Hut Clusters Research Articles

FinR Regulates Expression of nicC and nicX Operons, Involved in Nicotinic Acid Degradation in Pseudomonas putida KT2440.

Many proteobacteria harbor FinR homologues in their genomes as putative LysR-type proteins; however, the function of FinR is poorly studied except in the induction of fpr-1 under superoxide stress conditions in Pseudomonas putida and Pseudomonas aeruginosa Here, by analyzing the influence of finR deletion on the transcriptomic profile of P. putida KT2440 through RNA sequencing and real-time quantitative PCR (RT-qPCR), we found 11 operons that are potentially regulated by FinR. Among them, the expression of nicC and nicX operons, which were reported to be responsible for the aerobic degradation of nicotinic acid (NA), was significantly decreased in the finR mutant, and complementation with intact finR restored the expression of the two operons. The results of bacterial NA utilization demonstrated that the deletion of finR impaired bacterial growth in minimal medium supplemented with NA/6HNA (6-hydroxynicotinic acid) as the sole carbon source and that complementation with intact finR restored the growth of the mutant strain. The expression of nicC and nicX operons was previously revealed to be repressed by the NicR repressor and induced by NA/6HNA. Our transcriptional assay revealed that the deletion of finR weakened the induction of nicC and nicX by NA/6HNA. Meanwhile, the deletion of finR largely decreased the effect of nicR deletion on the expression of nicC and nicX operons. These results suggest that finR plays a positive role and cooperates with NicR in the regulation of nicC and nicX operons. In vitro experiments showed that both FinR and NicR bound to nicX and nicC promoter regions directly. The results of this study deepened our knowledge of FinR function and nicotinic acid degradation in P. putidaIMPORTANCE This study analyzed the influence of finR deletion on the transcriptomic profile of Pseudomonas putida KT2440. The FinR regulator is widely distributed but poorly studied in diverse proteobacteria. Here, we found 11 operons that potentially are regulated by FinR in KT2440. We further demonstrated that FinR played a positive role and cooperated with the NicR repressor in bacterial nicotinic acid (NA) degradation via regulating the expression of nicC and nicX operons. Furthermore, a transcriptomic analysis also indicated a potentially negative role of FinR in the expression of the hut cluster involved in bacterial histidine utilization. The work deepened our knowledge of FinR function and nicotinic acid degradation in P. putida.

Ge2Pt hut clusters: A substrate for germanene

The formation and structure of Ge2Pt clusters was studied in order to understand their germanene termination layer. The Ge2Pt clusters are formed by depositing a few layers of Pt on a Ge(110) surface. Annealing at temperatures above 1043 K results in eutectic Ge-Pt droplets that etch grooves on the surface in the [11¯0] direction. Upon cooling down, they solidify and decompose into a Ge2Pt phase and a pure Ge phase. Electron diffraction reveals that the hut-shaped clusters have their (001) plane oriented parallel to the Ge(110) surface and their (100) plane facing in the Ge[11¯0] direction. The facets of the Ge2Pt hut clusters have been determined to be the {101} and {011} planes. The germanene layers which cover these facets are commensurate with the {101} and {011} facets of the Ge2Pt substrate.

Efficient Calculation of Electronic Structure Using O(N) Density Functional Theory.

We propose an efficient way to calculate the electronic structure of large systems by combining a large-scale first-principles density functional theory code, Conquest, and an efficient interior eigenproblem solver, the Sakurai-Sugiura method. The electronic Hamiltonian and charge density of large systems are obtained by Conquest, and the eigenstates of the Hamiltonians are then obtained by the Sakurai-Sugiura method. Applications to a hydrated DNA system and adsorbed P2 molecules and Ge hut clusters on large Si substrates demonstrate the applicability of this combination on systems with 10,000+ atoms with high accuracy and efficiency.

Nanoscale thermal transport in self-organized epitaxial Ge nanostructures on Si(001)

The thermal transport properties of self-organized Ge nanostructures on Si were studied by means of ultrafast surface sensitive time-resolved electron diffraction. The thermal boundary resistance was determined from the temperature response of the Ge nanostructures upon impulsive heating by fs-laser pulses. The transient temperature was determined through the Debye–Waller effect. Epitaxial growth of Ge hut and dome clusters was achieved by in-situ deposition of 8 monolayers of Ge on Si(001) at 550 °C under ultra-high vacuum conditions. Time-resolved spot profile analysis of different orders of diffraction spots was used to distinguish between the thermal response of hut and dome clusters. Dome clusters of 6 nm height and 50 nm width cool with a time constant of which agrees well with numerical simulations calculated in the framework of the diffuse mismatch model. The much smaller hut clusters with a height of 2.3 nm and width of 23 nm exhibit a cooling time of , which is a factor of 2 slower than predicted by theory.

