Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison

The hybridization kinetics for a series of designed 25mer probe�target pairs having varying degrees of secondary structure have been measured by UV absorbance and surface plasmon resonance (SPR) spectroscopy in solution and on the surface, respectively. Kinetic rate constants derived from the resultant data decrease with increasing probe and target secondary structure similarly in both solution and surface environments. Specifically, addition of three intramolecular base pairs in the probe and target structure slow hybridization by a factor of two. For individual strands containing four or more intramolecular base pairs, hybridization cannot be described by a traditional two-state model in solution-phase nor on the surface. Surface hybridization rates are also 20- to 40-fold slower than solution-phase rates for identical sequences and conditions. These quantitative findings may have implications for the design of better biosensors, particularly those using probes with deliberate secondary structure.

Angels: In Network Support for Minimum Distribution Time in P2P Overlays

This paper proposes the use of in-network caches (which we call Angels) to reduce the Minimum Distribution Time (MDT) of a file from a seeder – a node that possesses the file – to a set of leechers – nodes who are interested in downloading the file. An Angel is not a leecher in the sense that it is not interested in receiving the entire file, but rather it is interested in minimizing the MDT to all leechers, and as such uses its storage and up/down-link capacity to cache and forward parts of the file to other peers. We extend the analytical results by Kumar and Ross [1] to account for the presence of angels by deriving a new lower bound for the MDT. We show that this newly derived lower bound is tight by proposing a distribution strategy under assumptions of a fluid model. We present a GroupTree heuristic that addresses the impracticalities of the fluid model. We evaluate our designs through simulations that show that our Group-Tree heuristic outperforms other heuristics, that it scales well with the increase of the number of leechers, and that it closely approaches the optimal theoretical bounds.

Angels: In-Network Support for Minimum Distribution Time in P2P Overlays

This thesis proposes the use of in-network caches (which we call Angels) to reduce the Minimum Distribution Time (MDT) of a file from a seeder – a node that possesses the file – to a set of leechers – nodes who are interested in downloading the file. An Angel is not a leecher in the sense that it is not interested in receiving the entire file, but rather it is interested in minimizing the MDT to all leechers, and as such uses its storage and up/down-link capacity to cache and forward parts of the file to other peers. We extend the analytical results by Kumar and Ross (Kumar and Ross, 2006) to account for the presence of angels by deriving a new lower bound for the MDT. We show that this newly derived lower bound is tight by proposing a distribution strategy under assumptions of a fluid model. We present a GroupTree heuristic that addresses the impracticalities of the fluid model. We evaluate our designs through simulations that show that our GroupTree heuristic outperforms other heuristics, that it scales well with the increase of the number of leechers, and that it closely approaches the optimal theoretical bounds.

Correlations in low dimensional quantum systems

In this thesis I present the work done during my PhD in the area of low dimensional quantum gases. The chapters of this thesis are self contained and represent individual projects which have been peer reviewed and accepted for publication in respected international journals. Various systems are considered, the first of which is a two particle model which possesses an exact analytical solution. I investigate the non-classical correlations that exist between the particles as a function of the tunable properties of the system. In the second work I consider the coherences and out of equilibrium dynamics of a one-dimensional Tonks-Girardeau gas. I show how the coherence of the gas can be inferred from various properties of the reduced state and how this may be observed in experiments. I then present a model which can be used to probe a one-dimensional Fermi gas by performing a measurement on an impurity which interacts with the gas. I show how this system can be used to observe the so-called orthogonality catastrophe using modern interferometry techniques. In the next chapter I present a simple scheme to create superposition states of particles with special emphasis on the NOON state. I explore the effect of inter-particle interactions in the process and then characterise the usefulness of these states for interferometry. Finally I present my contribution to a project on long distance entanglement generation in ion chains. I show how carefully tuning the environment can create decoherence-free subspaces which allows one to create and preserve entanglement.

