The crystal structure and vibrational spectroscopy of jarosite and alunite minerals

The alunite supergroup of minerals is a large hydroxy-sulfate mineral group, which has seen renewed interest following their discovery on Mars. Numerous reviews exist concerning nomenclature, formation, and natural occurrence of this mineral group. Sulfate minerals in general are widely studied and their vibrational spectra are well characterized. However, no specific review concerning alunite and jarosite spectroscopy and crystal structure has been forthcoming. This review focuses on the controversial aspects of the crystal structure and vibrational spectroscopy of jarosite and alunite minerals. Inconsistencies regarding band assignments especially in the 1000–400 cm−1 region plague these two mineral groups and result in different band assignments among the various spectroscopic studies. There are significant crystallographic and magnetic structure ambiguities with regards to ammonium and hydronium end-members, namely, the geometry these two ions assume in the structure and the fact that hydronium jarosite is a spin glass. It was also found that the synthetic causes for the super cell in plumbojarosite, minamiite, huangite, and walthierite are not known.

A New Approach to the Prediction of Partition Coefficients in Water/Organic Interfaces

In the present work, a new approach for the determination of the partition coefficient in different interfaces based on the density function theory is proposed. Our results for log P(ow) considering a n-octanol/water interface for a large super cell for acetone -0.30 (-0.24) and methane 0.95 (0.78) are comparable with the experimental data given in parenthesis. We believe that these differences are mainly related to the absence of van der Walls interactions and the limited number of molecules considered in the super cell. The numerical deviations are smaller than that observed for interpolation based tools. As the proposed model is parameter free, it is not limited to the n-octanol/water interface.

Quantum Mechanics Insight into the Microwave Nucleation of SrTiO3 Nanospheres

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Um estudo sobre a influência de defeitos de diferente natureza nas propriedades eletrônicas de nanotubos usando o método das ondas cilindricas linearizadas aumentadas

Os nanotubos de carbono e nitreto de boro são nano estruturas unidimensionais que apresentam comportamento tanto metálico quanto semicondutor, dependendo da sua quiralidade, exceto para os nanotubos de nitreto de boro que apresentam sempre características semicondutoras, caso não estejam dopados. Devido suas características eletrônicas, os nanotubos apresentam grandes possibilidades de aplicação em dispositivos de nanoeletrônica, tais como nanodiodos, nanotransistores e como elementos de interconexão, dentre outros. Por esta razão, é importante compreender como fatores externos agem sobre as propriedades de tais materiais. Um desses fatores externos é a introdução de defeitos nos nanotubos. Tais defeitos são a ausência de um ou mais átomos de carbono, pertencente ao nanotubo de carbono e, de nitrogênio ou boro, para os nanotubos de nitreto de boro, ou ainda, a substituição de átomos de carbono, nitrogênio ou boro por diferentes átomos na estrutura dos correspondentes nanotubos. Este trabalho apresenta um estudo teórico dos efeitos da introdução de defeitos, por substituição, nas propriedades eletrônicas dos nanotubos de carbono e nitreto de boro, via simulação ab-initio. Avaliam-se as estruturas de banda de energia e densidade de estados de nanotubos de carbono semicondutores e metálicos tipos armchair e zig-zag e apenas do tipo armchair para os nanotubos de nitreto de boro usando o método LACW – método das ondas cilíndricas linearizadas aumentadas. Além disso, devido a crescente importância dos nanotubos de nitreto de boro, fazemos um estudo sistematizado da estrutura eletrônica desses nanotubos, para uma supercélula formada por três células unitárias, usando dopagem intrínseca, bem como uma análise quantitativa, baseada na energia total e banda proibida, de estabilidade dessas estruturas.

Analysis of electronic structure of boron nitride nanotubes with different positions of intrinsic impurities

The pristine boron nitride nanotubes have a large direct band gap around 5 eV. This band gap can be engineered by doping. We investigate electronic structure of the doped hexagonal boron nitride (5,5) nanotubes using the linearized augmented cylindrical wave method. In particular, this work focuses on systematical study of the band gap and the density of states around the Fermi-level when the nanotubes are doped by intrinsic impurities of two substitutional boron atoms in a super cell and a comparative analysis of the relative stability of three structures studied here. This corresponds to 3.3% of impurity concentration. We calculate 29 configurations of the nanotubes with different positions of the intrinsic impurities in the nanotube. The band gap and density of states around the Fermi level show strong dependence on the relative positions of the impurity atoms. The two defect sub bands called D^∏(B) appear in the band gap of the pristine nanotube. The doped nanotubes possess p-type semiconductor properties with the band gap of 1.3-1.9 eV.

