Electrical, electrochemical, and optical characterization of ceria films

Acceptor-doped ceria has been recognized as a promising intermediate temperature solid oxide fuel cell electrode/electrolyte material. For practical implementation of ceria as a fuel cell electrolyte and for designing model experiments for electrochemical activity, it is necessary to fabricate thin films of ceria. Here, metal-organic chemical vapor deposition was carried out in a homemade reactor to grow ceria films for further electrical, electrochemical, and optical characterization. Doped/undoped ceria films are grown on single crystalline oxide wafers with/without Pt line pattern or Pt solid layer. Deposition conditions were varied to see the effect on the resultant film property. Recently, proton conduction in nanograined polycrystalline pellets of ceria drew much interest. Thickness-mode (through-plane, z-direction) electrical measurements were made to confirm the existence of proton conductivity and investigate the nature of the conduction pathway: exposed grain surfaces and parallel grain boundaries. Columnar structure presumably favors proton conduction, and we have found measurable proton conductivity enhancement. Electrochemical property of gas-columnar ceria interface on the hydrogen electrooxidation is studied by AC impedance spectroscopy. Isothermal gas composition dependence of the electrode resistance was studied to elucidate Sm doping level effect and microstructure effect. Significantly, preferred orientation is shown to affect the gas dependence and performance of the fuel cell anode. A hypothesis is proposed to explain the origin of this behavior. Lastly, an optical transmittance based methodology was developed to obtain reference refractive index and microstructural parameters (thickness, roughness, porosity) of ceria films via subsequent fitting procedure.

Oxidative chemisorption of SO_2 on γ - Al_2O_3 and deposition of H_2-permselective SiO_2 films

The interaction of SO_2 with γ - Al_2O_3 and the deposition of H_2 permselective SiO_2 films have been investigated. The adsorption and oxidative adsorption of SO_2 on γ - Al_2O_3 have been examined at temperatures 500-700°C by Fourier transform infrared spectroscopy (FTIR) and thermogravimetric analysis (TGA). At temperatures above 500°C most of SO_2 adsorbed on the strong sites on alumina. The adsorbed SO_2 species was characterized by an IR band at 1065 cm^(-1). The equilibrium coverage and initial rate of adsorption decreased with temperature suggesting a two-step adsorption. When γ - Al_2O_3 was contacted with a mixture of SO_2 and O_2, adsorption of SO_2 and oxidation of the adsorbed SO_2 to a surface sulfate characterized by broad IR bands at 1070 cm^(-1), 1390 cm^(-1) took place. The results of a series of TGA experiments under different atmospheres strongly suggest that surface SO_2 and surface sulfate involve the same active sites such that SO_2 adsorption is inhibited by already formed sulfate. The results also indicate a broad range of site strengths.

The desorption of adsorbed SO_2 and the reductive desorption of oxidatively adsorbed SO_2 have been investigated by microreactor experiments and thermogravimetric analysis (TGA). Temperature programmed reduction (TPR) of adsorbed SO_2 showed that SO_2 was desorbed without significant reaction with H_2 when H_2 concentration was low while considerable reaction occurred when 100% H_2 was used. SO_2 adsorbed on the strong sites on alumina was reduced to sulfur and H_2S. The isothermal reduction experiments of oxidatively adsorbed SO_2 reveal that the rate of reduction is very slow below 550°C even with 100% H_2. The reduction product is mainly composed of SO_2. TPR experiments of oxidatively adsorbed SO_2 showed that H_2S arose from a sulfate strongly chemisorbed on the surface.

Films of amorphous SiO_2 were deposited within the walls of porous Vycor tubes by SiH_4 oxidation in an opposing reactants geometry : SiH_4 was passed inside the tube while O_2 was passed outside the tube. The two reactants diffused opposite to each other and reacted within a narrow front inside the tube wall to form a thin SiO_2 film. Once the pores were plugged the reactants could not reach each other and the reaction stopped. At 450°C and 0.1 and 0.33 atm of SiH_4 and O_2, the reaction was complete within 15 minutes. The thickness of the SiO_2 film was estimated to be about 0.1 µm. Measurements of H_2 and N_2 permeation rates showed that the SiO_2 film was highly selective to H_2 permeation. The H_2:N_2 flux at 450°C varied between 2000-3000.

