Automated Structure Discovery for Scanning Tunneling Microscopy.

Scanning tunneling microscopy (STM) with a functionalized tip apex reveals the geometric and electronic structures of a sample within the same experiment. However, the complex nature of the signal makes images difficult to interpret and has so far limited most research to planar samples with a known chemical composition. Here, we present automated structure discovery for STM (ASD-STM), a machine learning tool for predicting the atomic structure directly from an STM image, by building upon successful methods for structure discovery in noncontact atomic force microscopy (nc-AFM). We apply the method on various organic molecules and achieve good accuracy on structure predictions and chemical identification on a qualitative level while highlighting future development requirements for ASD-STM. This method is directly applicable to experimental STM images of organic molecules, making structure discovery available for a wider scanning probe microscopy audience outside of nc-AFM. This work also allows more advanced machine learning methods to be developed for STM structure discovery.

Accelerated Lignocellulosic Molecule Adsorption Structure Determination.

Here, we present a study combining Bayesian optimization structural inference with the machine learning interatomic potential Neural Equivariant Interatomic Potential (NequIP) to accelerate and enable the study of the adsorption of the conformationally flexible lignocellulosic molecules ß-d-xylose and 1,4-ß-d-xylotetraose on a copper surface. The number of structure evaluations needed to map out the relevant potential energy surfaces are reduced by Bayesian optimization, while NequIP minimizes the time spent on each evaluation, ultimately resulting in cost-efficient and reliable sampling of large systems and configurational spaces. Although the applicability of Bayesian optimization for the conformational analysis of the more flexible xylotetraose molecule is restricted by the sample complexity bottleneck, the latter can be effectively bypassed with external conformer search tools, such as the Conformer-Rotamer Ensemble Sampling Tool, facilitating the subsequent lower-dimensional global minimum adsorption structure determination. Finally, we demonstrate the applicability of the described approach to find adsorption structures practically equivalent to the density functional theory counterparts at a fraction of the computational cost.

On-Surface Synthesis of Silole and Disila-Cyclooctene Derivatives.

The incorporation of Si atoms into organic compounds significantly increases a variety of functionality, facilitating further applications. Recently, on-surface synthesis was introduced into organosilicon chemistry as 1,4-disilabenzene bridged nanostructures were obtained via coupling between silicon atoms and brominated phenyl groups at the ortho position on Au(111). Here, we demonstrate a high generality of this strategy via syntheses of silole derivatives and nanoribbon structures with eight-membered sila-cyclic rings from dibrominated molecules at the bay and peri positions on Au(111), respectively. Their structures and electronic properties were investigated by a combination of scanning tunneling microscopy/spectroscopy and density functional theory calculations. This work demonstrates a great potential to deal with heavy group 14 elements in on-surface silicon chemistry.

Structure Discovery in Atomic Force Microscopy Imaging of Ice.

The interaction of water with surfaces is crucially important in a wide range of natural and technological settings. In particular, at low temperatures, unveiling the atomistic structure of adsorbed water clusters would provide valuable data for understanding the ice nucleation process. Using high-resolution atomic force microscopy (AFM) and scanning tunneling microscopy, several studies have demonstrated the presence of water pentamers, hexamers, and heptamers (and of their combinations) on a variety of metallic surfaces, as well as the initial stages of 2D ice growth on an insulating surface. However, in all of these cases, the observed structures were completely flat, providing a relatively straightforward path to interpretation. Here, we present high-resolution AFM measurements of several water clusters on Au(111) and Cu(111), whose understanding presents significant challenges due to both their highly 3D configuration and their large size. For each of them, we use a combination of machine learning, atomistic modeling with neural network potentials, and statistical sampling to propose an underlying atomic structure, finally comparing its AFM simulated images to the experimental ones. These results provide insights into the early phases of ice formation, which is a ubiquitous phenomenon ranging from biology to astrophysics.

Select Cover Crop Residue and Soil Microbiomes Contribute to Suppression of Fusarium Root and Crown Rot in Barley and Soybean.

Fusarium root and crown rot (FRCR) negatively impact several economically important plant species. Cover crops host different soil and residue microbiomes, thereby potentially influencing pathogen load and disease severity. The carryover effect of cover crops on FRCR in barley and soybean was investigated. Field trials were conducted in Prince Edward Island, Canada. Two cover crops from each plant group, including forbs, brassicas, legumes, and grasses, were grown in a randomized complete block design with barley and soybean planted in split plots the following year. Barley and soybean roots were assessed for FRCR through visual disease rating and Fusarium spp. were isolated from diseased tissue. Fungal and bacterial communities in cover crop residues were quantified using amplicon sequencing. The disease-suppressive effects of soil were tested in greenhouse studies. The results indicated that sorghum-sudangrass-associated microbiomes suppress Fusarium spp., leading to reduced FRCR in both barley and soybean. The oilseed radish microbiome had the opposite effect, consequently increasing FRCR incidence in barley and soybean. The results from this study indicate that cover crop residue and the associated soil microbiome influence the incidence and severity of FRCR in subsequent crops. This information can be used to determine cover cropping strategies in barley and soybean production systems.

