Light scattering spectroscopy: studies of electronic excitations and atomic vibrations in matter

This thesis comprises a compendium of forty-two publications on various research topics unified by a common theme s light scattering spectroscopy. The research work presented ranges from experimental studies of the dynamics of atoms in various phases of matter through to theoretical investigations of the light scattering process. The topics discussed are the dynamics of structural phase transitions in proper and improper ferroelectrics, and in antiferroelectrics, for both ordered and disordered systems; the magnetic phase transitions in ordered and disordered compounds; the electronic properties of divalent transition metal ions in pure and dilute systems; the lattice vibrations of ionic, covalent and molecular crystals; the selection rules governing higher-order light scattering processes; the weak interactions occurring between chemical species in both aqueous and non-aqueous solvents; and the use of automation techniques in light scattering spectroscopy

Quantum confinement in Si and Ge nanostructures: Effect of crystallinity

We look at the relationship between the preparation method of Si and Ge nanostructures (NSs) and the structural, electronic, and optical properties in terms of quantum confinement (QC). QC in NSs causes a blue shift of the gap energy with decreasing NS dimension. Directly measuring the effect of QC is complicated by additional parameters, such as stress, interface and defect states. In addition, differences in NS preparation lead to differences in the relevant parameter set. A relatively simple model of QC, using a `particle-in-a-box'-type perturbation to the effective mass theory, was applied to Si and Ge quantum wells, wires and dots across a variety of preparation methods. The choice of the model was made in order to distinguish contributions that are solely due to the effects of QC, where the only varied experimental parameter was the crystallinity. It was found that the hole becomes de-localized in the case of amorphous materials, which leads to stronger confinement effects. The origin of this result was partly attributed to differences in the effective mass between the amorphous and crystalline NS as well as between the electron and hole. Corrections to our QC model take into account a position dependent effective mass. This term includes an inverse length scale dependent on the displacement from the origin. Thus, when the deBroglie wavelength or the Bohr radius of the carriers is on the order of the dimension of the NS the carriers `feel' the confinement potential altering their effective mass. Furthermore, it was found that certain interface states (Si-O-Si) act to pin the hole state, thus reducing the oscillator strength.Comment: arXiv admin note: substantial text overlap with arXiv:1111.201

Light emission in silicon nanostructures

The many and diverse approaches to materials science problems have greatly enhanced our ability in recent times to engineer the physical properties of semiconductors. Silicon, of all semiconductors, underpins nearly all microelectronics today and will continue to do so for some time to come. However, in optoelectronics, the severe disadvantage of an indirect band gap has limited the application of elemental silicon. Here we review a number of diverse approaches to engineering efficient light emission in silicon nanostructures. These different approaches are placed in context and their prospects for application in silicon-based optoelectronics are assessed.NRC publication: Ye

Phonon-assisted optical absorption in germanium

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Protein Delivery of an Artificial Transcription Factor Restores Widespread Ube3a Expression in an Angelman Syndrome Mouse Brain.

Angelman syndrome (AS) is a neurological genetic disorder caused by loss of expression of the maternal copy of UBE3A in the brain. Due to brain-specific genetic imprinting at this locus, the paternal UBE3A is silenced by a long antisense transcript. Inhibition of the antisense transcript could lead to unsilencing of paternal UBE3A, thus providing a therapeutic approach for AS. However, widespread delivery of gene regulators to the brain remains challenging. Here, we report an engineered zinc finger-based artificial transcription factor (ATF) that, when injected i.p. or s.c., crossed the blood-brain barrier and increased Ube3a expression in the brain of an adult mouse model of AS. The factor displayed widespread distribution throughout the brain. Immunohistochemistry of both the hippocampus and cerebellum revealed an increase in Ube3a upon treatment. An ATF containing an alternative DNA-binding domain did not activate Ube3a. We believe this to be the first report of an injectable engineered zinc finger protein that can cause widespread activation of an endogenous gene in the brain. These observations have important implications for the study and treatment of AS and other neurological disorders

Plasma exchange in focal necrotizing glomerulonephritis without anti-GBM antibodies

Plasma exchange in focal necrotizing glomerulonephritis without anti-GBM antibodies. To determine whether plasma exchange was of additional benefit in patients treated with oral immunosuppressive drugs for focal necrotizing glomerulonephritis (without anti-GBM antibodies), we performed a randomized controlled trial with stratification for renal function on entry Forty-eight cases were analyzed, 25 in the treatment group (plasma exchange, prednisolone, cyclophosphamide and azathioprine) and 23 in the control group (drug therapy only). There was no difference in outcome in patients presenting with serum creatinine < 500 µmol/liter (N = 17), or > 500 µmol/liter but not on dialysis (N = 12), all but one of whom had improved by four weeks. However, patients who were initially dialysis-dependent (N = 19) were more likely to have recovered renal function (P = 0.041) if treated with plasma exchange as well as drugs (10 of 11) rather than with drugs alone (3 of 8). Long-term follow-up showed that improvement in renal function was generally maintained. The results of this trial confirm that focal necrotizing glomerulonephritis related to systemic vasculitis responds well to immunosuppressive drugs when treatment is started early, and suggest that plasma exchange is of additional benefit in dialysis-dependent cases

Structural modeling of an outer membrane electron conduit from a metal-reducing bacterium suggests electron transfer via periplasmic redox partners

