Selective Antisite Defect Formation in WS2 Monolayers via Reactive Growth on Dilute W-Au Alloy Substrates.

Defects are ubiquitous in 2D materials and can affect the structure and properties of the materials and also introduce new functionalities. Methods to adjust the structure and density of defects during bottom-up synthesis are required to control the growth of 2D materials with tailored optical and electronic properties. Here, the authors present an Au-assisted chemical vapor deposition approach to selectively form SW and S2W antisite defects, whereby one or two sulfur atoms substitute for a tungsten atom in WS2 monolayers. Guided by first-principles calculations, they describe a new method that can maintain tungsten-poor growth conditions relative to sulfur via the low solubility of W atoms in a gold/W alloy, thereby significantly reducing the formation energy of the antisite defects during the growth of WS2 . The atomic structure and composition of the antisite defects are unambiguously identified by Z-contrast scanning transmission electron microscopy and electron energy-loss spectroscopy, and their total concentration is statistically determined, with levels up to ≈5.0%. Scanning tunneling microscopy/spectroscopy measurements and first-principles calculations further verified these antisite defects and revealed the localized defect states in the bandgap of WS2 monolayers. This bottom-up synthesis method to form antisite defects should apply in the synthesis of other 2D materials.

Polymer Dots with Enhanced Photostability, Quantum Yield, and Two-Photon Cross-Section using Structurally Constrained Deep-Blue Fluorophores.

Semiconducting polymer dots (Pdots) have emerged as versatile probes for bioanalysis and imaging at the single-particle level. Despite their utility in multiplexed analysis, deep blue Pdots remain rare due to their need for high-energy excitation and sensitivity to photobleaching. Here, we describe the design of deep blue fluorophores using structural constraints to improve resistance to photobleaching, two-photon absorption cross sections, and fluorescence quantum yields using the hexamethylazatriangulene motif. Scanning tunneling microscopy was used to characterize the electronic structure of these chromophores on the atomic scale as well as their intrinsic stability. The most promising fluorophore was functionalized with a polymerizable acrylate handle and used to give deep-blue fluorescent acrylic polymers with Mn > 18 kDa and D < 1.2. Nanoprecipitation with amphiphilic polystyrene-graft-(carboxylate-terminated poly(ethylene glycol)) gave water-soluble Pdots with blue fluorescence, quantum yields of 0.81, and molar absorption coefficients of (4 ± 2) × 108 M-1 cm-1. This high brightness facilitated single-particle visualization with dramatically improved signal-to-noise ratio and photobleaching resistance versus an unencapsulated dye. The Pdots were then conjugated with antibodies for immunolabeling of SK-BR3 human breast cancer cells, which were imaged using deep blue fluorescence in both one- and two-photon excitation modes.

Nanoscale Superconducting States in the Fe-Based Filamentary Superconductor of Pr-Doped CaFe2As2.

The low-temperature scanning tunneling microscope and spectroscopy (STM/STS) are used to visualize superconducting states in the cleaved single crystal of 9% praseodymium-doped CaFe2As2 (Pr-Ca122) with Tc ≈ 30 K. The spectroscopy shows strong spatial variations in the density of states (DOS), and the superconducting map constructed from spectroscopy discloses a localized superconducting phase, as small as a single unit cell. The comparison of the spectra taken at 4.2 K and 22 K (below vs. close to the bulk superconducting transition temperature) from the exact same area confirms the superconducting behavior. Nanoscale superconducting states have been found near Pr dopants, which can be identified using dI/dV conductance maps at +300 mV. There is no correlation of the local superconductivity to the surface reconstruction domain and surface defects, which reflects its intrinsic bulk behavior. We, therefore, suggest that the local strain of Pr dopants is competing with defects induced local magnetic moments; this competition is responsible for the local superconducting states observed in this Fe-based filamentary superconductor.

Atomically Precise PdSe2 Pentagonal Nanoribbons.

We report atomically precise pentagonal PdSe2 nanoribbons (PNRs) fabricated on a pristine PdSe2 substrate with a hybrid method of top-down and bottom-up processes. The PNRs form a uniform array of dimer structure with a width of 2.4 nm and length of more than 200 nm. In situ four-probe scanning tunneling microscopy (STM) reveals metallic behavior of PNRs with ballistic transport for at least 20 nm in length. Density functional theory calculations produce a semiconducting density of states of isolated PNRs and find that the band gap narrows and disappears quickly once considering coupling between PNR stacking layers or interaction with the PdSe2 substrate. The coupling of PNRs is further corroborated by Raman spectroscopy and field-effect transistor measurements. The facile method of fabricating atomically precise PNRs offers an air-stable functional material for dimensional control.