Mechanistic study on spraying of blended biodiesel using phase Doppler anemometry

Droplet size and dynamics of blended palm oil-based fatty acid methyl ester (FAME) and diesel oil spray were mechanistically investigated using a phase Doppler anemometry. A two-fluid atomizer was applied for dispersing viscous blends of blended biodiesel oil with designated flow rates. It was experimentally found that the atomizer could generate a spray with large droplets with Sauter mean diameters of ca. 30 mm at low air injection pressure. Such large droplets traveled with a low velocity along their trajectory after emerging from the nozzle tip. The viscosity of blended biodiesel could significantly affect the atomizing process, resulting in the controlled droplet size distribution. Blended biodiesel with a certain fraction of palm oil-based FAME would be consistently atomized owing to its low viscosity. However, the viscosity could exert only a small effect on the droplet velocity profile with the air injection pressure higher than 0.2 MPa.

Effect of biodiesel oil composition on droplet size distribution

Droplet size distribution of biodiesel oil with various compositions was investigated in this work. The droplets generated by a two-fluid atomizer were measured by a commercial PDA. It was found that viscosity of the fuel has a strong effect on the drop size distribution. Additionally, effect of air injection pressures applied to atomize the spray was taken into account. Shear force induced by flow field exerts an effect on distribution of biodiesel droplets in atomized spray.

Response decision processes and externalizing behavior problems in adolescents.

Externalizing behavior problems of 124 adolescents were assessed across Grades 7-11. In Grade 9, participants were also assessed across social-cognitive domains after imagining themselves as the object of provocations portrayed in six videotaped vignettes. Participants responded to vignette-based questions representing multiple processes of the response decision step of social information processing. Phase 1 of our investigation supported a two-factor model of the response evaluation process of response decision (response valuation and outcome expectancy). Phase 2 showed significant relations between the set of these response decision processes, as well as response selection, measured in Grade 9 and (a) externalizing behavior in Grade 9 and (b) externalizing behavior in Grades 10-11, even after controlling externalizing behavior in Grades 7-8. These findings suggest that on-line behavioral judgments about aggression play a crucial role in the maintenance and growth of aggressive response tendencies in adolescence.

Impaired formation of beta-adrenergic receptor-nucleotide regulatory protein complexes in pseudohypoparathyroidism.

Decreased activity of the guanine nucleotide regulatory protein (N) of the adenylate cyclase system is present in cell membranes of some patients with pseudohypoparathyrodism (PHP-Ia) whereas others have normal activity of N (PHP-Ib). Low N activity in PHP-Ia results in a decrease in hormone (H)-stimulatable adenylate cyclase in various tissues, which might be due to decreased ability to form an agonist-specific high affinity complex composed of H, receptor (R), and N. To test this hypothesis, we compared beta-adrenergic agonist-specific binding properties in erythrocyte membranes from five patients with PHP-Ia (N = 45% of control), five patients with PHP-Ib (N = 97%), and five control subjects. Competition curves that were generated by increasing concentrations of the beta-agonist isoproterenol competing with [125I]pindolol were shallow (slope factors less than 1) and were computer fit to a two-state model with corresponding high and low affinity for the agonist. The agonist competition curves from the PHP-Ia patients were shifted significantly (P less than 0.02) to the right as a result of a significant (P less than 0.01) decrease in the percent of beta-adrenergic receptors in the high affinity state from 64 +/- 22% in PHP-Ib and 56 +/- 5% in controls to 10 +/- 8% in PHP-Ia. The agonist competition curves were computer fit to a "ternary complex" model for the two-step reaction: H + R + N in equilibrium HR + N in equilibrium HRN. The modeling was consistent with a 60% decrease in the functional concentration of N, and was in good agreement with the biochemically determined decrease in erythrocyte N protein activity. These in vitro findings in erythrocytes taken together with the recent observations that in vivo isoproterenol-stimulated adenylate cyclase activity is decreased in patients with PHP (Carlson, H. E., and A. S. Brickman, 1983, J. Clin. Endocrinol. Metab. 56:1323-1326) are consistent with the notion that N is a bifunctional protein interacting with both R and the adenylate cyclase. It may be that in patients with PHP-Ia a single molecular and genetic defect accounts for both decreased HRN formation and decreased adenylate cyclase activity, whereas in PHP-Ib the biochemical lesion(s) appear not to affect HRN complex formation.