Atomic structure and water arrangement on K-feldspar microcline (001).

The properties of clouds, such as their reflectivity or their likelihood to precipitate, depend on whether the cloud droplets are liquid or frozen. Thus, understanding the ice nucleation mechanisms is essential for the development of reliable climate models. Most ice nucleation in the atmosphere is heterogeneous, i.e., caused by ice nucleating particles such as mineral dusts or organic aerosols. In this regard, K-feldspar minerals have attracted great interest recently as they have been identified as one of the most important ice nucleating particles under mixed-phase cloud conditions. The mechanism by which feldspar minerals facilitate ice nucleation remains, however, elusive. Here, we present atomic force microscopy (AFM) experiments on microcline (001) performed in an ultrahigh vacuum and at the solid-water interface together with density functional theory (DFT) and molecular dynamics (MD) calculations. Our ultrahigh vacuum data reveal features consistent with a hydroxyl-terminated surface. This finding suggests that water in the residual gas readily reacts with the surface. Indeed, the corresponding DFT calculations confirm a dissociative water adsorption. Three-dimensional AFM measurements performed at the mineral-water interface unravel a layered hydration structure with two features per surface unit cell. A comparison with MD calculations suggests that the structure observed in AFM corresponds to the second hydration layer rather than the first water layer. In agreement with previous computation results, no ice-like structure is seen, questioning an explanation of the ice nucleation ability by lattice match. Our results provide an atomic-scale benchmark for the clean and water-covered microcline (001) plane, which is mandatory for understanding the ice nucleation mechanism on feldspar minerals.

Droplet slipperiness despite surface heterogeneity at molecular scale.

Friction determines whether liquid droplets slide off a solid surface or stick to it. Surface heterogeneity is generally acknowledged as the major cause of increased contact angle hysteresis and contact line friction of droplets. Here we challenge this long-standing premise for chemical heterogeneity at the molecular length scale. By tuning the coverage of self-assembled monolayers (SAMs), water contact angles change gradually from about 10° to 110° yet contact angle hysteresis and contact line friction are low for the low-coverage hydrophilic SAMs as well as high-coverage hydrophobic SAMs. Their slipperiness is not expected based on the substantial chemical heterogeneity of the SAMs featuring uncoated areas of the substrate well beyond the size of a water molecule as probed by metal reactants. According to molecular dynamics simulations, the low friction of both low- and high-coverage SAMs originates from the mobility of interfacial water molecules. These findings reveal a yet unknown and counterintuitive mechanism for slipperiness, opening new avenues for enhancing the mobility of droplets.

Local probe-induced structural isomerization in a one-dimensional molecular array.

Synthesis of one-dimensional molecular arrays with tailored stereoisomers is challenging yet has great potential for application in molecular opto-, electronic- and magnetic-devices, where the local array structure plays a decisive role in the functional properties. Here, we demonstrate the construction and characterization of dehydroazulene isomer and diradical units in three-dimensional organometallic compounds on Ag(111) with a combination of low-temperature scanning tunneling microscopy and density functional theory calculations. Tip-induced voltage pulses firstly result in the formation of a diradical species via successive homolytic fission of two C-Br bonds in the naphthyl groups, which are subsequently transformed into chiral dehydroazulene moieties. The delicate balance of the reaction rates among the diradical and two stereoisomers, arising from an in-line configuration of tip and molecular unit, allows directional azulene-to-azulene and azulene-to-diradical local probe structural isomerization in a controlled manner. Furthermore, our theoretical calculations suggest that the diradical moiety hosts an open-shell singlet with antiferromagnetic coupling between the unpaired electrons, which can undergo an inelastic spin transition of 91 meV to the ferromagnetically coupled triplet state.

Water adsorption lifts the (2 × 1) reconstruction of calcite(104).

The adsorption of water on calcite(104) is investigated in ultra-high vacuum by density functional theory (DFT) and non-contact atomic force microscopy (NC-AFM) in the coverage regime of up to one monolayer (ML). DFT calculations reveal a clear preference for water to adsorb on the bulk-like carbonate group rows of the (2 × 1) reconstructed surface. Additionally, an apparent water attraction due to carbonate group reorientation suggest island formation for water adsorbed on the reconstructed carbonate group rows. Experimentally, water is found to exclusively occupy specific positions within the (2 × 1) unit cell up to 0.5 ML, to form islands at coverage between 0.5 and 1 ML, and to express a (1 × 1) structure at coverage of a full monolayer.

