High indium non-polar InGaN clusters with infrared sensitivity grown by PAMBE

Studies on the optical properties of InGaN alloy of relatively higher indium content are of potential interest to understand the effect of indium content on the optical band gap of epitaxial InGaN. We report the growth of self assembled non-polar high indium clusters of In0.55Ga0.45N over non-polar (11-20) a-plane In0.17Ga0.83N epilayer grown on a-plane (11-20) GaN/(1-102) r-plane sapphire substrate using plasma assisted molecular beam epitaxy (PAMBE). Such structures are potential candidates for high brightness LEDs emitting in longer wavelengths. The high resolution X-ray diffraction studies revealed the formation of two distinct compositions of InxGa1-xN alloys, which were further confirmed by photoluminescence studies. A possible mechanism for the formation of such structure was postulated which was supported with the results obtained by energy dispersive X-ray analysis. The structure hence grown when investigated for photo-detecting properties, showed sensitivity to both infrared and ultraviolet radiations due to the different composition of InGaN region. (C) 2015 Author(s).

Polaron effects on the optical absorptions in asymmetrical semi-parabolic quantum wells

The linear and nonlinear optical absorptions considering the weak-coupling electron-LO-phonon interaction in asymmetrical semiparabolic quantum wells are theoretically investigated. The numerical results for the typical GaAs/AlxGa1-xAs material show that the factors of Al content x, the relaxation time and the photon energy have great influence on the optical absorption coefficients. Moreover, the theoretical values of the optical absorptions are more than a factor of 2-3 higher than the one in the structure without considering the electron-LO-phonon interaction by calculating. (C) 2007 Elsevier B.V. All rights reserved.

Models of the Oxygen-Evolving Complex of Photosystem II

In the five chapters that follow, I delineate my efforts over the last five years to synthesize structurally and chemically relevant models of the Oxygen Evolving Complex (OEC) of Photosystem II. The OEC is nature’s only water oxidation catalyst, in that it forms the dioxygen in our atmosphere necessary for oxygenic life. Therefore understanding its structure and function is of deep fundamental interest and could provide design elements for artificial photosynthesis and manmade water oxidation catalysts. Synthetic endeavors towards OEC mimics have been an active area of research since the mid 1970s and have mutually evolved alongside biochemical and spectroscopic studies, affording ever-refined proposals for the structure of the OEC and the mechanism of water oxidation. This research has culminated in the most recent proposal: a low symmetry Mn₄CaO₅ cluster with a distorted Mn₃CaO₄ cubane bridged to a fourth, dangling Mn. To give context for how my graduate work fits into this rich history of OEC research, Chapter 1 provides a historical timeline of proposals for OEC structure, emphasizing the role that synthetic Mn and MnCa clusters have played, and ending with our Mn₃CaO₄ heterometallic cubane complexes.

In Chapter 2, the triarylbenzene ligand framework used throughout my work is introduced, and trinuclear clusters of Mn, Co, and Ni are discussed. The ligand scaffold consistently coordinates three metals in close proximity while leaving coordination sites open for further modification through ancillary ligand binding. The ligands coordinated could be varied, with a range of carboxylates and some less coordinating anions studied. These complexes’ structures, magnetic behavior, and redox properties are discussed.

Chapter 3 explores the redox chemistry of the trimanganese system more thoroughly in the presence of a fourth Mn equivalent, finding a range of oxidation states and oxide incorporation dependent on oxidant, solvent, and Mn salt. Oxidation states from Mn^II₄ to Mn^IIIMn^IV₃ were observed, with 1-4 O^2– ligands incorporated, modeling the photoactivation of the OEC. These complexes were studied by X-ray diffraction, EPR, XAS, magnetometry, and CV.

As Ca²⁺ is a necessary component of the OEC, Chapter 4 discusses synthetic strategies for making highly structurally accurate models of the OEC containing both Mn and Ca in the Mn₃CaO₄ cubane + dangling Mn geometry. Structural and electrochemical characterization of the first Mn₃CaO₄ heterometallic cubane complex— and comparison to an all-Mn Mn₄O₄ analog—suggests a role for Ca²⁺ in the OEC. Modification of the Mn₃CaO₄ system by ligand substitution affords low symmetry Mn₃CaO₄ complexes that are the most accurate models of the OEC to date.

