Dimer Rows Research Articles

On the Nature of the Mitochondrial Permeability Transition

The mitochondrial inner membrane (IM) undergoes a dramatic permeability transition (mPT) associated with exposure to reactive oxygen species (ROS) and/or abnormally high Ca+2. The mPT is characterized by matrix swelling, loss of membrane potential and increased solute permeability. While changes are initially transient and partly reversible, repeated insult leads to irreversible loss in function associated with outer membrane (OM) rupture. While the onset of mPT is attributed to opening of a pore whose molecular identity remains undefined, much of what is known about mPT can be explained without invoking a pore. The IM has a complicated topology established by two high-curvature features: (1) catenoid-shaped junctions that connect cristae with the IM periphery, formed by proteins (MICOS, OPA1) and cardiolipin, and (2) acute folds in cristae induced and/or stabilized by dimer rows of the ATP synthase which interacts with MICOS and cardiolipin. There is considerable evidence that the ATP synthase and cardiolipin, stabilizers of IM topology, are disrupted by high Ca+2and by ROS respectively. The consequence of destabilizing regions of high IM curvature is increased mechanical stress, normally balanced by osmotic forces, which would drive water into the matrix through aquaporins. The increased membrane strain in the high-curvature regions could cause discrete, transient losses of local IM integrity, resulting in stepwise depolarization and solute influx that would mimic pore opening and closing. Predictions of mPT membrane stress models vs pore models will be compared against experimental data.

“Boron + vacancy” complexes on the hydrogenated diamond surface С(100)-(2×1)

The paper presents the results of quantum-chemical modeling of structural and electronic states of “boron + vacancy” complex defects on the hydrogenated and clean diamond surface, with a variation in the position of BV complexes in the upper six surface layers. Neutral, positive and negatively charged states of the complexes are considered. Two different positions of impurity and intrinsic defects in the composition of the BV complex have been considered for the third and fourth layers: under the dimer row and between the rows. The influence of the surface passivation on the position of BV complexes on the energy scale is analyzed. It has been found that hydrogenation of the surface leads to a change in the configuration of the most stable BV complex. The formation of a local graphite-like structure with π-conjugation is the main stabilizing factor for the defect structures, regardless of the considered charge state. It was shown that the distribution of the spin density of the studied negative BV complexes located directly in the near-surface layers of the clean and hydrogenated surface is similar to the spin properties of complexes in the bulk of diamond.

Density Functional Theory Calculations of the Adsorption of Cytosine on Si(100)

We have performed density functional theory (DFT) calculations to investigate the adsorption structures of cytosine on Si(100). Multiple adsorption configurations that could result from Lewis acid–base reactions or cycloadditions were optimized, and the structural and energetic parameters of the obtained adsorption structures were compared. Row‐bridged bidentate configurations with SiOCNCNSi linkages to two silicon atoms in adjacent dimer rows were found to be more stable than other configurations. The SiN bond was formed by NH dissociative adsorption, while the SiO bond was dative. In the monodentate structures, the CH or NH dissociative adsorption structures were more energetically favorable than the datively bonded ones. Cycloaddition through the π‐electrons of the CN or CC bonds of the cytosine ring resulted in relatively unstable adsorption products.

Effect of H Defects on Li Transport during the Deposition Process on an H‐Diamond Surface: A First‐Principles Calculation Analysis

AbstractTo explore the feasibility and rationality of a hydrogen‐terminated diamond surface film as an solid electrolyte interface (SEI) for lithium‐sulfur batteries, the adsorption and migration behavior of lithium atoms on the hydrogen‐terminated diamond surface with different amounts of hydrogen defects are determined by first‐principles calculations. Since a hydrogen deficiency in the row direction is denser than a hydrogen deficiency in the chain direction, hydrogen deficiency can drive lithium‐ion deposition. Thus, lithium atoms are more stable on the surface of hydrogen‐terminated diamonds with a hydrogen deficiency in the direction of the dimer row. The adsorption of lithium atoms on hydrogen‐terminated diamond films lacking three hydrogens is more stable due to the absence of dangling chemical bonds on the surface of the hydrogen‐terminated diamond. Therefore, lithium atoms cannot be adsorbed on an all‐H‐diamond surface. The low adsorption energy of lithium atoms on a clean diamond surface indicates that it is a simple physical adsorption. H termination increases the adsorption energy and migration activation energy of Li on the diamond surface. H termination changes the migration path of Li on the diamond surface. The atomic deposition of Li is driven by the center of the H defect region on the H‐diamond surface.