Unanticipated Large-Scale Deletion in Fusarium graminearum Genome Using CRISPR/Cas9 and Its Impact on Growth and Virulence.

Fusarium graminearum, a filamentous fungus, and causal agent of Fusarium head blight (FHB) in wheat and other cereals, leads to significant economic losses globally. This study aimed to investigate the roles of specific genes in F. graminearum virulence using CRISPR/Cas9-mediated gene deletions. Illumina sequencing was used to characterize the genomic changes due to editing. Unexpectedly, a large-scale deletion of 525,223 base pairs on chromosome 2, comprising over 222 genes, occurred in two isolates. Many of the deleted genes were predicted to be involved in essential molecular functions, such as oxidoreductase activity, transmembrane transporter activity, hydrolase activity, as well as biological processes, such as carbohydrate metabolism and transmembrane transport. Despite the substantial loss of genetic material, the mutant isolate exhibited normal growth rates and virulence on wheat under most conditions. However, growth rates were significantly reduced under high temperatures and on some media. Additionally, wheat inoculation assays using clip dipping, seed inoculation, and head point inoculation methods were performed. No significant differences in virulence were observed, suggesting that these genes were not involved in infection or alternative compensatory pathways, and allow the fungi to maintain pathogenicity despite the extensive genomic deletion.

Differences in Molecular Adsorption Emanating from the (2 × 1) Reconstruction of Calcite(104).

Calcite, in the natural environment the most stable polymorph of calcium carbonate (CaCO3), not only is an abundant mineral in the Earth's crust but also forms a central constituent in the biominerals of living organisms. Intensive studies of calcite(104), the surface supporting virtually all processes, have been performed, and the interaction with a plethora of adsorbed species has been studied. Surprisingly, there is still serious ambiguity regarding the properties of the calcite(104) surface: effects such as a row-pairing or a (2 × 1) reconstruction have been reported, yet so far without physicochemical explanation. Here, we unravel the microscopic geometry of calcite(104) using high-resolution atomic force microscopy (AFM) data acquired at 5 K combined with density functional theory (DFT) and AFM image calculations. A (2 × 1) reconstruction of a pg-symmetric surface is found to be the thermodynamically most stable form. Most importantly, a decisive impact of the (2 × 1) reconstruction on adsorbed species is revealed for carbon monoxide.

Control of Molecular Orbital Ordering Using a van der Waals Monolayer Ferroelectric.

2D ferroelectric materials provide a promising platform for the electrical control of quantum states. In particular, due to their 2D nature, they are suitable for influencing the quantum states of deposited molecules via the proximity effect. Here, electrically controllable molecular states in phthalocyanine molecules adsorbed on monolayer ferroelectric material SnTe are reported. The strain and ferroelectric order in SnTe are found to create a transition between two distinct orbital orders in the adsorbed phthalocyanine molecules. By controlling the polarization of the ferroelectric domain using scanning tunneling microscopy (STM), it is successfully demonstrated that orbital order can be manipulated electrically. The results show how ferroelastic coupling in 2D systems allows for control of molecular states, providing a starting point for ferroelectrically switchable molecular orbital ordering and ultimately, electrical control of molecular magnetism.

On-surface synthesis of disilabenzene-bridged covalent organic frameworks.

Substituting carbon with silicon in organic molecules and materials has long been an attractive way to modify their electronic structure and properties. Silicon-doped graphene-based materials are known to exhibit exotic properties, yet conjugated organic materials with atomically precise Si substitution have remained difficult to prepare. Here we present the on-surface synthesis of one- and two-dimensional covalent organic frameworks whose backbones contain 1,4-disilabenzene (C4Si2) linkers. Silicon atoms were first deposited on a Au(111) surface, forming a AuSix film on annealing. The subsequent deposition and annealing of a bromo-substituted polyaromatic hydrocarbon precursor (triphenylene or pyrene) on this surface led to the formation of the C4Si2-bridged networks, which were characterized by a combination of high-resolution scanning tunnelling microscopy and photoelectron spectroscopy supported by density functional theory calculations. Each Si in a hexagonal C4Si2 ring was found to be covalently linked to one terminal Br atom. For the linear structure obtained with the pyrene-based precursor, the C4Si2 rings were converted into C4Si pentagonal siloles by further annealing.

Precise atom manipulation through deep reinforcement learning.