Finally, in Chapter 5 the reactivity of the Mn₃CaO₄ cubane complexes toward O- atom transfer is discussed. The metal M strongly affects the reactivity. The mechanisms of O-atom transfer and water incorporation from and into Mn₄O₄ and Mn₄O₃ clusters, respectively, are studied through computation and ¹⁸O-labeling studies. The μ3-oxos of the Mn₄O₄ system prove fluxional, lending support for proposals of O^2– fluxionality within the OEC.

Investigations of DNA-mediated protein oxidation

DNA charge transport (CT) involves the efficient transfer of electrons or electron holes through the DNA π-stack over long molecular distances of at least 100 base-pairs. Despite this shallow distance dependence, DNA CT is sensitive to mismatches or lesions that disrupt π-stacking and is critically dependent on proper electronic coupling of the donor and acceptor moieties into the base stack. Favorable DNA CT is very rapid, occurring on the picosecond timescale. Because of this speed, electron holes equilibrate along the DNA π-stack, forming a characteristic pattern of DNA damage at low oxidation potential guanine multiplets. Furthermore, DNA CT may be used in a biological context. DNA processing enzymes with 4Fe4S clusters can perform DNA-mediated electron transfer (ET) self-exchange reactions with other 4Fe4S cluster proteins, even if the proteins are quite dissimilar, as long as the DNA-bound [4Fe4S]^3+/2+ redox potentials are conserved. This mechanism would allow low copy number DNA repair proteins to find their lesions efficiently within the cell. DNA CT may also be used biologically for the long-range, selective activation of redox-active transcription factors. Within this work, we pursue other proteins that may utilize DNA CT within the cell and further elucidate aspects of the DNA-mediated ET self-exchange reaction of 4Fe4S cluster proteins.

Dps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. One aspect of their protection involves ferroxidase activity, whereby ferrous iron is bound and oxidized selectively by hydrogen peroxide, thereby preventing formation of damaging hydroxyl radicals via Fenton chemistry. Understanding the specific mechanism by which Dps proteins protect the bacterial genome could inform the development of new antibiotics. We investigate whether DNA-binding E. coli Dps can utilize DNA CT to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate oxidative DNA damage via the flash-quench technique, which localizes to a low potential guanine triplet. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps which lack available reducing equivalents, significantly attenuates the yield of oxidative DNA damage at the guanine triplet. These data demonstrate that ferrous iron-loaded Dps is selectively oxidized to fill guanine radical holes, thereby restoring the integrity of the DNA. Luminescence studies indicate no direct interaction between the ruthenium photooxidant and Dps, supporting the DNA-mediated oxidation of ferrous iron-loaded Dps. Thus DNA CT may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance.

Further work focused on spectroscopic characterization of the DNA-mediated oxidation of ferrous iron-loaded Dps. X-band EPR was used to monitor the oxidation of DNA-bound Dps after DNA photooxidation via the flash-quench technique. Upon irradiation with poly(dGdC)₂, a signal arises with g = 4.3, consistent with the formation of mononuclear high-spin Fe(III) sites of low symmetry, the expected oxidation product of Dps with one iron bound at each ferroxidase site. When poly(dGdC)₂ is substituted with poly(dAdT)₂, the yield of Dps oxidation is decreased significantly, indicating that guanine radicals facilitate Dps oxidation. The more favorable oxidation of Dps by guanine radicals supports the feasibility of a long-distance protection mechanism via DNA CT where Dps is oxidized to fill guanine radical holes in the bacterial genome produced by reactive oxygen species.

We have also explored possible electron transfer intermediates in the DNA-mediated oxidation of ferrous iron-loaded Dps. Dps proteins contain a conserved tryptophan residue in close proximity to the ferroxidase site (W52 in E. coli Dps). In comparison to WT Dps, in EPR studies of the oxidation of ferrous iron-loaded Dps following DNA photooxidation, W52Y and W52A mutants were deficient in forming the characteristic EPR signal at g = 4.3, with a larger deficiency for W52A compared to W52Y. In addition to EPR, we also probed the role of W52 Dps in cells using a hydrogen peroxide survival assay. Bacteria containing W52Y Dps survived the hydrogen peroxide challenge more similarly to those containing WT Dps, whereas cells with W52A Dps died off as quickly as cells without Dps. Overall, these results suggest the possibility of W52 as a CT hopping intermediate.