Chlorine insertion and manipulation on the Si(100)- 2×1 -Cl surface in the regime of local supersaturation

We insert and manipulate a single chlorine atom in chlorine monolayer on a Si(100)-2x1 surface using a scanning tunneling microscope. Two objects were created - a Cl atom in a groove between two dimer rows, and bridge-bonded Cl on a silicon dimer. Changing the voltage polarity leads to conversion of the objects into each other. Anisotropic movement of the objects at 77 K is mediated by two different diffusion mechanisms: hopping and crowdion-like motion. Insertion of a Cl atom in a groove between two dimer rows leads to the formation of a dangling bond on a third-layer Si atom. At positive sample voltage bias, the first object is positively charged, while the second object can be neutral or negatively charged depending on silicon sample doping.

Atomic-scale control of tunneling in donor-based devices

Atomically precise donor-based quantum devices are a promising candidate for solid-state quantum computing and analog quantum simulations. However, critical challenges in atomically precise fabrication have meant systematic, atomic scale control of the tunneling rates and tunnel coupling has not been demonstrated. Here using a room temperature grown locking layer and precise control over the entire fabrication process, we reduce unintentional dopant movement while achieving high quality epitaxy in scanning tunnelling microscope (STM)-patterned devices. Using the Si(100)2 × 1 surface reconstruction as an atomically-precise ruler to characterize the tunnel gap in precision-patterned single electron transistors, we demonstrate the exponential scaling of the tunneling resistance on the tunnel gap as it is varied from 7 dimer rows to 16 dimer rows. We demonstrate the capability to reproducibly pattern devices with atomic precision and a donor-based fabrication process where atomic scale changes in the patterned tunnel gap result in the expected changes in the tunneling rates.

Molecular dynamics simulations of the growth of Ge on Si

The initial stages of the growth of germanium on the dimer reconstructed Si(100) surface is modelled using molecular dynamics (MD). Pyramidal island structures are observed to form despite MD being carried out at a deposition rate faster than experiment. By an examination of transitions that can occur from intermediate structures that form in the MD simulations, growth mechanisms can be identified. The initial wetting occurs as a result of Ge atoms diffusing into the trenches between the dimer rows. This results in Ge–Ge or Ge–Si dimer chains growing in rows perpendicular to the original Si–Si dimer rows on the surface. It is shown how strained Ge pyramids with square bases can form by diffusing atoms joining together adjacent dimer rows. From these initial square-based structures, complex concerted motions are observed in which atoms in lower layers ‘climb up’ to higher layers. Similar structures grown in the pure Si case exhibit much higher energies barriers for the ‘climbing up’ process indicating that the effect of strain is to reduce the energy barriers for pyramid formation. In addition to the investigation of atomistic growth processes, surface energy effects are also examined, which show that a germanium-covered Si(100) surface containing shallow-angled pyramids is energetically more favourable than that grown as a flat monolayer.

Hydrogen inserted into the Si(100)-2 × 1-H surface: a first-principles study.

Hydrogen can be inserted into Si(100)-2 × 1-H during surface preparation or during the hydrogen desorption lithography used to create atomic-scale devices. Here, a hydrogen atom inserted into a hydrogen monolayer on the Si(100)-2 × 1 surface has been studied using density functional theory. Hydrogen-induced defects were considered in their neutral, negative, and positive charge states. It was found that hydrogen forms a dihydride unit on the surface in the most stable neutral and negative charge states. Hydrogen located in the groove between dimer rows is also one of the most stable negative charge states. In the positive charge state, hydrogen forms a three-center bond inside a Si dimer, Si-H-Si, similar to the bulk case. A comparison of simulated scanning tunneling microscopy (STM) images with the experimental data available in the literature showed that neutral and negatively charged hydrogen-induced defects were already observed in experiments. The results reveal that the H atom inserted into a hydrogen monolayer on the Si(100)-2 × 1 surface can lead to the formation of a positively or negatively charged defect. It is shown that H atoms in the considered configurations can play a role in various surface reactions.