Quantum Mechanics Insight into the Microwave Nucleation of SrTiO3 Nanospheres

An extensive investigation of strontium titanate, SrTiO3 (STO), nanospheres synthesized via a microwave-assisted hydrothermal (MAH) method has been conducted to gain a better insight into thermodynamic, kinetic, and reaction phenomena involved in STO nucleation and crystal growth processes. To this end, quantum chemical modeling based on the density functional theory and periodic super cell models were done. Several experimental techniques were employed to get a deep characterization of structural and optical features of STO nanospheres. A possible formation mechanism was proposed, based on dehydration of titanium and strontium clusters followed by mesoscale transformation and a self-assembly process along an oriented attachment mechanism resulting in spherical like shape. Raman and XANES analysis renders a noncentrosymmetric environment for the octahedral titanium, while infrared and first order Raman modes reveal OH groups which are unsystematically incorporated into uncoordinated superficial sites. These results seem to indicate that the key component is the presence of distorted TiO6 clusters to engender a luminescence property. Analysis of band structure, density Of states, and charge map shows that there is a close relationship among local broken symmetry, polarization, and energy split of the 3d orbitals of titanium. The interplay among these electronic and structural features provides necessary conditions to evaluate its luminescent properties under two energy excitation.

A microfluidic device for high density hydrodynamic cell trapping, growth and super-resolution imaging

Super-Resolution imaging techniques such as Fluorescent Photo-Activation Localisation Microscopy (FPALM) have created a powerful new toolkit for investigating living cells, however a simple platform for growing, trapping, holding and controlling the cells is needed before the approach can become truly widespread. We present a microfluidic device formed in polydimethylsiloxane (PDMS) with a fluidic design which traps cells in a high-density array of wells and holds them very still throughout the life cycle, using hydrodynamic forces only. The device meets or exceeds all the necessary criteria for FPALM imaging of Schizosaccharomyces pombe and is designed to remain flexible, robust and easy to use. © 2011 IEEE.

IL-23 is pro-proliferative, epigenetically regulated and modulated by chemotherapy in non-small cell lung cancer

Background IL-23 is a member of the IL-6 super-family and plays key roles in cancer. Very little is currently known about the role of IL-23 in non-small cell lung cancer (NSCLC). Methods RT-PCR and chromatin immunopreciptiation (ChIP) were used to examine the levels, epigenetic regulation and effects of various drugs (DNA methyltransferase inhibitors, Histone Deacetylase inhibitors and Gemcitabine) on IL-23 expression in NSCLC cells and macrophages. The effects of recombinant IL-23 protein on cellular proliferation were examined by MTT assay. Statistical analysis consisted of Student's t-test or one way analysis of variance (ANOVA) where groups in the experiment were three or more. Results In a cohort of primary non-small cell lung cancer (NSCLC) tumours, IL-23A expression was significantly elevated in patient tumour samples (p<0.05). IL-23A expression is epigenetically regulated through histone post-translational modifications and DNA CpG methylation. Gemcitabine, a chemotherapy drug indicated for first-line treatment of NSCLC also induced IL-23A expression. Recombinant IL-23 significantly increased cellular proliferation in NSCLC cell lines. Conclusions These results may therefore have important implications for treating NSCLC patients with either epigenetic targeted therapies or Gemcitabine. © 2012 Elsevier Ireland Ltd.

Super DNAging - New insights into DNA integrity, genome stability and telomeres in the oldest old

Reductions in DNA integrity, genome stability, and telomere length are strongly associated with the aging process, age-related diseases as well as the age-related loss of muscle mass. However, in people reaching an age far beyond their statistical life expectancy the prevalence of diseases, such as cancer, cardiovascular disease, diabetes or dementia, is much lower compared to “averagely” aged humans. These inverse observations in nonagenarians (90–99 years), centenarians (100–109 years) and super-centenarians (110 years and older) require a closer look into dynamics underlying DNA damage within the oldest old of our society. Available data indicate improved DNA repair and antioxidant defense mechanisms in “super old” humans, which are comparable with much younger cohorts. Partly as a result of these enhanced endogenous repair and protective mechanisms, the oldest old humans appear to cope better with risk factors for DNA damage over their lifetime compared to subjects whose lifespan coincides with the statistical life expectancy. This model is supported by study results demonstrating superior chromosomal stability, telomere dynamics and DNA integrity in “successful agers”. There is also compelling evidence suggesting that life-style related factors including regular physical activity, a well-balanced diet and minimized psycho-social stress can reduce DNA damage and improve chromosomal stability. The most conclusive picture that emerges from reviewing the literature is that reaching “super old” age appears to be primarily determined by hereditary/genetic factors, while a healthy lifestyle additionally contributes to achieving the individual maximum lifespan in humans. More research is required in this rapidly growing population of super old people. In particular, there is need for more comprehensive investigations including short- and long-term lifestyle interventions as well as investigations focusing on the mechanisms causing DNA damage, mutations, and telomere shortening.