Thin SiO_2 films were heat treated in different gas mixtures to determine their stability in functioning as high-temperature hydrogen-permselective membranes. The films were heat-treated at 450-700°C in dry N_2, dry O_2, N_2-H_2O, and O_2-H_2O mixtures. The permeation rates of H_2 and N_2 changed depending on the original conditions of film formation as well as on the heat treatment. Heating in dry N_2 slowly reduced the permeation rates of both H_2 and N_2. Heating in a N_2-H_2O atmosphere led to a steeper decline of H_2 permeability. But the permeation rate of N_2 increased or decreased according to whether the film deposition had been carried out in the absence or presence of H_2O vapor, respectively. Thermal treatment in O_2 caused rapid decline of the permeation rates of H_2 and N_2 in films that were deposited under dry conditions. The decline was moderate in films deposited under wet conditions.

Ultrafast dynamics in ZnO thin films irradiated by femtosecond lasers

The damage morphologies, threshold fluences in ZnO films were studied with femtosecond laser pulses. Time-resolved reflectivity and transmissivity have been measured by the pump-probe technique at different pump fluences and wavelengths. The results indicate that two-phase transition is the dominant damage mechanism, which is similar to that in narrow band gap semiconductors. The estimated energy loss rate of conduction electrons is 1.5 eV/ps. (c) 2005 Elsevier Ltd. All rights reserved.

Surface effects on spinwave resonance in thin magnetic films

Over the past few decades, ferromagnetic spinwave resonance in magnetic thin films has been used as a tool for studying the properties of magnetic materials. A full understanding of the boundary conditions at the surface of the magnetic material is extremely important. Such an understanding has been the general objective of this thesis. The approach has been to investigate various hypotheses of the surface condition and to compare the results of these models with experimental data. The conclusion is that the boundary conditions are largely due to thin surface regions with magnetic properties different from the bulk. In the calculations these regions were usually approximated by uniform surface layers; the spins were otherwise unconstrained except by the same mechanisms that exist in the bulk (i.e., no special "pinning" at the surface atomic layer is assumed). The variation of the ferromagnetic spinwave resonance spectra in YIG films with frequency, temperature, annealing, and orientation of applied field provided an excellent experimental basis for the study.

This thesis can be divided into two parts. The first part is ferromagnetic resonance theory; the second part is the comparison of calculated with experimental data in YIG films. Both are essential in understanding the conclusion that surface regions with properties different from the bulk are responsible for the resonance phenomena associated with boundary conditions.

The theoretical calculations have been made by finding the wave vectors characteristic of the magnetic fields inside the magnetic medium, and then combining the fields associated with these wave vectors in superposition to match the specified boundary conditions. In addition to magnetic boundary conditions required for the surface layer model, two phenomenological magnetic boundary conditions are discussed in detail. The wave vectors are easily found by combining the Landau-Lifshitz equations with Maxwell's equations. Mode positions are most easily predicted from the magnetic wave vectors obtained by neglecting damping, conductivity, and the displacement current. For an insulator where the driving field is nearly uniform throughout the sample, these approximations permit a simple yet accurate calculation of the mode intensities. For metal films this calculation may be inaccurate but the mode positions are still accurately described. The techniques necessary for calculating the power absorbed by the film under a specific excitation including the effects of conductivity, displacement current and damping are also presented.

In the second part of the thesis the properties of magnetic garnet materials are summarized and the properties believed associated with the two surface regions of a YIG film are presented. Finally, the experimental data and calculated data for the surface layer model and other proposed models are compared. The conclusion of this study is that the remarkable variety of spinwave spectra that arises from various preparation techniques and subsequent treatments can be explained by surface regions with magnetic properties different from the bulk.