DNA-modified electrodes have become an essential tool for the study of the redox chemistry of DNA processing enzymes with 4Fe4S clusters. In many cases, it is necessary to investigate different complex samples and substrates in parallel in order to elucidate this chemistry. Therefore, we optimized and characterized a multiplexed electrochemical platform with the 4Fe4S cluster base excision repair glycosylase Endonuclease III (EndoIII). Closely packed DNA films, where the protein has limited surface accessibility, produce EndoIII electrochemical signals sensitive to an intervening mismatch, indicating a DNA-mediated process. Multiplexed analysis allowed more robust characterization of the CT-deficient Y82A EndoIII mutant, as well as comparison of a new family of mutations altering the electrostatics surrounding the 4Fe4S cluster in an effort to shift the reduction potential of the cluster. While little change in the DNA-bound midpoint potential was found for this family of mutants, likely indicating the dominant effect of DNA-binding on establishing the protein redox potential, significant variations in the efficiency of DNA-mediated electron transfer were apparent. On the basis of the stability of these proteins, examined by circular dichroism, we proposed that the electron transfer pathway in EndoIII can be perturbed not only by the removal of aromatic residues but also through changes in solvation near the cluster.

While the 4Fe4S cluster of EndoIII is relatively insensitive to oxidation and reduction in solution, we have found that upon DNA binding, the reduction potential of the [4Fe4S]^3+/2+ couple shifts negatively by approximately 200 mV, bringing this couple into a physiologically relevant range. Demonstrated using electrochemistry experiments in the presence and absence of DNA, these studies do not provide direct molecular evidence for the species being observed. Sulfur K-edge X-ray absorbance spectroscopy (XAS) can be used to probe directly the covalency of iron-sulfur clusters, which is correlated to their reduction potential. We have shown that the Fe-S covalency of the 4Fe4S cluster of EndoIII increases upon DNA binding, stabilizing the oxidized [4Fe4S]³⁺ cluster, consistent with a negative shift in reduction potential. The 7% increase in Fe-S covalency corresponds to an approximately 150 mV shift, remarkably similar to DNA electrochemistry results. Therefore we have obtained direct molecular evidence for the shift in 4Fe4S reduction potential of EndoIII upon DNA binding, supporting the feasibility of our model whereby these proteins can utilize DNA CT to cooperate in order to efficiently find DNA lesions inside cells.

In conclusion, in this work we have explored the biological applications of DNA CT. We discovered that the DNA-binding bacterial ferritin Dps can protect the bacterial genome from a distance via DNA CT, perhaps contributing to pathogen survival and virulence. Furthermore, we optimized a multiplexed electrochemical platform for the study of the redox chemistry of DNA-bound 4Fe4S cluster proteins. Finally, we have used sulfur K-edge XAS to obtain direct molecular evidence for the negative shift in 4Fe4S cluster reduction potential of EndoIII upon DNA binding. These studies contribute to the understanding of DNA-mediated protein oxidation within cells.

Band-tail shape and transport near the metal-insulator transition in Si-doped

In the present work, an infrared light-emitting diode is used to photodope molecular-beam-epitaxy-grown Si: Al0.3Ga0.7As, a well-known persistent photoconductor, to vary the effective electron concentration of samples in situ. Using this technique, we examine the transport properties of two samples containing different nominal doping concentrations of Si [1 x 10(19) cm(-3) for sample 1 (S1) and 9 x 10(17) cm(-3) for sample 2 (S2)] and vary the effective electron density between 10(14) and 10(18) cm(-3). The metal-insulator transition for S1 is found to occur at a critical carrier concentration of 5.7 x 10(16) cm(-3) at 350 mK. The mobilities in both samples are found to be limited by ionized impurity scattering in the temperature range probed, and are adequately described by the Brooks-Herring screening theory for higher carrier densities. The shape of the band tail of the density of states in Al0.3Ga0.7As is found electrically through transport measurements. It is determined to have a power-law dependence, with an exponent of -1.25 for S1 and -1.38 for S2.