Rab8 and Rab8-interacting proteins as players in cell polarization

Rab8 and its interacting proteins as regulators of cell polarization During the development of a multi-cellular organism, progenitor cells have to divide and migrate appropriately as well as organize their differentiation with one another, in order to produce a viable embryo. To divide, differentiate and migrate cells have to undergo polarization, a process where internal and external components such as actin, microtubules and adhesion receptors are reorganized to produce a cell that is asymmetric, with functionally different surfaces. Also in the adult organism there is a continuous need for these processes, as cells need to migrate in response to tissue damage and to fight infection. Improper regulation of cell proliferation and migration can conversely lead to disease such as cancer. GTP-binding proteins function as molecular switches by cycling between a GTP-bound (active) conformation and a GDP-bound (inactive) conformation. The Ras super-family of small GTPases are found in all eukaryotic cells. They can be functionally divided into five subfamilies. The Ras family members mainly regulate gene expression, controlling cell proliferation and differentiation. Ras was in fact the first human oncogene to be characterized, and as much as 30% of all human tumors may be directly or indirectly caused by mutations of Ras molecules The Rho family members mainly regulate cytoskeletal reorganization. Arf proteins are known to regulate vesicle budding and Rab proteins regulate vesicular transport. Ran regulates nuclear transport as well as microtubule organization during mitosis. The focus of the thesis of Katarina Hattula, is on Rab8, a small GTPase of the Rab family. Activated Rab8 has previously been shown to induce the formation of new surface extensions, reorganizing both actin and microtubules, and to have a role in directed membrane transport to cell surfaces. However, the exact membrane route it regulates has remained elusive. In the thesis three novel interactors of Rab8 are presented. Rabin8 is a Rab8-specific GEF that localizes to vesicles where it presumably recruits and activates its target Rab8. Its expression in cells leads to remodelling of actin and the formation of polarized cell surface domains. Optineurin, known to be associated with a leading cause of blindness in humans (open-angle glaucoma), is shown to interact specifically with GTP-bound Rab8. Rab8 binds to an amino-terminal region and interestingly, the Huntingtin protein binds a carboxy-terminal region of optineurin. (Aberrant Huntingtin protein is known to be the cause Huntington s disease in humans.) Co-expression of Huntingtin and optineurin enhanced the recruitment of Huntingtin to Rab8-positive vesicular structures. Furthermore, optineurin promoted cell polarization in a similar way to Rab8. A third novel interactor of Rab8 presented in this thesis is JFC1, a member of the synaptogamin-like protein (Slp) family. JFC1 interacts with Rab8 specifically in its GTP-bound form, co-localizes with endogenous Rab8 on tubular and vesicular structures, and is probably involved in controlling Rab8 membrane dynamics. Rab8 is in this thesis work clearly shown to have a strong effect on cell shape. Blocking Rab8 activity by expression of Rab8 RNAi, or by expressing the dominant negative Rab8 (T22N) mutant leads to loss of cell polarity. Conversely, cells expressing the constitutively active Rab8 (Q67L) mutant exhibit a strongly polarized phenotype. Experiments in live cells show that Rab8 is associated with macropinosomes generated at ruffling areas of the membrane. These macropinosomes fuse with or transform into tubules that move toward the cell centre, from where they are recycled back to the leading edge to participate in protrusion formation. The biogenesis of these tubules is shown to be dependent on both actin and microtubule dynamics. The Rab8-specific membrane route studied contained several markers known to be internalized and recycled (1 integrin, transferrin, transferrin receptor, cholera toxin B subunit (CTxB), and major histocompatibility complex class I protein (MHCI)). Co-expression studies revealed that Rab8 localization overlaps with that of Rab11 and Arf6. Rab8 is furthermore clearly functionally linked to Arf6. The data presented in this thesis strongly suggests a role for Rab8 as a regulator for a recycling compartment, which is involved in providing structural and regulatory components to the leading edge to participate in protrusion formation.

