: A comparative technical study.

Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, molecular diagnostics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have taken center stage in the detection of infected individuals for isolation purposes but also in the mass surveillance as a preventive strategy to contain the virus spread. While nasopharyngeal swabs (NPS) have remained the golden standard substrate, salivary diagnostic for SARS-CoV-2 has been proposed as an alternative and noninvasive measure in vulnerable individuals. Nevertheless, there is a widespread assumption that salivary reverse-transcription polymerase chain reaction (RT-PCR) does not match the quality of testing using NPS and particular care should be taken in respect to food or beverage intake, when sampling saliva. Our study indicates that without any precaution in the selection of 190 patients, nor restriction over the time window of sampling, there is 99% match in the COVID-19 positivity between NPS and saliva when using RT-PCR, with a reported Delta in thermal cycles (Cts) values for the viral genes Envelope (E) and Open reading frame 1ab (Orf1ab) between 0 and 2, a 98.7% sensitivity and 100% specificity. This high accuracy is maintained in pooling configurations that can be used for mass-testing purposes in professional and educational settings. The further advantage to using crude saliva as compared to NPS or mouthwash is that direct methods yield robust results. Overall, our study validates and promotes the use of salivary diagnostic for COVID-19 eliminating the need of a medical practitioner for the sampling, resolving the unpleasantness of the NPS intervention and empowering the patient to do self-testing in times of need.

High-speed identification of suspended carbon nanotubes using Raman spectroscopy and deep learning.

The identification of nanomaterials with the properties required for energy-efficient electronic systems is usually a tedious human task. A workflow to rapidly localize and characterize nanomaterials at the various stages of their integration into large-scale fabrication processes is essential for quality control and, ultimately, their industrial adoption. In this work, we develop a high-throughput approach to rapidly identify suspended carbon nanotubes (CNTs) by using high-speed Raman imaging and deep learning analysis. Even for Raman spectra with extremely low signal-to-noise ratios (SNRs) of 0.9, we achieve a classification accuracy that exceeds 90%, while it reaches 98% for an SNR of 2.2. By applying a threshold on the output of the softmax layer of an optimized convolutional neural network (CNN), we further increase the accuracy of the classification. Moreover, we propose an optimized Raman scanning strategy to minimize the acquisition time while simultaneously identifying the position, amount, and metallicity of CNTs on each sample. Our approach can readily be extended to other types of nanomaterials and has the potential to be integrated into a production line to monitor the quality and properties of nanomaterials during fabrication.

Insurance and Epidemics: SARS, West Nile Virus and Nipah Virus.

Severe acute respiratory syndrome (SARS) reminds us that sudden disease emergence is a permanent part of our world-and should be anticipated in our planning. Historically the emergence of new diseases has had little or no impact beyond a small, localized cluster of infections. However, given just the right conditions, a highly virulent pathogen can suddenly spread across time and space with massive consequences, as has occurred on several occasions in human history. In the wake of the SARS outbreak, we are now forced to confront the unpleasant fact that human activities are increasing the frequency and severity of these kinds of emergences. The idea of more frequent biological ''invasions'' with economic and societal impacts comparable to SARS, presents stakeholders in the global economy with unprecedented new risks, challenges and even opportunities. As a major contributor to economic stability, the insurance industry must follow these trends very closely and develop scenarios to anticipate these events.

Combining polarized Raman spectroscopy and micropillar compression to study microscale structure-property relationships in mineralized tissues.

Bone is a natural composite possessing outstanding mechanical properties combined with a lightweight design. The key feature contributing to this unusual combination of properties is the bone hierarchical organization ranging from the nano- to the macro-scale. Bone anisotropic mechanical properties from two orthogonal planes (along and perpendicular to the main bone axis) have already been widely studied. In this work, we demonstrate the dependence of the microscale compressive mechanical properties on the angle between loading direction and the mineralized collagen fibril orientation in the range between 0° and 82°. For this, we calibrated polarized Raman spectroscopy for quantitative collagen fibril orientation determination and validated the method using widely used techniques (small angle X-ray scattering, micro-computed tomography). We then performed compression tests on bovine cortical bone micropillars with known mineralized collagen fibril angles. A strong dependence of the compressive micromechanical properties of bone on the fibril orientation was found with a high degree of anisotropy for both the elastic modulus (Ea/Et=3.80) and the yield stress (σay/σty=2.54). Moreover, the post-yield behavior was found to depend on the MCF orientation with a transition between softening to hardening behavior at approximately 50°. The combination of methods described in this work allows to reliably determine structure-property relationships of bone at the microscale, which may be used as a measure of bone quality.