Revealing the Local Electronic Structure of a Single-Layer Covalent Organic Framework through Electronic Decoupling.

Covalent organic frameworks (COFs) are molecule-based 2D and 3D materials that possess a wide range of mechanical and electronic properties. We have performed a joint experimental and theoretical study of the electronic structure of boroxine-linked COFs grown under ultrahigh vacuum conditions and characterized using scanning tunneling spectroscopy on Au(111) and hBN/Cu(111) substrates. Our results show that a single hBN layer electronically decouples the COF from the metallic substrate, thus suppressing substrate-induced broadening and revealing new features in the COF electronic local density of states (LDOS). The resulting sharpening of LDOS features allows us to experimentally determine the COF band gap, bandwidths, and the electronic hopping amplitude between adjacent COF bridge sites. These experimental parameters are consistent with the results of first-principles theoretical predictions.

Defects in Highly Anisotropic Transition-Metal Dichalcogenide PdSe2.

The atomic and electronic structures of pristine PdSe2 as well as various intrinsic vacancy defects in PdSe2 are studied comprehensively by combining scanning tunneling microscopy, spectroscopy, and density functional theory calculations. Other than the topmost Se atoms, sublayer Pd atoms and the intrinsic Pd and Se vacancy defects are identified. Both VSe and VPd defects induce defect states near the Fermi level. As a result, the vacancy defects can be negatively charged by a tip gating effect. At negative sample bias, the screened Coulomb interaction between the scanning tunneling microscopy (STM) tip and the charged vacancies creates a disk-like protrusion around the VPd and crater-like features around VSe. The magnification effect of the long-range charge localization at the charged defect site makes sublayer defects as deep as 1 nm visible even in STM images. This result proves that by gating the probe, scanning probe microscopy can be used as an easy tool for characterizing sublayer defects in a nondestructive way.

Length-Dependent Evolution of Type II Heterojunctions in Bottom-Up-Synthesized Graphene Nanoribbons.

The ability to tune the band-edge energies of bottom-up graphene nanoribbons (GNRs) via edge dopants creates new opportunities for designing tailor-made GNR heterojunctions and related nanoscale electronic devices. Here we report the local electronic characterization of type II GNR heterojunctions composed of two different nitrogen edge-doping configurations (carbazole and phenanthridine) that separately exhibit electron-donating and electron-withdrawing behavior. Atomically resolved structural characterization of phenanthridine/carbazole GNR heterojunctions was performed using bond-resolved scanning tunneling microscopy and noncontact atomic force microscopy. Scanning tunneling spectroscopy and first-principles calculations reveal that carbazole and phenanthridine dopant configurations induce opposite upward and downward orbital energy shifts owing to their different electron affinities. The magnitude of the energy offsets observed in carbazole/phenanthridine heterojunctions is dependent on the length of the GNR segments comprising each heterojunction with longer segments leading to larger heterojunction energy offsets. Using a new on-site energy analysis based on Wannier functions, we find that the origin of this behavior is a charge transfer process that reshapes the electrostatic potential profile over a long distance within the GNR heterojunction.

Accessing the Intrinsic Spin Transport in a Topological Insulator by Controlling the Crossover of Bulk-to-Surface Conductance.

We report a method to control contributions of bulk and surface states in the topological insulator Bi_{2}Te_{2}Se that allows accessing the spin-polarized transport endowed by topological surface states. An intrinsic surface dominant transport is established when cooling the sample to low temperature or reducing the conduction channel length, both achieved in situ in the transport measurements with a four-probe scanning tunneling microscope without the need of further tailoring the sample. The topological surface states show characteristic transport behaviors with mobility about an order of magnitude higher than reported before, and a spin polarization approaching the theoretically predicted value. Our result demonstrates accessibility to the intrinsic high mobility spin transport of topological surface states, which paves a way to realizing topological spintronic devices.

Coarse-grained modeling of multiphase interactions at microscale.

The objective of this study is to develop and test a coarse-grained molecular dynamics framework to model microscale multiphase systems with different inter-particle interactions and recover emerging thermodynamic and mechanical properties at the microscale. A water-vapor model and a fused silica model are developed to demonstrate the capability of our framework. The former can reproduce the water density and surface tension over a wide range of temperatures; the latter can reproduce experimental density, tensile strength, and Young's modulus of fused silica. Therefore, the deformable solid model is implemented in the proposed framework. Validations of spatial scaling methods for solid, liquid, and multiphase systems suggest that the proposed framework can be calibrated at an arbitrary microscale and used at a different length scale without recalibration. Different values of wettability for a solid-liquid-vapor system that is characterized by the contact angle can be achieved by changing the solid-liquid inter-particle potential. Thanks to these features, the proposed coarse-grained molecular dynamics framework can potentially find applications in modeling systems in which multiple phases coexist and have substantial interactions.