Electric Field Control of Interface Related Spin Splitting in Step Quantum Wells

Spin splitting of the AlyGa1-yAs/GaAs/AlxGa1-xAs/AlyGa1-yAs (x not equal y) step quantum wells (QWs) has been theoretically investigated with a model that includes both the interface and the external electric field contribution. The overall spin splitting is mainly determined by the interface contribution, which can be well manipulated by the external electric field. In the absence of the electric field, the Rashba effect exists due to the internal structure inversion asymmetry (SIA). The electric field can strengthen or suppress the internal SIA, resulting in an increase or decrease of the spin splitting. The step QW, which results in large spin splitting, has advantages in applications to spintronic devices compared with symmetrical and asymmetrical QWs. Due to the special structure design, the spin splitting does not change with the external electric field.

Well-width dependence of in-plane optical anisotropy in (001) GaAs/AlGaAs quantum wells induced by in-plane uniaxial strain and interface asymmetry

The well-width dependence of in-plane optical anisotropy (IPOA) in (001) GaAs/AlxGa1-xAs quantum wells induced by in-plane uniaxial strain and interface asymmetry has been studied comprehensively. Theoretical calculations show that the IPOA induced by in-plane uniaxial strain and interface asymmetry exhibits much different well-width dependence. The strain-induced IPOA is inversely proportional to the energy spacing between heavy- and light-hole subbands, so it increases with the well width. However, the interface-related IPOA is mainly determined by the probability that the heavy- and light-holes appear at the interfaces, so it decreases with the well width. Reflectance difference spectroscopy has been carried out to measure the IPOA of (001) GaAs/AlxGa1-xAs quantum wells with different well widths. Strain- and interface-induced IPOA have been distinguished by using a stress apparatus, and good agreement with the theoretical prediction is obtained. The anisotropic interface potential parameters are also determined. In addition, the energy shift between the interface- and strain-induced 1H1E reflectance difference (RD) structures, and the deviation of the 1L1E RD signal away from the prediction of the calculation model have been discussed.

Annealing study of carrier concentration in gradient-doped GaAs/GaAlAs epilayers grown by molecular beam epitaxy

We measured the carrier concentration distribution of gradient-doped GaAs/GqAlAs epilayers grown by molecular beam epitaxy before and after annealing at 600 degrees C, using electrochemical capacitance voltage profiling, to investigate the internal variation of transmission-mode GaAs photocathodes arising from the annealing process. The results show that the carrier concentration increased after annealing. As a result, the total band-bending energy in the gradient-doped GaAs emission layer increased by 25.24% after annealing, which improves the pbotoexcited electron movement toward the surface. On the other hand, the annealing process resulted in a worse carrier concentration discrepancy between the GaAs and the GaAlAs, which causes a lower back interface potential barrier, decreasing the amount of high-energy photoelectrons. (C) 2009 Optical Society of America

Spin splitting of conduction subbands in Al0.3Ga0.7As/GaAs/AlxGa1-x As/Al0.3Ga0.7As step quantum wells

By means of the transfer matrix technique, interface-induced Rashba spin splitting of conduction subbands in Al0.3Ga0.7As/GaAs/AlxGa1-xAs/Al0.3Ga0.7As step quantum wells which contain internal structure inversion asymmetry introduced by the insertion of AlxGa1-xAs step potential is investigated theoretically in the absence of electric field and magnetic field. The dependence of spin splitting on the well width, step width and Al concentration is investigated in detail. We find that the sign of the first excited subband spin splitting changes with well width and step width, and is opposite to that of the ground subband under certain conditions. The sign and strength of the spin splitting are shown to be sensitive to the components of the envelope function at three interfaces. Copyright (C) EPLA, 2009

Anisotropic Spin Splitting in Step Quantum Wells

By the method of finite difference, the anisotropic spin splitting of the AlxGa1-xAs/GaAs/AlyGa1-yAs/AlxGa1-xAs step quantum wells (QWs) are theoretically investigated considering the interplay of the bulk inversion asymmetry and structure inversion asymmetry induced by step quantum well structure and external electric field. We demonstrate that the anisotropy of the total spin splitting can be controlled by the shape of the QWs and the external electric field. The interface related Rashba effect plays an important effect on the anisotropic spin splitting by influencing the magnitude of the spin splitting and the direction of electron spin. The Rashba spin splitting presents in the step quantum wells due to the interface related Rashba effect even without external electric field or magnetic field.

