X-Pro peptides. A theoretical study of the hydrogen bonded conformations of (a-aminoisobutyryl-L -prolyl)n sequences

Intramolecularly hydrogen bonded conformations of (Aib-Pro)n sequences have been analysed theoretically. Both 4�1 (C10 and 3�1 (C7 hydrogen bonded regular structures are shown to be stereochemically feasible. Conformational energies for the helical structures have been estimated using classical potential energy methods. Both C10 and C7 conformations have very similar energies. Pyrrolidine ring puckering has a pronounced effect on the energies, and only Cγ-endo puckered Pro residues can be accommodated. The theoretical calculations using spectroscopic data suggest that the recently proposed novel 310 helical conformation for benzyloxycarbonyl(Aib-Pro)4-methyl ester is in solution, is indeed energetically and stereochemically favourable.

Theoretical studies on the conformations of aldopentopyranose tetraacetates

Abstract is not available.

Locality and order-invariant logics

Malli on logiikassa käytetty abstraktio monille matemaattisille objekteille. Esimerkiksi verkot, ryhmät ja metriset avaruudet ovat malleja. Äärellisten mallien teoria on logiikan osa-alue, jossa tarkastellaan logiikkojen, formaalien kielten, ilmaisuvoimaa malleissa, joiden alkioiden lukumäärä on äärellinen. Rajoittuminen äärellisiin malleihin mahdollistaa tulosten soveltamisen teoreettisessa tietojenkäsittelytieteessä, jonka näkökulmasta logiikan kaavoja voidaan ajatella ohjelmina ja äärellisiä malleja niiden syötteinä. Lokaalisuus tarkoittaa logiikan kyvyttömyyttä erottaa toisistaan malleja, joiden paikalliset piirteet vastaavat toisiaan. Väitöskirjassa tarkastellaan useita lokaalisuuden muotoja ja niiden säilymistä logiikkoja yhdistellessä. Kehitettyjä työkaluja apuna käyttäen osoitetaan, että Gaifman- ja Hanf-lokaalisuudeksi kutsuttujen varianttien välissä on lokaalisuuskäsitteiden hierarkia, jonka eri tasot voidaan erottaa toisistaan kasvavaa dimensiota olevissa hiloissa. Toisaalta osoitetaan, että lokaalisuuskäsitteet eivät eroa toisistaan, kun rajoitutaan tarkastelemaan äärellisiä puita. Järjestysinvariantit logiikat ovat kieliä, joissa on käytössä sisäänrakennettu järjestysrelaatio, mutta sitä on käytettävä siten, etteivät kaavojen ilmaisemat asiat riipu valitusta järjestyksestä. Määritelmää voi motivoida tietojenkäsittelyn näkökulmasta: vaikka ohjelman syötteen tietojen järjestyksellä ei olisi odotetun tuloksen kannalta merkitystä, on syöte tietokoneen muistissa aina jossakin järjestyksessä, jota ohjelma voi laskennassaan hyödyntää. Väitöskirjassa tutkitaan minkälaisia lokaalisuuden muotoja järjestysinvariantit ensimmäisen kertaluvun predikaattilogiikan laajennukset yksipaikkaisilla kvanttoreilla voivat toteuttaa. Tuloksia sovelletaan tarkastelemalla, milloin sisäänrakennettu järjestys lisää logiikan ilmaisuvoimaa äärellisissä puissa.

On Games on Non-Wellfounded Sets and Stationary Sets

In this thesis we study a few games related to non-wellfounded and stationary sets. Games have turned out to be an important tool in mathematical logic ranging from semantic games defining the truth of a sentence in a given logic to for example games on real numbers whose determinacies have important effects on the consistency of certain large cardinal assumptions. The equality of non-wellfounded sets can be determined by a so called bisimulation game already used to identify processes in theoretical computer science and possible world models for modal logic. Here we present a game to classify non-wellfounded sets according to their branching structure. We also study games on stationary sets moving back to classical wellfounded set theory. We also describe a way to approximate non-wellfounded sets with hereditarily finite wellfounded sets. The framework used to do this is domain theory. In the Banach-Mazur game, also called the ideal game, the players play a descending sequence of stationary sets and the second player tries to keep their intersection stationary. The game is connected to precipitousness of the corresponding ideal. In the pressing down game first player plays regressive functions defined on stationary sets and the second player responds with a stationary set where the function is constant trying to keep the intersection stationary. This game has applications in model theory to the determinacy of the Ehrenfeucht-Fraisse game. We show that it is consistent that these games are not equivalent.