Facile Fabrication of Large-Area Atomically Thin Membranes by Direct Synthesis of Graphene with Nanoscale Porosity.

Direct synthesis of graphene with well-defined nanoscale pores over large areas can transform the fabrication of nanoporous atomically thin membranes (NATMs) and greatly enhance their potential for practical applications. However, scalable bottom-up synthesis of continuous sheets of nanoporous graphene that maintain integrity over large areas has not been demonstrated. Here, it is shown that a simple reduction in temperature during chemical vapor deposition (CVD) on Cu induces in-situ formation of nanoscale defects (≤2-3 nm) in the graphene lattice, enabling direct and scalable synthesis of nanoporous monolayer graphene. By solution-casting of hierarchically porous polyether sulfone supports on the as-grown nanoporous CVD graphene, large-area (>5 cm2 ) NATMs for dialysis applications are demonstrated. The synthesized NATMs show size-selective diffusive transport and effective separation of small molecules and salts from a model protein, with ≈2-100× increase in permeance along with selectivity better than or comparable to state-of-the-art commercially available polymeric dialysis membranes. The membranes constitute the largest fully functional NATMs fabricated via bottom-up nanopore formation, and can be easily scaled up to larger sizes permitted by CVD synthesis. The results highlight synergistic benefits in blending traditional membrane casting with bottom-up pore creation during graphene CVD for advancing NATMs toward practical applications.

3D Imaging and Manipulation of Subsurface Selenium Vacancies in PdSe_{2}.

Two-dimensional materials such as layered transition-metal dichalcogenides (TMDs) are ideal platforms for studying defect behaviors, an essential step towards defect engineering for novel material functions. Here, we image the 3D lattice locations of selenium-vacancy V_{Se} defects and manipulate them using a scanning tunneling microscope (STM) near the surface of PdSe_{2}, a recently discovered pentagonal layered TMD. The V_{Se} show a characterisitc charging ring in a spatially resolved conductance map, based on which we can determine its subsurface lattice location precisely. Using the STM tip, not only can we reversibly switch the defect states between charge neutral and charge negative, but also trigger migrations of V_{Se} defects. This allows a demonstration of direct "writing" and "erasing" of atomic defects and tracing the diffusion pathways. First-principles calculations reveal a small diffusion barrier of V_{Se} in PdSe_{2}, which is much lower than S vacancy in MoS_{2} or an O vacancy in TiO_{2}. This finding opens an opportunity of defect engineering in PdSe_{2} for such as controlled phase transformations and resistive-switching memory device application.

Concentration Dependence of Dopant Electronic Structure in Bottom-up Graphene Nanoribbons.

Bottom-up fabrication techniques enable atomically precise integration of dopant atoms into the structure of graphene nanoribbons (GNRs). Such dopants exhibit perfect alignment within GNRs and behave differently from bulk semiconductor dopants. The effect of dopant concentration on the electronic structure of GNRs, however, remains unclear despite its importance in future electronics applications. Here we use scanning tunneling microscopy and first-principles calculations to investigate the electronic structure of bottom-up synthesized N = 7 armchair GNRs featuring varying concentrations of boron dopants. First-principles calculations of freestanding GNRs predict that the inclusion of boron atoms into a GNR backbone should induce two sharp dopant states whose energy splitting varies with dopant concentration. Scanning tunneling spectroscopy experiments, however, reveal two broad dopant states with an energy splitting greater than expected. This anomalous behavior results from an unusual hybridization between the dopant states and the Au(111) surface, with the dopant-surface interaction strength dictated by the dopant orbital symmetry.

Atomically precise graphene nanoribbon heterojunctions from a single molecular precursor.

The rational bottom-up synthesis of atomically defined graphene nanoribbon (GNR) heterojunctions represents an enabling technology for the design of nanoscale electronic devices. Synthetic strategies used thus far have relied on the random copolymerization of two electronically distinct molecular precursors to yield GNR heterojunctions. Here we report the fabrication and electronic characterization of atomically precise GNR heterojunctions prepared through late-stage functionalization of chevron GNRs obtained from a single precursor. Post-growth excitation of fully cyclized GNRs induces cleavage of sacrificial carbonyl groups, resulting in atomically well-defined heterojunctions within a single GNR. The GNR heterojunction structure was characterized using bond-resolved scanning tunnelling microscopy, which enables chemical bond imaging at T = 4.5 K. Scanning tunnelling spectroscopy reveals that band alignment across the heterojunction interface yields a type II heterojunction, in agreement with first-principles calculations. GNR heterojunction band realignment proceeds over a distance less than 1 nm, leading to extremely large effective fields.