Effects of a flash-flood on channel morphology and some insects of a small stony stream in the Peak District, Derbyshire

In this paper, some observations are made following a flash-flood that occurred in Stake Clough, a small tributary of the River Goyt, during the evening of 6 August 1996. The site was visited eight times between 8 August - 30 October 1996 to take samples and make observations on the stream. The flood scoured the bed of Stake Clough but more significantly, caused it to change course along the middle part of the floodplain. Initially after the flood, the numbers of insects in all stretches of the stream channel were low (100-200 m super(2)), but then gradually rose to population densities approaching ten times this figure. The benthos was dominated by the Chironomidae and also leuctrid stoneflies (Leuctra nigra, L. hippopus and L. inermis). On 8th August 1996, 12 mesh bags, each containing oak leaves, were placed in the stream and collected after 24 hours. These were also dominated by chironomids, and contained relatively high numbers of the caddis, Potamophylax cingulatus.

I. Reactively sputtered Ti-Si-N thin films for diffusion barrier applications. II. Oxidation, diffusion and crystallization of an amorphous Zr_(60)Al_(15)Ni_(25) alloy.

Films of Ti-Si-N obtained by reactively sputtering a TiSi_2, a Ti_5Si_3, or a Ti_3Si target are either amorphous or nanocrystalline in structure. The atomic density of some films exceeds 10^23 at./cm^3. The room-temperature resistivity of the films increases with the Si and the N content. A thermal treatment in vacuum at 700 °C for 1 hour decreases the resistivity of the Ti-rich films deposited from the Ti_5Si_3 or the Ti_3Si target, but increases that of the Si-rich films deposited from the TiSi_2 target when the nitrogen content exceeds about 30 at. %.

Ti_(34)Si_(23)N_(43) deposited from the Ti_5Si_3 target is an excellent diffusion barrier between Si and Cu. This film is a mixture of nanocrystalline TiN and amorphous SiN_x. Resistivity measurement from 80 K to 1073 K reveals that this film is electrically semiconductor-like as-deposited, and that it becomes metal-like after an hour annealing at 1000 °C in vacuum. A film of about 100 nm thick, with a resistivity of 660 µΩcm, maintains the stability of Si n+p shallow junction diodes with a 400 nm Cu overlayer up to 850 °C upon 30 min vacuum annealing. When used between Si and Al, the maximum temperature of stability is 550 °C for 30 min. This film can be etched in a CF_4/O_2 plasma.

The amorphous ternary metallic alloy Zr_(60)Al_(15)Ni_(25) was oxidized in dry oxygen in the temperature range 310 °C to 410 °C. Rutherford backscattering and cross-sectional transmission electron microscopy studies suggest that during this treatment an amorphous layer of zirconium-aluminum-oxide is formed at the surface. Nickel is depleted from the oxide and enriched in the amorphous alloy below the oxide/alloy interface. The oxide layer thickness grows parabolically with the annealing duration, with a transport constant of 2.8x10^(-5) m^2/s x exp(-1.7 eV/kT). The oxidation rate is most likely controlled by the Ni diffusion in the amorphous alloy.

At later stages of the oxidation process, precipitates of nanocrystalline ZrO_2 appear in the oxide near the interface. Finally, two intermetallic phases nucleate and grow simultaneously in the alloy, one at the interface and one within the alloy.

Rewriting Schemes for Flash Memory

Flash memory is a leading storage media with excellent features such as random access and high storage density. However, it also faces significant reliability and endurance challenges. In flash memory, the charge level in the cells can be easily increased, but removing charge requires an expensive erasure operation. In this thesis we study rewriting schemes that enable the data stored in a set of cells to be rewritten by only increasing the charge level in the cells. We consider two types of modulation scheme; a convectional modulation based on the absolute levels of the cells, and a recently-proposed scheme based on the relative cell levels, called rank modulation. The contributions of this thesis to the study of rewriting schemes for rank modulation include the following: we

•propose a new method of rewriting in rank modulation, beyond the previously proposed method of “push-to-the-top”;

•study the limits of rewriting with the newly proposed method, and derive a tight upper bound of 1 bit per cell;

•extend the rank-modulation scheme to support rankings with repetitions, in order to improve the storage density;

•derive a tight upper bound of 2 bits per cell for rewriting in rank modulation with repetitions;

•construct an efficient rewriting scheme that asymptotically approaches the upper bound of 2 bit per cell.