Air–sea fluxes of oxygenated volatile organic compounds across the Atlantic Ocean

We present air-sea fluxes of oxygenated volatile organics compounds (OVOCs) quantified by eddy covariance (EC) during the Atlantic Meridional Transect cruise in 2012. Measurements of acetone, acetaldehyde, and methanol in air as well as in water were made in several different oceanic provinces and over a wide range of wind speeds (1-18 m s(-1)). The ocean appears to be a net sink for acetone in the higher latitudes of the North Atlantic but a source in the subtropics. In the South Atlantic, seawater acetone was near saturation relative to the atmosphere, resulting in essentially zero net flux. For acetaldehyde, the two-layer model predicts a small oceanic emission, which was not well resolved by the EC method. Chemical enhancement of air-sea acetaldehyde exchange due to aqueous hydration appears to be minor. The deposition velocity of methanol correlates linearly with the transfer velocity of sensible heat, confirming predominant airside control. We examine the relationships between the OVOC concentrations in air as well as in water, and quantify the gross emission and deposition fluxes of these gases.

The Influence of Copper Binding on the Stability of the SCO Protein from Bacillus subtilis

Every aerobic organism expresses cytochrome c oxidase to catalyze reduction of molecular oxygen to water, and takes advantage of this energy releasing reaction to produce an electrochemical gradient used in cellular energy production. The protein SCO (Synthesis of cytochrome c oxidase) is a required assembly factor for the oxidase, conserved across many species. SCO is implicated in the assembly of one of two copper centres (ie., CuA) of cytochrome oxidase. The exact mechanism of SCO’s participation in CuA assembly is not known. SCO has been proposed to bind and deliver copper, or alternatively to act in reductive preparation of the CuA site within the oxidase. In this body of work, the strength and stability of Cu(II) binding to Bacillus subtilis SCO is explored via electronic absorption and fluorescence spectroscopies and by calorimetric methods. An equilibrium dissociation constant (Kd) of 3.5x10-12 M was determined as an upper limit for the BsSCO-Cu(II) interaction, via differential scanning calorimetry. In the first reported case for a SCO homolog, dissociation kinetics of Cu(II) from BsSCO were characterized, and found to be dependent on both ionic strength and the presence of free Cu(II) in solution. Further differential scanning calorimetry experiments performed at high ionic strength support a two-step model of BsSCO and Cu(II) binding. The implications of this model for the BsSCO-Cu(II) interaction are presented in relation to the mechanism of interaction between SCO and the CuA site of cytochrome c oxidase.

The extreme-ultraviolet structure and properties of a newly emerged active region

The structure and properties of a newly emerged solar active region (NOAA Active Region 7985) are discussed using the Coronal Diagnostic Spectrometer (CDS) and the Extreme- Ultraviolet Imaging Telescope (EIT) on board the Solar and Heliospheric Observatory. CDS obtained high-resolution EUV spectra in the 308-381 Angstrom and 513-633 Angstrom wavelength ranges, while EIT recorded full-disk EUV images in the He II (304 Angstrom), Fe IX/X (171 Angstrom), Fe xii (195 Angstrom), and Fe XV (284 Angstrom) bandpasses. Electron density measurements from Si rx, Si X, Fe xii, Fe XIII, and Fe xiv line ratios indicate that the region consists of a central high- density core with peak densities of the order of 1.2 x 10(10) cm(-3), which decrease monotonically to similar to5.0 X 10(8) cm(-3) at the active region boundary. The derived electron densities also vary systematically with temperature. Electron pressures as a function of both active region position and temperature were estimated using the derived electron densities and ion formation temperatures, and the constant pressure assumption was found to be an unrealistic simplification. Indeed, the active region is found to have a high-pressure core (1.3 x 10(16) cm(-3) K) that falls to 6.0 x 10(14) cm(-3) K just outside the region. CDS line ratios from different ionization stages of iron, specifically Fe xvi (335.4 Angstrom) and Fe xiv (334.4 Angstrom), were used to diagnose plasma temperatures within the active region. Using this method, peak temperatures of 2.1 x 10(6) K were identified. This is in good agreement with electron temperatures derived using EIT filter ratios and the two-temperature model of Zhang et al. The high- temperature emission is confined to the active region core, while emission from cooler (1-1.6) x 10(6) K lines originates in a system of loops visible in EIT 171 and 195 X images. Finally, the three-dimensional geometry of the active region is investigated using potential field extrapolations from a Kitt Peak magnetogram. The combination of EUV and magnetic field extrapolations extends the "core-halo" picture of active region structure to one in which the core is composed of a number of compact coronal loops that confine the hot, dense, high- pressure core plasma while the halo emission emerges from a system of cooler and more extended loops.