Detection of the Spin-Chemical Potential in Topological Insulators Using Spin-Polarized Four-Probe STM.

We demonstrate a new method for the detection of the spin-chemical potential in topological insulators using spin-polarized four-probe scanning tunneling microscopy on in situ cleaved Bi_{2}Te_{2}Se surfaces. Two-dimensional (2D) surface and 3D bulk conductions are separated quantitatively via variable probe-spacing measurements, enabling the isolation of the nonvanishing spin-dependent electrochemical potential from the Ohmic contribution. This component is identified as the spin-chemical potential arising from the 2D charge current through the spin momentum locked topological surface states (TSS). This method provides a direct measurement of spin current generation efficiency and opens a new avenue to access the intrinsic spin transport associated with pristine TSS.

Molecular Self-Assembly in a Poorly Screened Environment: F4TCNQ on Graphene/BN.

We report a scanning tunneling microscopy and noncontact atomic force microscopy study of close-packed 2D islands of tetrafluorotetracyanoquinodimethane (F4TCNQ) molecules at the surface of a graphene layer supported by boron nitride. While F4TCNQ molecules are known to form cohesive 3D solids, the intermolecular interactions that are attractive for F4TCNQ in 3D are repulsive in 2D. Our experimental observation of cohesive molecular behavior for F4TCNQ on graphene is thus unexpected. This self-assembly behavior can be explained by a novel solid formation mechanism that occurs when charged molecules are placed in a poorly screened environment. As negatively charged molecules coalesce, the local work function increases, causing electrons to flow into the coalescing molecular island and increase its cohesive binding energy.

Site-Specific Substitutional Boron Doping of Semiconducting Armchair Graphene Nanoribbons.

A fundamental requirement for the development of advanced electronic device architectures based on graphene nanoribbon (GNR) technology is the ability to modulate the band structure and charge carrier concentration by substituting specific carbon atoms in the hexagonal graphene lattice with p- or n-type dopant heteroatoms. Here we report the atomically precise introduction of group III dopant atoms into bottom-up fabricated semiconducting armchair GNRs (AGNRs). Trigonal-planar B atoms along the backbone of the GNR share an empty p-orbital with the extended π-band for dopant functionality. Scanning tunneling microscopy (STM) topography reveals a characteristic modulation of the local density of states along the backbone of the GNR that is superimposable with the expected position and concentration of dopant B atoms. First-principles calculations support the experimental findings and provide additional insight into the band structure of B-doped 7-AGNRs.

The role of H1 linker histone subtypes in preserving the fidelity of elaboration of mesendodermal and neuroectodermal lineages during embryonic development.

H1 linker histone proteins are essential for the structural and functional integrity of chromatin and for the fidelity of additional epigenetic modifications. Deletion of H1c, H1d and H1e in mice leads to embryonic lethality by mid-gestation with a broad spectrum of developmental alterations. To elucidate the cellular and molecular mechanisms underlying H1 linker histone developmental functions, we analyzed embryonic stem cells (ESCs) depleted of H1c, H1d and H1e subtypes (H1-KO ESCs) by utilizing established ESC differentiation paradigms. Our study revealed that although H1-KO ESCs continued to express core pluripotency genes and the embryonic stem cell markers, alkaline phosphatase and SSEA1, they exhibited enhanced cell death during embryoid body formation and during specification of mesendoderm and neuroectoderm. In addition, we demonstrated deregulation in the developmental programs of cardiomyocyte, hepatic and pancreatic lineage elaboration. Moreover, ectopic neurogenesis and cardiomyogenesis occurred during endoderm-derived pancreatic but not hepatic differentiation. Furthermore, neural differentiation paradigms revealed selective impairments in the specification and maturation of glutamatergic and dopaminergic neurons with accelerated maturation of glial lineages. These impairments were associated with deregulation in the expression profiles of pro-neural genes in dorsal and ventral forebrain-derived neural stem cell species. Taken together, these experimental observations suggest that H1 linker histone proteins are critical for the specification, maturation and fidelity of organ-specific cellular lineages derived from the three cardinal germ layers.

Infrared spectroscopy of molecular submonolayers on surfaces by infrared scanning tunneling microscopy: tetramantane on Au111.