The next part of this thesis studies rewriting schemes for a conventional absolute-levels modulation. The considered model is called “write-once memory” (WOM). We focus on WOM schemes that achieve the capacity of the model. In recent years several capacity-achieving WOM schemes were proposed, based on polar codes and randomness extractors. The contributions of this thesis to the study of WOM scheme include the following: we

•propose a new capacity-achievingWOM scheme based on sparse-graph codes, and show its attractive properties for practical implementation;

•improve the design of polarWOMschemes to remove the reliance on shared randomness and include an error-correction capability.

The last part of the thesis studies the local rank-modulation (LRM) scheme, in which a sliding window going over a sequence of real-valued variables induces a sequence of permutations. The LRM scheme is used to simulate a single conventional multi-level flash cell. The simulated cell is realized by a Gray code traversing all the relative-value states where, physically, the transition between two adjacent states in the Gray code is achieved by using a single “push-to-the-top” operation. The main results of the last part of the thesis are two constructions of Gray codes with asymptotically-optimal rate.

Investigation of competitive antagonist binding to the nicotinic acetylcholine receptor using voltage-jump and light-flash techniques

1. The effect of 2,2’-bis-[α-(trimethylammonium)methyl]azobenzene (2BQ), a photoisomerizable competitive antagonist, was studied at the nicotinic acetycholine receptor of Electrophorus electroplaques using voltage-jump and light-flash techniques.

2. 2BQ, at concentrations below 3 μΜ, reduced the amplitude of voltage-jump relaxations but had little effect on the voltage-jump relaxation time constants under all experimental conditions. At higher concentrations and voltages more negative than -150 mV, 2BQ caused significant open channel blockade.

3. Dose-ratio studies showed that the cis and trans isomers of 2BQ have equilibrium binding constants (K _ᵢ) of .33 and 1.0 μΜ, respectively. The binding constants determined for both isomers are independent of temperature, voltage, agonist concentration, and the nature of the agonist.

4. In a solution of predominantly cis-2BQ, visible-light flashes led to a net cis→trans isomerization and caused an increase in the agonist-induced current. This increase had at least two exponential components; the larger amplitude component had the same time constant as a subsequent voltage-jump relaxation; the smaller amplitude component was investigated using ultraviolet light flashes.

5. In a solution of predominantly trans-2BQ, UV-light flashes led to a net trans→cis isomerization and caused a net decrease in the agonist-induced current. This effect had at least two exponential components. The smaller and faster component was an increase in agonist-induced current and had a similar time constant to the voltage-jump relaxation. The larger component was a slow decrease in the agonist-induced current with rate constant approximately an order of magnitude less than that of the voltage-jump relaxation. This slow component provided a measure of the rate constant for dissociation of cis-2BQ (k_ = 60/s at 20°C). Simple modelling of the slope of the dose-rate curves yields an association rate constant of 1.6 x 10⁸/M/s. This agrees with the association rate constant of 1.8 x 10⁸/M/s estimated from the binding constant (K_i). The Q₁₀ of the dissociation rate constant of cis-2BQ was 3.3 between 6° and 20°C. The rate constants for association and dissociation of cis-28Q at receptors are independent of voltage, agonist concentration, and the nature of the agonist.

6. We have measured the molecular rate constants of a competitive antagonist which has roughly the same K _ᵢ as d-tubocurarine but interacts more slowly with the receptor. This leads to the conclusion that curare itself has an association rate constant of 4 x 10⁹/M/s or roughly as fast as possible for an encounter-limited reaction.

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.