The array of In-Bi heterodimers on the Si(100) surface

Studying the In and Bi coadsorption onto the Si(100) surface at elevated temperatures using Scanning Tunneling Microscopy, Angle-Resolved Photoelectron Spectroscopy, and Density Functional Theory, we have found the formation of a 2 × 4 array of In-Bi heterogeneous dimers. The surface is closely related to a Bi-induced Si(100)2 × n-Bi (n=5−12) reconstruction and can be visualized as that with one Bi atom in a Bi-Bi dimer replaced by In atom, and the length of dimer rows stabilized on 4 periods. The In-Bi dimers are buckled, with Bi atoms being 0.62 Å higher than In. STM simulations revealed that the contribution of a Bi atom into experimental STM contrast is dominant. The asymmetric In-Bi heterodimers orient in a unit cell independent of each other producing chaotically looking STM images despite the 2 × 4 lattice itself is well-ordered. The surface is semiconductor featuring noticeable Rashba-type spin-splitting of surface states. This structure is believed to be an interesting object for theoretical and experimental studies on the influence of lack of symmetry and chemical disorder to spin polarization in the low-dimensional materials.

Scanning Tunneling Microscope Study on C2H2 Adsorption on a Ge(100) Surface

Adsorption configurations of C2H2 on the Ge(001) surface at room temperature were investigated using scanning tunneling microscope (STM). Two adsorption features, occupying one dimer and two dimers, respectively, were observed as major species. Both of them appear in rounded or elongated bean shapes in filled-state images. In empty-state images, they reveal atomically resolved details: two and four local maxima for the one-dimer and the two-dimer features, respectively. The empty-state double maximum of the one-dimer feature confirms the adsorption of a C2H2 molecule on top of a dimer. Based on the empty-state quadruple maximum of the two-dimer feature, we propose the adsorption of a pair of C2H2 molecules across the ends of two adjacent dimers in the same dimer row (paired end-bridge). This differs from the previous interpretation of the two-dimer feature as a single C2H2 molecule adsorbed in a tetra-σ-bonding configuration. We also observed C2H2 molecules adsorbed in the unpaired end-bridge configuration, but none in tetra-σ-bonding configurations. These observations and interpretations are consistent with the energetics predicted by using theoretical calculations.

STM-Induced Desorption and Lithographic Patterning of Cl-Si(100)-(2 × 1).

A scanning tunneling microscope (STM) was used to investigate tip-induced chlorine desorption and lithographic patterning of Cl-terminated Si(100)-(2 × 1) surfaces from 4 to 600 K in ultrahigh vacuum. Until now, STM lithography has exclusively focused on hydrogen-based chemistry for donor device fabrication. As the initial step in developing halogen-based chemistries for STM fabrication of acceptor-based devices, we substituted the hydrogen resist with chlorine. We found that chlorine can be selectively desorbed by the STM tip using both electron and hole injection. Observations show that targeted chlorine was not driven into the surface but desorbed completely as both individual and pairs of atoms. Chlorine depassivation lithography is demonstrated using both field-emission patterning to desorb chlorine from large areas with high efficiency (0.83(1)) and atomic-precision patterning to desorb one to two dimer rows at a time, resulting in 1.5 nm wide lines. Further, varying the experimental parameters for lithography revealed a positive correlation between pattern line widths and both positive sample bias voltage (1.7(2) nm/V) and total electron dose (0.15(2) nm/(mC/cm)), demonstrating that the energy and total number of electrons play a role in desorption from multiple sites.

Predictions of Pattern Formation in Amino Acid Adlayers at the In Vacuo Graphene Interface: Influence of Termination State.

Controlled self-assembly of biomolecules on graphene offers a pathway for realizing its full potential in biological applications. Microscopy has revealed the self-assembly of amino acid adlayers into dimer rows on nonreactive substrates. However, neither the spontaneous formation of these patterns, nor the influence of amino acid termination state on the formation of patterns has been directly resolved to date. Molecular dynamics simulations, with the ability to reveal atomic level details and exert full control over the termination state, are used here to model initially disordered adlayers of neutral, zwitterionic, and neutral-zwitterionic mixtures for two types of amino acids, tryptophan and methionine, adsorbed on graphene in vacuo. The simulations of the zwitterion-containing adlayers exhibit the spontaneous emergence of dimer row ordering, mediated by charge-driven intermolecular interactions. In contrast, adlayers containing only neutral species do not assemble into ordered patterns. It is also found that the presence of trace amounts of water reduces the interamino acid interactions in the adlayers, but does not induce or disrupt pattern formation. Overall, the findings reveal the balance between the lateral interamino acid interactions and amino acid-graphene interactions, providing foundational insights for ultimately realizing the predictable pattern formation of biomolecules adsorbed on unreactive surfaces.