We have developed a new scanning-tunneling-microscopy-based spectroscopy technique to characterize infrared (IR) absorption of submonolayers of molecules on conducting crystals. The technique employs a scanning tunneling microscope as a precise detector to measure the expansion of a molecule-decorated crystal that is irradiated by IR light from a tunable laser source. Using this technique, we obtain the IR absorption spectra of [121]tetramantane and [123]tetramantane on Au(111). Significant differences between the IR spectra for these two isomers show the power of this new technique to differentiate chemical structures even when single-molecule-resolved scanning tunneling microscopy (STM) images look quite similar. Furthermore, the new technique was found to yield significantly better spectral resolution than STM-based inelastic electron tunneling spectroscopy, and to allow determination of optical absorption cross sections. Compared to IR spectroscopy of bulk tetramantane powders, infrared scanning tunneling microscopy (IRSTM) spectra reveal narrower and blueshifted vibrational peaks for an ordered tetramantane adlayer. Differences between bulk and surface tetramantane vibrational spectra are explained via molecule-molecule interactions.

Functions of huntingtin in germ layer specification and organogenesis.

Huntington's disease (HD) is a neurodegenerative disease caused by abnormal polyglutamine expansion in the huntingtin protein (Htt). Although both Htt and the HD pathogenic mutation (mHtt) are implicated in early developmental events, their individual involvement has not been adequately explored. In order to better define the developmental functions and pathological consequences of the normal and mutant proteins, respectively, we employed embryonic stem cell (ESC) expansion, differentiation and induction experiments using huntingtin knock-out (KO) and mutant huntingtin knock-in (Q111) mouse ESC lines. In KO ESCs, we observed impairments in the spontaneous specification and survival of ectodermal and mesodermal lineages during embryoid body formation and under inductive conditions using retinoic acid and Wnt3A, respectively. Ablation of BAX improves cell survival, but failed to correct defects in germ layer specification. In addition, we observed ensuing impairments in the specification and maturation of neural, hepatic, pancreatic and cardiomyocyte lineages. These developmental deficits occurred in concert with alterations in Notch, Hes1 and STAT3 signaling pathways. Moreover, in Q111 ESCs, we observed differential developmental stage-specific alterations in lineage specification and maturation. We also observed changes in Notch/STAT3 expression and activation. Our observations underscore essential roles of Htt in the specification of ectoderm, endoderm and mesoderm, in the specification of neural and non-neural organ-specific lineages, as well as cell survival during early embryogenesis. Remarkably, these developmental events are differentially deregulated by mHtt, raising the possibility that HD-associated early developmental impairments may contribute not only to region-specific neurodegeneration, but also to non-neural co-morbidities.

Selective roles of normal and mutant huntingtin in neural induction and early neurogenesis.

Huntington's disease (HD) is a neurodegenerative disorder caused by abnormal polyglutamine expansion in the amino-terminal end of the huntingtin protein (Htt) and characterized by progressive striatal and cortical pathology. Previous reports have shown that Htt is essential for embryogenesis, and a recent study by our group revealed that the pathogenic form of Htt (mHtt) causes impairments in multiple stages of striatal development. In this study, we have examined whether HD-associated striatal developmental deficits are reflective of earlier maturational alterations occurring at the time of neurulation by assessing differential roles of Htt and mHtt during neural induction and early neurogenesis using an in vitro mouse embryonic stem cell (ESC) clonal assay system. We demonstrated that the loss of Htt in ESCs (KO ESCs) severely disrupts the specification of primitive and definitive neural stem cells (pNSCs, dNSCs, respectively) during the process of neural induction. In addition, clonally derived KO pNSCs and dNSCs displayed impaired proliferative potential, enhanced cell death and altered multi-lineage potential. Conversely, as observed in HD knock-in ESCs (Q111 ESCs), mHtt enhanced the number and size of pNSC clones, which exhibited enhanced proliferative potential and precocious neuronal differentiation. The transition from Q111 pNSCs to fibroblast growth factor 2 (FGF2)-responsive dNSCs was marked by potentiation in the number of dNSCs and altered proliferative potential. The multi-lineage potential of Q111 dNSCs was also enhanced with precocious neurogenesis and oligodendrocyte progenitor elaboration. The generation of Q111 epidermal growth factor (EGF)-responsive dNSCs was also compromised, whereas their multi-lineage potential was unaltered. These abnormalities in neural induction were associated with differential alterations in the expression profiles of Notch, Hes1 and Hes5. These cumulative observations indicate that Htt is required for multiple stages of neural induction, whereas mHtt enhances this process and promotes precocious neurogenesis and oligodendrocyte progenitor cell elaboration.