Correction to: A suite of 19F based relaxation dispersion experiments to assess biomolecular motions.

In the original publication, Figures 3 and 6 were displayed incorrectly due to a mistake made by the publisher. The correct version of Figs. 3 and 6 are given below.

A suite of 19F based relaxation dispersion experiments to assess biomolecular motions.

Proteins and nucleic acids are highly dynamic bio-molecules that can populate a variety of conformational states. NMR relaxation dispersion (RD) methods are uniquely suited to quantify the associated kinetic and thermodynamic parameters. Here, we present a consistent suite of 19F-based CPMG, on-resonance R1ρ and off-resonance R1ρ RD experiments. We validate these experiments by studying the unfolding transition of a 7.5 kDa cold shock protein. Furthermore we show that the 19F RD experiments are applicable to very large molecular machines by quantifying dynamics in the 360 kDa half-proteasome. Our approach significantly extends the timescale of chemical exchange that can be studied with 19F RD, adds robustness to the extraction of exchange parameters and can determine the absolute chemical shifts of excited states. Importantly, due to the simplicity of 19F NMR spectra, it is possible to record complete datasets within hours on samples that are of very low costs. This makes the presented experiments ideally suited to complement static structural information from cryo-EM and X-ray crystallography with insights into functionally relevant motions.

Controlled Quantum Dot Formation in Atomically Engineered Graphene Nanoribbon Field-Effect Transistors.

Graphene nanoribbons (GNRs) have attracted strong interest from researchers worldwide, as they constitute an emerging class of quantum-designed materials. The major challenges toward their exploitation in electronic applications include reliable contacting, complicated by their small size (<50 nm), and the preservation of their physical properties upon device integration. In this combined experimental and theoretical study, we report on the quantum dot behavior of atomically precise GNRs integrated in a device geometry. The devices consist of a film of aligned five-atom-wide GNRs (5-AGNRs) transferred onto graphene electrodes with a sub 5 nm nanogap. We demonstrate that these narrow-bandgap 5-AGNRs exhibit metal-like behavior at room temperature and single-electron transistor behavior for temperatures below 150 K. By performing spectroscopy of the molecular levels at 13 K, we obtain addition energies in the range of 200-300 meV. DFT calculations predict comparable addition energies and reveal the presence of two electronic states within the bandgap of infinite ribbons when the finite length of the 5-AGNR is accounted for. By demonstrating the preservation of the 5-AGNRs' molecular levels upon device integration, as demonstrated by transport spectroscopy, our study provides a critical step forward in the realization of more exotic GNR-based nanoelectronic devices.

Massive Dirac Fermion Behavior in a Low Bandgap Graphene Nanoribbon Near a Topological Phase Boundary.

Graphene nanoribbons (GNRs) have attracted much interest due to their largely modifiable electronic properties. Manifestation of these properties requires atomically precise GNRs which can be achieved through a bottom-up synthesis approach. This has recently been applied to the synthesis of width-modulated GNRs hosting topological electronic quantum phases, with valence electronic properties that are well captured by the Su-Schrieffer-Heeger (SSH) model describing a 1D chain of interacting dimers. Here, ultralow bandgap GNRs with charge carriers behaving as massive Dirac fermions can be realized when their valence electrons represent an SSH chain close to the topological phase boundary, i.e., when the intra- and interdimer coupling become approximately equal. Such a system has been achieved via on-surface synthesis based on readily available pyrene-based precursors and the resulting GNRs are characterized by scanning probe methods. The pyrene-based GNRs (pGNRs) can be processed under ambient conditions and incorporated as the active material in a field effect transistor. A quasi-metallic transport behavior is observed at room temperature, whereas at low temperature, the pGNRs behave as quantum dots showing single-electron tunneling and Coulomb blockade. This study may enable the realization of devices based on carbon nanomaterials with exotic quantum properties.

Optical Imaging and Spectroscopy of Atomically Precise Armchair Graphene Nanoribbons.

We report the optical imaging and absorption spectroscopy on atomically precise armchair graphene nanoribbons (GNRs) on insulating fused silica substrates. This is achieved by controlling light polarization on macroscopically aligned GNRs which greatly enhances the optical contrast of the submonolayer GNRs on the insulating substrates. We measure the linear absorption spectra of 7-armchair and 9-armchair GNRs in this study, and the experimental data agree qualitatively with ab inito calculation results. The polarization spectroscopy technique enables an unambiguous optical identification of GNRs and provides a rapid tool to characterize the transferred film over a large area.

A non-oxidizing fabrication method for lithographic break junctions of sensitive metals.