A 100MHz to 1GHz, 0.35V to 1.5V supply 256 x 64 SRAM mock using symmetrized 9T SRAM cell with controlled read

In this paper, we present Dynamic Voltage and Frequency Managed 256 x 64 SRAM block in 65nm technology, for frequency ranging from 100MHz to 1GHz. The total energy is minimized for any operating frequency in the above range and leakage energy is minimized during standby mode. Since noise margin of SRAM cell deteriorates at low voltages, we propose Static Noise Margin improvement circuitry, which symmetrizes the SRAM cell by controlling the body bias of pull down NMOS transistor. We used a 9T SRAM cell that isolates Read and Hold Noise Margin and has less leakage. We have implemented an efficient technique of pushing address decoder into zigzag-super-cut-off in stand-by mode without affecting its performance in active mode of operation. The Read Bit Line (RBL) voltage drop is controlled and pre-charge of bit lines is done only when needed for reducing power wastage.

A 100MHz to 1GHz, 0.35V to 1.5V Supply 256 x 64 SRAM Block Using Symmetrized 9T SRAM Cell with Controlled Read

In this paper, we present dynamic voltage and frequency Managed 256 x 64 SRAM block in 65 nm technology, for frequency ranging from 100 MHz to 1 GHz. The total energy is minimized for any operating frequency in the above range and leakage energy is minimized during standby mode. Since noise margin of SRAM cell deteriorates at low voltages, we propose static noise margin improvement circuitry, which symmetrizes the SRAM cell by controlling the body bias of pull down NMOS transistor. We used a 9T SRAM cell that isolates Read and hold noise margin and has less leakage. We have implemented an efficient technique of pushing address decoder into zigzag- super-cut-off in stand-by mode without affecting its performance in active mode of operation. The read bit line (RBL) voltage drop is controlled and pre-charge of bit lines is done only when needed for reducing power wastage.

Spatial filtering nearly eliminates the side-lobes in single- and multi-photon 4pi-type-C super-resolution fluorescence microscopy

Super-resolution microscopy has tremendously progressed our understanding of cellular biophysics and biochemistry. Specifically, 4pi fluorescence microscopy technique stands out because of its axial super-resolution capability. All types of 4pi-microscopy techniques work well in conjugation with deconvolution techniques to get rid of artifacts due to side-lobes. In this regard, we propose a technique based on spatial filter in a 4pi-type-C confocal setup to get rid of these artifacts. Using a special spatial filter, we have reduced the depth-of-focus. Interference of two similar depth-of-focus beams in a 4 pi geometry result in substantial reduction of side-lobes. Studies show a reduction of side-lobes by 46% and 76% for single and two photon variant compared to 4pi - type - C confocal system. This is incredible considering the resolving capability of the existing 4pi - type - C confocal microscopy. Moreover, the main lobe is found to be 150 nm for the proposed spatial filtering technique as compared to 690 nm of the state-of-art confocal system. Reconstruction of experimentally obtained 2PE - 4pi data of green fluorescent protein (GFP)-tagged mitocondrial network shows near elimination of artifacts arising out of side-lobes. Proposed technique may find interesting application in fluorescence microscopy, nano-lithography, and cell biology. (C) 2013 AIP Publishing LLC.

Engineering a nanostructured ``super surface'' with superhydrophobic and superkilling properties

We present a nanostructured ``super surface'' fabricated using a simple recipe based on deep reactive ion etching of a silicon wafer. The topography of the surface is inspired by the surface topographical features of dragonfly wings. The super surface is comprised of nanopillars 4 mm in height and 220 nm in diameter with random inter-pillar spacing. The surface exhibited superhydrophobicity with a static water contact angle of 154.0 degrees and contact angle hysteresis of 8.3 degrees. Bacterial studies revealed the bactericidal property of the surface against both gram negative (Escherichia coli) and gram positive (Staphylococcus aureus) strains through mechanical rupture of the cells by the sharp nanopillars. The cell viability on these nanostructured surfaces was nearly six-fold lower than on the unmodified silicon wafer. The nanostructured surface also killed mammalian cells (mouse osteoblasts) through mechanical rupture of the cell membrane. Thus, such nanostructured super surfaces could find applications for designing selfcleaning and anti-bacterial surfaces in diverse applications such as microfluidics, surgical instruments, pipelines and food packaging.