Effect of the InAlAs and InGaAs combination strain-reducing layer on 1.3 mu m emission self-assembled InAs/GaAs quantum dots

Self-assembled InAs quantum dots (QDs) with differing deposition thicknesses covered by InxAl1-xAs (x = 0.2, 0.3) and In0.2Ga0.8As combination strain-reducing layers (CSRLs) were grown by molecular beam epitaxy. Their structural and optical properties were investigated by atomic force microscopy and photoluminescence spectroscopy, respectively. The emission peak position of InAs QDs capped by CSRL can reach 1.34 mum at room temperature with a relatively larger energy splitting of 93 meV between the ground and first excited states.

Self-organized superlattices along the [001] growth direction in In0.52Al0.48As layers grown on nominally (001) InP substrates by molecular beam epitaxy

Horizontal self-organized superlattice structures consisting of alternating In-rich and Al-rich layers formed naturally during solid-source molecular beam epitaxy (MBE) growth of In0.52Al0.48As on exactly (001) InP substrates, with In and At fluxes unchanged. The growth temperatures were changed from 490 to 510 degrees C, the most commonly used growth temperature for In0.52Al0.48As alloy. No self-organized superlattices (SLs) were observed at the growth temperature 490 degrees C, and self-organized SLs were observed in InAlAs layers at growth temperatures ranging from 498 to 510 degrees C. The results show that the period of the SLs is very highly regular, with the value of similar to 6 nm, and the composition of In or Al varies approximately sinusoidally along the [001] growth direction. The theoretical simulation results confirm that the In composition modulation amplitude is less than 0.02 relative the In composition of the In0.52Al0.48As lattice matched with the InP substrate. The influence of InAs self-organized quantum wires on the spontaneously formed InxAl1-xAs/InyAl1-yAs SLs was also studied and the formation of self-organized InxAl1-xAs/InyAl1-yAs SLs was attributed to the strain-mediated surface segregation process during MBE growth of In0.52Al0.48As alloy. (C) 2005 Published by Elsevier Ltd.

Interface of wet oxidized AlGaAs/GaAs distributed Bragg reflectors

The interface of wet oxidized Al0.97Ga0.03As/GaAs in a distributed Bragg reflector (DBR) structure has been studied by means of transmission electron microscopy and Raman spectroscopy. With the extension of oxidation time, the oxide/GaAs interfaces are not abrupt any more. There is an amorphous film near the oxide/GaAs interface, which is Ga2O3 related to the prolonged heating. In the samples oxidized for 10 and 20 min, there are some fissures along the oxidized AlGaAs/GaAs interfaces. In the samples oxidized or in situ annealed for long time, no such fissures are present due to the complete removal of the volatile products.

Aluminium doping induced enhancement of p-d coupling in ZnO

Valence-band type Auger lines in Al doped and undoped ZnO were comparatively studied with the corresponding core level x-ray photoelectron spectrography (XPS) spectra as references. Then the shift trend of energy levels in the valence band was that p and p-s-d states move upwards but e and p-d states downwards with increasing Al concentration. The decreased energy of the Zn 3d state is larger than the increased energy of the 0 2p state, indicating the lowering of total energy. This may indicate that Al doping could induce the enhancement of p-d coupling in ZnO, which originates from stronger Al-O hybridization. The shifts of these states and the mechanism were confirmed by valence band XPS spectra and 0 K-edge x-ray absorption spectrography (XAS) spectra. Finally, some previously reported phenomena are explained based on the Al doping induced enhancement of p-d coupling.

Study of persistent photoconductivity and subband electronic properties of the two-dimensional electron gas in modulation doped GaAs/AlGaAs structure

We obtained the high mobility Of mu(2K) = 1.78 x 10(6) cm(2)/V . s in Si-doped GaAs/AlGaAs two-dimensional electron gas (2DEG) structures. After the sample was illuminated by a light-emitting diode in magnetic fields up to 6 T at T = 2K, we did observe the persistent photoconductivity effect and the electron density increased obviously. The electronic properties of 2DEG have been studied by Quantum-Hall-effect and Shubnikov-de Haas (SdH) oscillation measurements. We found that the electron concentrations of two subbands increase simultaneity with the increasing total electron concentration, and the electron mobility also increases obviously after being illuminated. At the same time, we also found that the electronic quantum lifetime becomes shorter, and a theoretical explunation is given through the widths of integral quantum Hall plateaus.