Bayesian statistical analysis of bacterial diversity

Bacteria play an important role in many ecological systems. The molecular characterization of bacteria using either cultivation-dependent or cultivation-independent methods reveals the large scale of bacterial diversity in natural communities, and the vastness of subpopulations within a species or genus. Understanding how bacterial diversity varies across different environments and also within populations should provide insights into many important questions of bacterial evolution and population dynamics. This thesis presents novel statistical methods for analyzing bacterial diversity using widely employed molecular fingerprinting techniques. The first objective of this thesis was to develop Bayesian clustering models to identify bacterial population structures. Bacterial isolates were identified using multilous sequence typing (MLST), and Bayesian clustering models were used to explore the evolutionary relationships among isolates. Our method involves the inference of genetic population structures via an unsupervised clustering framework where the dependence between loci is represented using graphical models. The population dynamics that generate such a population stratification were investigated using a stochastic model, in which homologous recombination between subpopulations can be quantified within a gene flow network. The second part of the thesis focuses on cluster analysis of community compositional data produced by two different cultivation-independent analyses: terminal restriction fragment length polymorphism (T-RFLP) analysis, and fatty acid methyl ester (FAME) analysis. The cluster analysis aims to group bacterial communities that are similar in composition, which is an important step for understanding the overall influences of environmental and ecological perturbations on bacterial diversity. A common feature of T-RFLP and FAME data is zero-inflation, which indicates that the observation of a zero value is much more frequent than would be expected, for example, from a Poisson distribution in the discrete case, or a Gaussian distribution in the continuous case. We provided two strategies for modeling zero-inflation in the clustering framework, which were validated by both synthetic and empirical complex data sets. We show in the thesis that our model that takes into account dependencies between loci in MLST data can produce better clustering results than those methods which assume independent loci. Furthermore, computer algorithms that are efficient in analyzing large scale data were adopted for meeting the increasing computational need. Our method that detects homologous recombination in subpopulations may provide a theoretical criterion for defining bacterial species. The clustering of bacterial community data include T-RFLP and FAME provides an initial effort for discovering the evolutionary dynamics that structure and maintain bacterial diversity in the natural environment.

Modeling Asymmetries in Financial Data with Multiplicative Error Models

This thesis addresses modeling of financial time series, especially stock market returns and daily price ranges. Modeling data of this kind can be approached with so-called multiplicative error models (MEM). These models nest several well known time series models such as GARCH, ACD and CARR models. They are able to capture many well established features of financial time series including volatility clustering and leptokurtosis. In contrast to these phenomena, different kinds of asymmetries have received relatively little attention in the existing literature. In this thesis asymmetries arise from various sources. They are observed in both conditional and unconditional distributions, for variables with non-negative values and for variables that have values on the real line. In the multivariate context asymmetries can be observed in the marginal distributions as well as in the relationships of the variables modeled. New methods for all these cases are proposed. Chapter 2 considers GARCH models and modeling of returns of two stock market indices. The chapter introduces the so-called generalized hyperbolic (GH) GARCH model to account for asymmetries in both conditional and unconditional distribution. In particular, two special cases of the GARCH-GH model which describe the data most accurately are proposed. They are found to improve the fit of the model when compared to symmetric GARCH models. The advantages of accounting for asymmetries are also observed through Value-at-Risk applications. Both theoretical and empirical contributions are provided in Chapter 3 of the thesis. In this chapter the so-called mixture conditional autoregressive range (MCARR) model is introduced, examined and applied to daily price ranges of the Hang Seng Index. The conditions for the strict and weak stationarity of the model as well as an expression for the autocorrelation function are obtained by writing the MCARR model as a first order autoregressive process with random coefficients. The chapter also introduces inverse gamma (IG) distribution to CARR models. The advantages of CARR-IG and MCARR-IG specifications over conventional CARR models are found in the empirical application both in- and out-of-sample. Chapter 4 discusses the simultaneous modeling of absolute returns and daily price ranges. In this part of the thesis a vector multiplicative error model (VMEM) with asymmetric Gumbel copula is found to provide substantial benefits over the existing VMEM models based on elliptical copulas. The proposed specification is able to capture the highly asymmetric dependence of the modeled variables thereby improving the performance of the model considerably. The economic significance of the results obtained is established when the information content of the volatility forecasts derived is examined.