Structural and electronic properties of boron-induced defects on the Si(001) surface

The (001) surface of heavily boron (B) doped silicon is investigated by employing the scanning tunneling microscopy measurements and the density functional theory calculations. Two different defect structures are found in the surface layers, both of which evolve the characteristic spectral features near the valence band maximum. One of the two incorporates a B atom in the second layer with the Si dimers intact and is scattered randomly in the layer. The other one incorporates a B atom in the fourth layer with a dimer vacancy produced directly above it and tends to get together with nearby dimer vacancies to grow the extended or line defects along the perpendicular direction to the dimer rows. Such defect formation is energetically favored to enhance the B populations in the second and fourth layers by $\ensuremath{\sim}120$ and $\ensuremath{\sim}80$ times, respectively, when compared to that in the bulk layer.

Role of Electronic Structures and Dispersion Interactions in Adsorption Selectivity of Pyrimidine Molecules with a Si(5 5 12) Surface

We show that the resonance energy and dispersion interactions (DIs) are critical factors in determining the selectivity and configuration in the reaction of pyrimidine molecules with a silicon surface. The atomic structures of the pyrimidine molecules after they reacted with a Si(5 5 12)–2 × 1 surface were studied. Binding configurations of the pyrimidines were distinct from those of other molecules with N lone-pair electrons and aromaticity. The pyrimidine molecules were adsorbed to produce two σ bonds to silicon with N2 and C5 on the adatom row (Adr) and honeycomb chain (Hnc) sites and with C1 and C4 on the dimer row (Dmr) and the tetramer row (Ttr) sites. The reactions occurred via a [4 + 2]-type cycloaddition to produce planar-type configurations with loss of aromaticity. That is, the atoms of the aromatic ring of pyrimidine form chemical bonds with silicon atoms, which is in contrast to the adsorption behaviors reported for other N-containing aromatic molecules. When pyrimidine is adsorbed, its molec...

Electron Attachment Leads to Unidirectional In-Plane Molecular Rotation of Para-Chlorostyrene on Si(100)

We report the observation of electron-induced unidirectional planar molecular rotation of para-chlorostyrene on Si(100), studied by scanning tunneling microscopy (STM) at room temperature and by ab initio theory. This bifunctional molecule is shown to be favorable to the electron-induced rotation since the phenyl group acts as a pivot and the vinyl as a lever arm. In the initial configuration, both phenyl and vinyl are attached to silicon dimers along the same row of the substrate. The first electron from the STM tip is observed to induce a lateral shift of the vinyl to “state 1” in which the vinyl is bound asymmetrically to one side of a silicon dimer. The second electron is found to give rise to a ∼60° rotation to “state 2”, a configuration in which the vinyl has swung around the phenyl to an adjacent dimer row. The impulsive two-state (I2S) model was employed to explain the conversion of the initial state to state 1 and the conversion of state 1 to state 2. These two successive impulses were computed b...

Photomodulation of Two-Dimensional Self-Assembly of Azobenzene–Hexa-peri-hexabenzocoronene–Azobenzene Triads

Achieving exquisite control over self-assembly of functional polycyclic aromatic hydrocarbons (PAH) and nanographene (NG) is essential for their exploitation as active elements in (nano)technological applications. In the framework of our effort to leverage their functional complexity, we designed and synthesized two hexa-peri-hexabenzocoronene (HBC) triads, pAHA and oAHA, decorated with two light-responsive azobenzene moieties at the pseudo-para and ortho positions, respectively. Their photoisomerization in solution is demonstrated by UV–vis absorption. 1H NMR measurements of oAHA suggested 23% of Z-form can be obtained at a photostationary state with UV irradiation (366 nm). Scanning tunneling microscopy imaging revealed that the self-assembly of pAHA and oAHA at the solid–liquid interface between highly oriented pyrolytic graphite (HOPG) and their solution in 1,2,4-trichlorobenzene can be modulated upon light irradiation. This is in contrast to our previous work using HBC bearing a single azobenzene moiety, which did not show such photomodulation of the self-assembled structure. Upon E-Z isomerization both pAHA and oAHA displayed an increased packing density on the surface of graphite. Moreover, pAHA revealed a change of self-assembled pattern from an oblique unit cell to a dimer row rectangular crystal lattice whereas the assembly of oAHA retained a dimer row structure before and after light irradiation, yet with a modification of the inter-row molecular orientation. Molecular mechanics/molecular dynamics simulations validated the self-assembly patterns of pAHA and oAHA, comprising azobenzenes in their Z-forms. These results pave the way toward use of suitably functionalized large PAHs, as well as NGs, to develop photoswitchable devices.