Electrochemically active metals offer advanced functionalities with respect to the well-established gold electrode arrangements in various electronic transport experiments on atomic scale objects. Such functionalities can arise from stronger interactions with the leads which provide better coupling to specific molecules and may also facilitate metallic filament formation in atomic switches. However, the higher reactivity of the electrode metal also imposes challenges in the fabrication and reliability of nanometer scale platforms, limiting the number of reported applications. Here we present a high-yield lithographic fabrication procedure suitable to extend the experimental toolkit with mechanically controllable break junctions of oxygen sensitive metallic electrodes. We fabricate and characterize silver break junctions exhibiting single-atomic conductance and superior mechanical and electrical stability at room temperature. As a proof-of-principle application, we demonstrate resistive switching between metastable few-atom configurations at finite voltage bias.

A Universal Length-Dependent Vibrational Mode in Graphene Nanoribbons.

Graphene nanoribbons (GNRs) have attracted considerable interest, as their atomically tunable structure makes them promising candidates for future electronic devices. However, obtaining detailed information about the length of GNRs has been challenging and typically relies on low-temperature scanning tunneling microscopy. Such methods are ill-suited for practical device application and characterization. In contrast, Raman spectroscopy is a sensitive method for the characterization of GNRs, in particular for investigating their width and structure. Here, we report on a length-dependent, Raman-active low-energy vibrational mode that is present in atomically precise, bottom-up-synthesized armchair graphene nanoribbons (AGNRs). Our Raman study demonstrates that this mode is present in all families of AGNRs and provides information on their length. Our spectroscopic findings are corroborated by scanning tunneling microscopy images and supported by first-principles calculations that allow us to attribute this mode to a longitudinal acoustic phonon. Finally, we show that this mode is a sensitive probe for the overall structural integrity of the ribbons and their interaction with technologically relevant substrates.

In Situ Strain Tuning in hBN-Encapsulated Graphene Electronic Devices.

Using a simple setup to bend a flexible substrate, we demonstrate deterministic and reproducible in situ strain tuning of graphene electronic devices. Central to this method is the full hBN encapsulation of graphene, which preserves the exceptional quality of pristine graphene for transport experiments. In addition, the on-substrate approach allows one to exploit strain effects in the full range of possible sample geometries and at the same time guarantees that changes in the gate capacitance remain negligible during the deformation process. We use Raman spectroscopy to spatially map the strain magnitude in devices with two different geometries and demonstrate the possibility to engineer a strain gradient, which is relevant for accessing the valley degree of freedom with pseudomagnetic fields. Comparing the transport characteristics of a suspended device with those of an on-substrate device, we demonstrate that our new approach does not suffer from the ambiguities encountered in suspended devices.

In-situ formation of one-dimensional coordination polymers in molecular junctions.

We demonstrate the bottom-up in-situ formation of organometallic oligomer chains at the single-molecule level. The chains are formed using the mechanically controllable break junction technique operated in a liquid environment, and consist of alternating isocyano-terminated benzene monomers coordinated to gold atoms. We show that the chaining process is critically determined by the surface density of molecules. In particular, we demonstrate that by reducing the local supply of molecules within the junction, either by lowering the molecular concentration or by adding side groups, the oligomerization process can be suppressed. Our experimental results are supported by ab-initio simulations, confirming that the isocyano terminating groups display a high tendency to form molecular chains, as a result of their high affinity for gold. Our findings open the road for the controlled formation of one-dimensional, single coordination-polymer chains as promising model systems of organometallic frameworks.

Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme.

Crystal structures of enzymes are indispensable to understanding their mechanisms on a molecular level. It, however, remains challenging to determine which structures are adopted in solution, especially for dynamic complexes. Here, we study the bilobed decapping enzyme Dcp2 that removes the 5' cap structure from eukaryotic mRNA and thereby efficiently terminates gene expression. The numerous Dcp2 structures can be grouped into six states where the domain orientation between the catalytic and regulatory domains significantly differs. Despite this wealth of structural information it is not possible to correlate these states with the catalytic cycle or the activity of the enzyme. Using methyl transverse relaxation-optimized NMR spectroscopy, we demonstrate that only three of the six domain orientations are present in solution, where Dcp2 adopts an open, a closed, or a catalytically active state. We show how mRNA substrate and the activator proteins Dcp1 and Edc1 influence the dynamic equilibria between these states and how this modulates catalytic activity. Importantly, the active state of the complex is only stably formed in the presence of both activators and the mRNA substrate or the m7GDP decapping product, which we rationalize based on a crystal structure of the Dcp1:Dcp2:Edc1:m7GDP complex. Interestingly, we find that the activating mechanisms in Dcp2 also result in a shift of the substrate specificity from bacterial to eukaryotic mRNA.