Spot profile analysis and lifetime mapping in ultrafast electron diffraction: Lattice excitation of self-organized Ge nanostructures on Si(001).

Ultrafast high energy electron diffraction in reflection geometry is employed to study the structural dynamics of self-organized Germanium hut-, dome-, and relaxed clusters on Si(001) upon femtosecond laser excitation. Utilizing the difference in size and strain state the response of hut- and dome clusters can be distinguished by a transient spot profile analysis. Surface diffraction from {105}-type facets provide exclusive information on hut clusters. A pixel-by-pixel analysis of the dynamics of the entire diffraction pattern gives time constants of 40, 160, and 390 ps, which are assigned to the cooling time constants for hut-, dome-, and relaxed clusters.

Nanoscale heat transport from Ge hut, dome, and relaxed clusters on Si(001) measured by ultrafast electron diffraction

The thermal transport properties of crystalline nanostructures on Si were studied by ultra-fast surface sensitive time-resolved electron diffraction. Self-organized growth of epitaxial Ge hut, dome, and relaxed clusters was achieved by in-situ deposition of 8 monolayers of Ge on Si(001) at 550 °C under UHV conditions. The thermal response of the three different cluster types subsequent to impulsive heating by fs laser pulses was determined through the Debye-Waller effect. Time resolved spot profile analysis and life-time mapping was employed to distinguish between the thermal response of the different cluster types. While dome clusters are cooling with a time constant of τ = 150 ps, which agrees well with numerical simulations, the smaller hut clusters with a height of 2.3 nm exhibit a cooling time constant of τ = 50 ps, which is a factor of 1.4 slower than expected.

Influence of composition and substrate miscut on the evolution of {105}-terminated in-plane Si1−xGex quantum wires on Si(001)

Isolated in-plane wires on Si(001) are promising nanostructures for quantum transport applications. They can be fabricated in a catalyst-free process by thermal annealing of self-organized Si1−xGex hut clusters. Here, we report on the influence of composition and small substrate miscuts on the unilateral wire growth during annealing at 570 °C. The addition of up to 20% of Si mainly affects the growth kinetics in the presence of energetically favorable sinks for diffusing Ge atoms, but does not significantly change the wire base width. For the investigated substrate miscuts of <0.12°, we find geometry-induced wire tapering, but no strong influence on the wire lengths. Miscuts <0.02° lead to almost perfect quantum wires terminated by virtually step-free {105} and {001} facets over lengths of several 100 nm. Generally, the investigated Si1−xGex wires are metastable: Annealing at ≥600 °C under otherwise identical conditions leads to the well-known coexistence of Si1−xGex pyramids and domes.

On atomic structure of Ge huts growing on the Ge/Si(001) wetting layer

Structural models of growing Ge hut clusters—pyramids and wedges—are proposed on the basis of data of recent STM investigations of nucleation and growth of Ge huts on the Si(001) surface in the process of molecular beam epitaxy. It is shown that extension of a hut base along ⟨110⟩ directions goes non-uniformly during the cluster growth regardless of its shape. Growing pyramids, starting from the second monolayer, pass through cyclic formation of slightly asymmetrical and symmetrical clusters, with symmetrical ones appearing after addition of every fourth monolayer. We suppose that pyramids of symmetrical configurations composed by 2, 6, 10, etc., monolayers over the wetting layer are more stable than asymmetrical ones. This might explain less stability of pyramids in comparison with wedges in dense arrays forming at low temperatures of Ge deposition. Possible nucleation processes of pyramids and wedges on wetting layer patches from identical embryos composed by 8 dimers through formation of 1 monolayer high 16-dimer nuclei different only in their symmetry is discussed. Schematics of these processes are presented. It is concluded from precise STM measurements that top layers of wetting layer patches are relaxed when huts nucleate on them.