Electromigration Effect on Vacancy Islands Nucleation on Si(100) Surface during Sublimation

By means of in situ ultrahigh vacuum reflection electron microscopy, the nucleation of vacancy islands on wide terraces of the Si(100) surface is investigated. The temperature dependence of the displacement of a vacancy island nucleation center is determined in the process of heating a sample with a dc electric current. On the basis of a theoretical model, the effective electric charge of addimers is estimated in the direction across dimer rows of the surface. The effective charge has a positive sign and does not exceed 15 units of the elementary charge in the temperature range of 1020–1120°C.

Electronic transport in planar atomic-scale structures measured by two-probe scanning tunneling spectroscopy

Miniaturization of electronic circuits into the single-atom level requires novel approaches to characterize transport properties. Due to its unrivaled precision, scanning probe microscopy is regarded as the method of choice for local characterization of atoms and single molecules supported on surfaces. Here we investigate electronic transport along the anisotropic germanium (001) surface with the use of two-probe scanning tunneling spectroscopy and first-principles transport calculations. We introduce a method for the determination of the transconductance in our two-probe experimental setup and demonstrate how it captures energy-resolved information about electronic transport through the unoccupied surface states. The sequential opening of two transport channels within the quasi-one-dimensional Ge dimer rows in the surface gives rise to two distinct resonances in the transconductance spectroscopic signal, consistent with phase-coherence lengths of up to 50 nm and anisotropic electron propagation. Our work paves the way for the electronic transport characterization of quantum circuits engineered on surfaces.

Self-assembly of 8-; 5- and 2-hydroxylquinolines on Au(111) single crystal in perchloric acid

Self-assembled monolayers of 8-; 5-; and 2-hydroxyquinolines (8-; 5- & 2-hqs) are obtained for the first time at the electrified Au(111)|100mM HClO4 interface via electrochemical scanning tunneling microscopy (EC-STM). We observed that 8- and 2-hqs form stripe patterns, both on the negatively charged reconstructed Au(111)-(p×√3) as well as on unreconstructed Au(111)-(1×1) surfaces. The adlayers are composed of dimer rows stabilized by both cyclic O-H···N hydrogen bonds and van der Waal interaction between the neighboring molecules. The O-H···N bond is made between the 8 and 2 position -OH acting as hydrogen bond donor and N in the pyridine ring as the hydrogen bond acceptor. When the 8 and 2 position of hydroxyl group in the pyridine ring is replaced to the 5 position in the benzene ring, we observed a monolayer with grid-like structure (trimeric pattern) that are qualitatively different from those of 8- and 2-hqs. Dimer formation is completely broken in the case of 5-hq, in which C-H···O and C-H···N hydrogen bonds play a key role in company with coadsorption of solvent molecules or electrolyte ions to support the stability of the adlayer. However, the H-bond networks of these adlayers are destabilized at the positive charge densities of Au(111). While 2-hq molecules form disordered chemisorbed adlayer, 8- and 5-hqs are subjected to electrochemical oxidation.

Scanning tunneling microscopy study of Cu-induced surface restructuring of Si(100)-(2 × 1)

We used scanning tunneling microscopy (STM) to study the Cu-induced restructuring of Si(100)-(2 × 1) surface at the atomic scale. Copper was deposited onto silicon substrates kept at room temperature (RT) or 500 °C. Submonolayer amounts of Cu were found to be sufficient to induce a visible restructuring of the Si(100)-(2 × 1) surface manifested by the disappearance of the vacancy line defects (VLDs), as well as dimer rows disordering (for the RT deposition) or the formation of a c(4 × 4) surface reconstruction (for the 500 °C deposition) not reported for the Cu/Si(100) system so far. Higher amounts of Cu deposited onto the RT-disordered surface at 500 °C led to the formation of 3D CuSi crystallites, accompanied by a significant surface roughening. In contrast, deposition of large amounts of Cu onto a pristine Si(100) at 500 °C resulted in the formation of a near-(1 × 1) local surface atoms ordering.