The Galactic metallicity gradient

We have previously published intermediate to hi,oh resolution spectroscopic observations of approximately 80 early B-type main-sequence stars situated in 19 Galactic open clusters/associations with Galactocentric distances distributed over 6 less than or equal to R-g less than or equal to 18 kpc. This current study collates and re-analyses these equivalent- width datasets using LTE and non-LTE model atmosphere techniques, in order to determine the stellar atmospheric parameters and abundance estimates for C, N, O, Mg, Al and Si. The latter should be representative of the present-day Galactic interstellar medium. Our extensive observational dataset permits the identification of sub-samples of stars with similar atmospheric parameters and of homogeneous subsets of lines. As such, this investigation represents the most extensive and systematic study of its kind to date. We conclude that the distribution of light elements (CI O, Mg & Si) in the Galactic disk can be represented by a linear, radial gradient of -0.07 +/- 0.01 dex kpc(-1) Our results for nitrogen and oxygen viz. (-0.09 +/- 0.01 dex kpc(-1) and -0.067 +/- 0.008 dex kpc(-1)) are in excellent agreement with that found from the study of HII regions. We have also examined our datasets for evidence of an abrupt discontinuity in the metallicity of the Galactic disk near a Galactocentric distance of 10 kpc (see Twarog et al. 1997). However, there is no evidence to suggest that our data would be better fitted with a two-zone model. Moreover, we observe a N/O gradient of -0.04 +/- 0.02 dex kpc(-1) which is consistent with that found for other spiral galaxies (Vila- Costas gr Edmunds 1993).

A Van der Pol-Mathieu equation for the dynamics of dust grain charge in dusty plasmas

The chaotic profile of dust grain dynamics associated with dust-acoustic oscillations in a dusty plasma is considered. The collective behaviour of the dust plasma component is described via a multi-fluid model, comprising Boltzmann distributed electrons and ions, as well as an equation of continuity possessing a source term for the dust grains, the dust momentum and Poisson's equations. A Van der Pol–Mathieu-type nonlinear ordinary differential equation for the dust grain density dynamics is derived. The dynamical system is cast into an autonomous form by employing an averaging method. Critical stability boundaries for a particular trivial solution of the governing equation with varying parameters are specified. The equation is analysed to determine the resonance region, and finally numerically solved by using a fourth-order Runge–Kutta method. The presence of chaotic limit cycles is pointed out.

Graphical determination of network limits for wind power integration

A graphical method is presented for determining the capability of individual system nodes to accommodate wind power generation. The method is based upon constructing a capability chart for each node at which a wind farm is to be connected. The capability chart defines the domain of allowable power injections at the candidate node, subject to constraints imposed by voltage limits, voltage stability and equipment capability limits being satisfied. The chart is first derived for a two-bus model, before being extended to a multi-node power system. The graphical method is employed to derive the chart for a two-node system, as well as its application to a multi-node power system, considering the IEEE 30-bus test system as a case study. Although the proposed method is derived with the intention of determining the wind farm capacity to be connected at a specific node, it can be used for the analysis of a PQ bus loading as well as generation.

Carbon leakage revisited: unilateral climate policy with directed technical change

Using a stylized theoretical model, we argue that current economic analyses of climate policy tend to over-estimate the degree of carbon leakage, as they abstract from the effects of induced technological change. We analyse carbon leakage in a two-country model with directed technical change, where only one of the countries enforces an exogenous cap on emissions. Climate policy induces changes in relative prices, that cause carbon leakage through a terms-of-trade effect. However, these changes in relative prices also affect the incentives to innovate in different sectors. This leads to a counterbalancing induced-technology effect, which always reduces carbon leakage. We therefore conclude that the leakage rates reported in the literature may be too high, as these estimates neglect the effect of price changes on the incentives to innovate.