Morphological Evaluation of Ge Nanoclusters by Spot Shape of Surface Electron Diffraction

Nanoclusters of Ge, such as hut clusters and pyramidal clusters, were grown on Si(001) substrates and evaluated by surface electron diffraction methods such as reflection high-energy electron diffraction (RHEED) and low-energy electron diffraction (LEED). Observations of the same sample by both RHEED and LEED were carried out for the first time. The diffraction spots had a characteristic shape and intensity distribution depending on the morphology of the clusters. The spot shapes in RHEED and LEED were simulated by kinematic calculations, which reproduced the experimental results fairly well. It was confirmed that the characteristic spot shapes can be explained by refraction effects and Laue function of diffraction intensity. [DOI: 10.1380/ejssnt.2012.18]

Nanoscale Heat Transport in Self-Organized Ge Clusters on Si(001)

ABSTRACTUltrafast time resolved transmission electron diffraction (TED) in a reflection geometry was used to study the cooling behavior of self-organized, well defined nanoscale germanium hut and dome clusters on Si(001). The clusters were heated in a pump-probe scheme by fs-laser pulses. The resulting transient temperature rise was then determined from the drop in diffraction intensity caused by the Debye-Waller effect. From a cooling time of τ =177 ps we estimated a strongly reduced heat transfer compared with homogeneous films of equivalent thickness.

Molecular Dynamics Study on Mechanical Properties in the Structure of Self-Assembled Quantum Dot

Stress and strain in the structure of self-assembled quantum dots constructed in the Ge/Si(001) system is calculated by using molecular dynamics simulation. Pyramidal hut cluster composed of Ge crystal with {105} facets surfaces observed in the early growth stage are computationally modeled. We calculate atomic stress and strain in relaxed pyramidal structure. Atomic stress for triplet of atoms is approximately defined as an average value of pairwise (virial) quantity inside triplet, which is the product of vectors between each two atoms. Atomic strain by means of atomic strain measure (ASM) which is formulated on the Green’s definition of continuum strain. We find the stress (strain) relaxation in pyramidal structure and stress (strain) concentration in the edge of pyramidal structure. We discuss size dependency of stress and strain distribution in pyramidal structure. The relationship between hydrostatic stress and atomic volumetric strain is basically linear for all models, but for the surface of pyramidal structure and Ge-Si interface. This means that there is a reasonable correlation between atomic stress proposed in the present study and atomic strain measure, ASM.

CMOS-compatible dense arrays of Ge quantum dots on the Si(001) surface: hut cluster nucleation, atomic structure and array life cycle during UHV MBE growth.

We report a direct observation of Ge hut nucleation on Si(001) during UHV molecular beam epitaxy at 360°C. Nuclei of pyramids and wedges were observed on the wetting layer (WL) (M × N) patches starting from the coverage of 5.1 Å and found to have different structures. Atomic models of nuclei of both hut species have been built as well as models of the growing clusters. The growth of huts of each species has been demonstrated to follow generic scenarios. The formation of the second atomic layer of a wedge results in rearrangement of its first layer. Its ridge structure does not repeat the nucleus. A pyramid grows without phase transitions. A structure of its vertex copies the nucleus. Transitions between hut species turned out to be impossible. The wedges contain point defects in the upper corners of the triangular faces and have preferential growth directions along the ridges. The derived structure of the {105} facet follows the paired dimer model. Further growth of hut arrays results in domination of wedges, and the density of pyramids exponentially drops. The second generation of huts arises at coverages >10 Å; new huts occupy the whole WL at coverages ~14 Å. Nanocrystalline Ge 2D layer begins forming at coverages >14 Å.

Absorption of terahertz radiation in Ge/Si(001) heterostructures with quantum dots

The terahertz spectra of the dynamic conductivity and radiation absorption coefficient in germanium-silicon heterostructures with arrays of Ge hut clusters (quantum dots) have been measured for the first time in the frequency range of 0.3-1.2 THz at room temperature. It has been found that the effective dynamic conductivity and effective radiation absorption coefficient in the heterostructure due to the presence of germanium quantum dots in it are much larger than the respective quantities of both the bulk Ge single crystal and Ge/Si(001) without arrays of quantum dots. The possible microscopic mechanisms of the detected increase in the absorption in arrays of quantum dots have been discussed.

Nucleation of Ge quantum dots on the Si(001) surface

A direct observation of nucleation of Ge hut clusters formed by ultrahigh-vacuum molecular-beam epitaxy is reported. The nuclei of the pyramidal and wedgelike clusters have been observed on the wetting layer blocks and found to have different structures. The growth of the clusters of both species goes on following different scenarios: Formation of the second atomic layer of the wedgelike cluster results in rearrangement of its first layer. Its ridge structure does not replicate the structure of the nucleus. The pyramidal cluster grows without phase transitions. The structure of its vertex copies the structure of the nucleus. The wedgelike clusters contain point defects on the triangular faces and have preferential directions of growth along the ridges.