Atomic-scale manipulation in scanning tunneling microscopy has enabled the creation of quantum states of matter based on artificial structures and extreme miniaturization of computational circuitry based on individual atoms. The ability to autonomously arrange atomic structures with precision will enable the scaling up of nanoscale fabrication and expand the range of artificial structures hosting exotic quantum states. However, the a priori unknown manipulation parameters, the possibility of spontaneous tip apex changes, and the difficulty of modeling tip-atom interactions make it challenging to select manipulation parameters that can achieve atomic precision throughout extended operations. Here we use deep reinforcement learning (DRL) to control the real-world atom manipulation process. Several state-of-the-art reinforcement learning (RL) techniques are used jointly to boost data efficiency. The DRL agent learns to manipulate Ag adatoms on Ag(111) surfaces with optimal precision and is integrated with path planning algorithms to complete an autonomous atomic assembly system. The results demonstrate that state-of-the-art DRL can offer effective solutions to real-world challenges in nanofabrication and powerful approaches to increasingly complex scientific experiments at the atomic scale.

Molecular insights on the crystalline cellulose-water interfaces via three-dimensional atomic force microscopy.

Cellulose, a renewable structural biopolymer, is ubiquitous in nature and is the basic reinforcement component of the natural hierarchical structures of living plants, bacteria, and tunicates. However, a detailed picture of the crystalline cellulose surface at the molecular level is still unavailable. Here, using atomic force microscopy (AFM) and molecular dynamics (MD) simulations, we revealed the molecular details of the cellulose chain arrangements on the surfaces of individual cellulose nanocrystals (CNCs) in water. Furthermore, we visualized the three-dimensional (3D) local arrangement of water molecules near the CNC surface using 3D AFM. AFM experiments and MD simulations showed anisotropic water structuring, as determined by the surface topologies and exposed chemical moieties. These findings provide important insights into our understanding of the interfacial interactions between CNCs and water at the molecular level. This may allow the establishment of the structure-property relationship of CNCs extracted from various biomass sources.

Water Dimer-Driven DNA Base Superstructure with Mismatched Hydrogen Bonding.

The existence of water dimers in equilibrium water vapor at room temperature and their anomalous properties revealed by recent studies suggest the benchmark role of water dimers in both experiment and theory. However, there has been a limited observation of individual water dimers due to the challenge of water separation and generation at the single-molecule level. Here, we achieve real-space imaging of individual confined water dimers embedded inside a self-assembled layer of a DNA base, adenine, on Ag(111). The hydration of the adenine layers by these water dimers causes a local surface chiral inversion in such a way that the neighboring homochiral adenine molecules become heterochiral after hydration, resulting in a mismatched hydrogen-bond pattern between neighboring adenine molecules. Furthermore, the mutual influence between the adenine superstructure and these dynamic confined water dimers is corroborated by theoretical simulation and calculations. The observation of single confined water dimers offers an unprecedented approach to studying the fundamental forms of water clusters and their interaction with the local chemical environment.

Practical considerations for feature assignment in high-speed AFM of live cell membranes.

High speed atomic force microscopy (HS-AFM) is, in principle, capable of yielding nanometer level detail about the surface of static structures. However, for highly dynamic samples HS-AFM may struggle with the correct feature assignment both within and between frames. Feature assignment in HS-AFM is dependent on (i) the intrinsic sampling rate, and (ii) the rate of internal redistribution of the sample. Whilst the first quantity (the sampling rate) is defined by the device parameters, the second quantity is frequently unknown, and is often the desired target of the measurement. This work examines how, even in the absence of gross cell morphological change, the rapid dynamics of living cell membranes, may impose an upper spatial limit to the frame-to-frame assignment of cell micro-topography and other related properties (such as local elasticity) whose motion may be described stochastically. Such a practical maximum may prove useful in the setup of HS-AFM experiments involving dynamic surfaces thereby facilitating selection of the most parsimonious relationship between observation size, image pixilation and sampling rates. To assist with performing the described calculations a graphical user interface-based software package called HS-AFM UGOKU is made freely available.

Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality.

Three-dimensional atomic force microscopy (3D-AFM) has resolved three-dimensional distributions of solvent molecules at solid-liquid interfaces at the subnanometer scale. This method is now being extended to the imaging of biopolymer assemblies such as chromosomes or proteins in cells, with the expectation of being able to resolve their three-dimensional structures. Here, we have developed a computational method to simulate 3D-AFM images of biopolymers by using the Jarzynski equality. It is found that some parts of the fiber structure of biopolymers are indeed resolved in the 3D-AFM image. The dependency of 3D-AFM images on the vertical scanning velocity is investigated, and optimum scanning velocities are found. It is also clarified that forces in nonequilibrium processes are measured in 3D-AFM measurements when the dynamics of polymers are slower than the scanning of the probe.