Many subsurface microorganisms couple their metabolism to the reduction or oxidation of extracellular substrates. For example, anaerobic mineral-respiring bacteria can use external metal oxides as terminal electron acceptors during respiration. Porin–cytochrome complexes facilitate the movement of electrons generated through intracellular catabolic processes across the bacterial outer membrane to these terminal electron acceptors. In the mineral-reducing model bacterium Shewanella oneidensis MR-1, this complex is composed of two decaheme cytochromes (MtrA and MtrC) and an outer-membrane β-barrel (MtrB). However, the structures and mechanisms by which porin–cytochrome complexes transfer electrons are unknown. Here, we used small-angle neutron scattering (SANS) to study the molecular structure of the transmembrane complexes MtrAB and MtrCAB. Ab initio modeling of the scattering data yielded a molecular envelope with dimensions of ∼105 × 60 × 35 Å for MtrAB and ∼170 × 60 × 45 Å for MtrCAB. The shapes of these molecular envelopes suggested that MtrC interacts with the surface of MtrAB, extending ∼70 Å from the membrane surface and allowing the terminal hemes to interact with both MtrAB and an extracellular acceptor. The data also reveal that MtrA fully extends through the length of MtrB, with ∼30 Å being exposed into the periplasm. Proteoliposome models containing membrane-associated MtrCAB and internalized small tetraheme cytochrome (STC) indicate that MtrCAB could reduce Fe(III) citrate with STC as an electron donor, disclosing a direct interaction between MtrCAB and STC. Taken together, both structural and proteoliposome experiments support porin–cytochrome–mediated electron transfer via periplasmic cytochromes such as STC

Results from the CERN pilot CLOUD experiment

During a 4-week run in October–November 2006, a pilot experiment was performed at the CERN Proton Synchrotron in preparation for the Cosmics Leaving OUtdoor Droplets (CLOUD) experiment, whose aim is to study the possible influence of cosmic rays on clouds. The purpose of the pilot experiment was firstly to carry out exploratory measurements of the effect of ionising particle radiation on aerosol formation from trace H2SO4 vapour and secondly to provide technical input for the CLOUD design. A total of 44 nucleation bursts were produced and recorded, with formation rates of particles above the 3 nm detection threshold of between 0.1 and 100 cm−3 s−1, and growth rates between 2 and 37 nm h−1. The corresponding H2SO4 concentrations were typically around 106 cm−3 or less. The experimentally-measured formation rates and H2SO4 concentrations are comparable to those found in the atmosphere, supporting the idea that sulphuric acid is involved in the nucleation of atmospheric aerosols. However, sulphuric acid alone is not able to explain the observed rapid growth rates, which suggests the presence of additional trace vapours in the aerosol chamber, whose identity is unknown. By analysing the charged fraction, a few of the aerosol bursts appear to have a contribution from ion-induced nucleation and ion-ion recombination to form neutral clusters. Some indications were also found for the accelerator beam timing and intensity to influence the aerosol particle formation rate at the highest experimental SO2 concentrations of 6 ppb, although none was found at lower concentrations. Overall, the exploratory measurements provide suggestive evidence for ion-induced nucleation or ion-ion recombination as sources of aerosol particles. However in order to quantify the conditions under which ion processes become significant, improvements are needed in controlling the experimental variables and in the reproducibility of the experiments. Finally, concerning technical aspects, the most important lessons for the CLOUD design include the stringent requirement of internal cleanliness of the aerosol chamber, as well as maintenance of extremely stable temperatures (variations below 0.1 _C)

The metaphysics of mental files

There is much to be said for a diachronic or interpersonal individuation of singular modes of presentation (MOPs) in terms of a criterion of epistemic transparency between thought tokens. This way of individuating MOPs has been discussed recently within the mental files framework, though the issues discussed here arise for all theories that individuate MOPs in terms of relations among tokens. All such theories face objections concerning apparent failures of the transitivity of the ‘same MOP’ relation. For mental files, these transitivity failures most obviously occur because mental files can merge or undergo fission. In this paper I argue that this problem is easily resolved once mental files are properly construed as continuants, whose metaphysics is analogous to that of persons or physical objects. All continuants can undergo fission or fusion, leading to similar transitivity problems, but there are well-established theories of persistence that accommodate this. I suggest that, in particular, the stage theory best suits the purposes of a continuant theory of MOPs.PostprintPeer reviewe

Photoreduction of Shewanella oneidensis Extracellular Cytochromes by Organic Chromophores and Dye-Sensitized TiO2.

The transfer of photoenergized electrons from extracellular photosensitizers across a bacterial cell envelope to drive intracellular chemical transformations represents an attractive way to harness nature's catalytic machinery for solar-assisted chemical synthesis. In $\textit{Shewanella oneidensis}$ MR-1 (MR-1), trans-outer-membrane electron transfer is performed by the extracellular cytochromes MtrC and OmcA acting together with the outer-membrane-spanning porin$\cdot$cytochrome complex (MtrAB). Here we demonstrate photoreduction of solutions of MtrC, OmcA, and the MtrCAB complex by soluble photosensitizers: namely, eosin Y, fluorescein, proflavine, flavin, and adenine dinucleotide, as well as by riboflavin and flavin mononucleotide, two compounds secreted by MR-1. We show photoreduction of MtrC and OmcA adsorbed on Ru$^{\text{II}}$-dye-sensitized TiO$_2$ nanoparticles and that these protein-coated particles perform photocatalytic reduction of solutions of MtrC, OmcA, and MtrCAB. These findings provide a framework for informed development of strategies for using the outer-membrane-associated cytochromes of MR-1 for solar-driven microbial synthesis in natural and engineered bacteria.This work was supported by the UK Biotechnology and Biological Sciences Research Council (grants BB/K009753/1, BB/K010220/1, BB/K009885/1, and BB/K00929X/1), the Engineering and Physical Sciences Research Council (EP/M001989/1, PhD studentship 1307196 to E.V.A.), a Royal Society Leverhulme Trust Senior Research Fellowship to J.N.B., the Christian Doppler Research Association, and OMV group