Classification of Ge hut clusters in arrays formed by molecular beam epitaxy at low temperatures on the Si(001) surface

Ge hut clusters forming quantum dot arrays on the Si(001) surface in the process of low-temperature ultrahigh-vacuum molecular beam epitaxy are morphologically investigated and classified using in situ scanning tunnelling microscopy. It is found that two main Ge hut cluster types—pyramidal and wedge-shaped—have different atomic structures, and it is concluded that shape transitions between the two are impossible. Derivative cluster species — obelisks (or truncated wedges) and accreted wedges — are revealed and investigated for the first time and shown to start dominating at high Ge coverages. The uniformity of cluster arrays is shown to be controlled by the scatter in the lengths of wedge-like clusters. At low growth temperatures (360 °C), cluster nucleation during the growth of the array is observed for all values of Ge coverage except for a particular point at which the arrays are more uniform than at higher or lower coverages. At higher temperatures (530 °C), no cluster nucleation is observed after the initial formation of the array.

Atomic structure of Ge quantum dots on the Si(001) surface

In situ morphological investigation of the “105” faceted Ge islands on the Si(001) surface (hut clusters) have been carried out using an ultra high vacuum instrument integrating a high resolution scanning tunnelling microscope and a molecular beam epitaxy vessel. Both species of hut clusters-pyramids and wedges-were found to have the same structure of the “105” facets which was visualized. Structures of vertexes of the pyramidal clusters and ridges of the wedge-shaped clusters were revealed as well and found to be different. This allowed us to propose a crystallographic model of the “105” facets as well as models of the atomic structure of both species of the hut clusters. An inference is made that transitions between the cluster shapes are impossible.

Klassifikatsiya hut-klasterov Ge v massivakh, formiruemykh na poverkhnosti Si(001) metodom molekulyarno-luchevoi epitaksii pri nizkikh temperaturakh

Классификация hut-кластеров Ge в массивах, формируемых на поверхности Si(001) методом молекулярно-лучевой эпитаксии при низких температурах, Арапкина Л.В., Юрьев В.А.

Kinetic frustration of Ostwald ripening in Ge/Si(100) hut ensembles

We show that low area density Ge/Si(100) island ensembles comprised solely of hut and pyramid clusters do not undergo Ostwald ripening during days-long growth temperature anneals. In contrast, a very low density of large, low chemical potential Ge islands reduce the supersaturation causing the huts and pyramids to ripen. By assuming that huts lengthen by adding single {105} planes that grow from apex-to-base, we use a mean-field facet nucleation model to interpret these experimental observations. We find that each newly completed plane replenishes the nucleation site at the hut apex and depletes the Ge supersaturation by a fixed amount. This provides a feedback mechanism that reduces the island growth rate. As long as the supersaturation remains high enough to support nucleation of additional planes on the narrowest hut cluster, Ostwald ripening is suppressed on an experimental time scale.

Electron charging in epitaxial Ge quantum dots on Si(100)

Electron confinement to heteroepitaxial Ge/Si(100) quantum dots encapsulated in a Si matrix was investigated using capacitance-voltage measurements. Optimized growth conditions produced dot ensembles comprised of either huts and pyramids or dome clusters allowing investigation of electron confinement to these distinct dot morphologies. At room temperature, 20–40 nm diameter hut and pyramid clusters confine ∼0.7 electrons, while 60–80 nm diameter dome clusters confine ∼6 electrons. The greater capacity of dome clusters may be attributed to the four distinct conduction band minima that are deeper than the single minimum found for pyramid clusters using a simple band structure model.

The Energetics of Hut-Cluster Self-Assembly in Ge/Si(001) from Linear-Scaling DFT Calculations

Density functional theory (DFT) in a linear-scaling implementation is used to study the energetics of three-dimensional (3D) Ge islands (hut clusters) grown on Si(001) surface. DFT calculations on the fully relaxed energies of a series of hut clusters of increasing size are reported, finding a 2D to 3D cross-over near three monolayers; the number of atoms in the largest simulated system is over 20,000. A variety of technical issues which are important in addressing the accuracy and validity of the calculations are described and assessed. The results suggest that energetics alone is responsible for the initial transition from 2D to 3D growth.