Generalised quaternion methods in conformal geometry

A new approach to Penrose's twistor algebra is given. It is based on the use of a generalised quaternion algebra for the translation of statements in projective five-space into equivalent statements in twistor (conformal spinor) space. The formalism leads toSO(4, 2)-covariant formulations of the Pauli-Kofink and Fierz relations among Dirac bilinears, and generalisations of these relations.

New lads or ladettes? A critique of current theoretical explanations for young women’s violence proliferated over social media

Current theoretical explanations for young women’s violence examine physical violence as a masculine behaviour. This means that young women are constructed as rejecting elements of their femininity in favour of masculine behaviours in order to perform violence in an acceptable way, which results in them being constructed as violent femmes, new lads or ladettes. Alternatively, theoretical explanations construct young women as adhering to a feminine gender performance when avoiding physical violence, or engaging what are traditionally considered to be feminine characteristics of aggression. This paper critiques existing theoretical approaches applied to young women’s violence, by drawing on empirical research that examined young women’s physical altercations proliferated through social media. Preliminary research findings illustrate how continuing to construct young women’s violence through a gendered paradigm offers inadequate explanations for what young women’s violence actually entails. It concludes by suggesting how young women’s violence may be more adequately explained using a theoretical framework of embodying gender that moves away from gender dichotomies and constructs violence as a series of bodily practices.

Tutoring with higher mathematics and the use of technology

We discuss three approaches to the use of technology as a teaching and learning tool that we are currently implementing for a target group of about one hundred second level engineering mathematics students. Central to these approaches is the underlying theme of motivating relatively poorly motivated students to learn, with the aim of improving learning outcomes. The approaches to be discussed have been used to replace, in part, more traditional mathematics tutorial sessions and lecture presentations. In brief, the first approach involves the application of constructivist thinking in the tertiary education arena, using technology as a computational and visual tool to create motivational knowledge conflicts or crises. The central idea is to model a realistic process of how scientific theory is actually developed, as proposed by Kuhn (1962), in contrast to more standard lecture and tutorial presentations. The second approach involves replacing procedural or algorithmic pencil-and-paper skills-consolidation exercises by software based tasks. Finally, the third approach aims at creating opportunities for higher order thinking via "on-line" exploratory or discovery mode tasks. The latter incorporates the incubation period method, as originally discussed by Rubinstein (1975) and others.

Korteweg-De Vries Equation for Non-Linear Ion-Acoustic Waves in a Plasma with Negative Ions

The theoretical analysis, based on the perturbation technique, of ion-acoustic waves in the vicinity of a Korteweg-de Vries (K-dV) equation derived in a plasma with some negative ions has been made. The investigation shows that the negative ions in plasma with isothermal electrons introduced a critical concentration at which the ion-acoustic wave plays an important role of wave-breaking and forming a precursor while the plasma with non-isothermal electrons has no such singular behaviour of the wave. These two distinct features of ion waves lead to an overall different approach of present study of ion-waves. A distinct feature of non-uniform transition from the nonisothermal case to isothermal case has been shown. Few particular plasma models have been chosen to show the characteristics behaviour of the ion-waves existing in different cases

Geometry of the de-Sitter universe

By making use of the fact that the de-Sitter metric corresponds to a hyperquadric in a five-dimensional flat space, it is shown that the three Robertson-Walker metrics for empty spacetime and positive cosmological constant, corresponding to 3-space of positive, negative and zero curvative, are geometrically equivalent. The 3-spaces correspond to intersections of the hyperquadric by hyperplanes, and the time-like geodesics perpendicular to them correspond to intersections by planes, in all three cases.

Theoretical gain optimization studies in 10.6 µm CO2-N2 gasdynamic lasers. IV. Further results of parametric study

Based on a method proposed by Reddy and Shanmugasundaram, similar solutions have been obtained for the steady inviscid quasi-one-dimensional nonreacting flow in the supersonic nozzle of CO2-N2-H2O and CO2-N2-He gasdynamic laser systems. Instead of using the correlations of a nonsimilar function NS for pure N2 gas, as is done in previous publications, the NS correlations are computed here for the actual gas mixtures used in the gasdynamic lasers. Optimum small-signal optical gain and the corresponding optimum values of the operating parameters like reservoir pressure and temperature and nozzle area ratio are computed using these correlations. The present results are compared with the previous results and the main differences are discussed. Journal of Applied Physics is copyrighted by The American Institute of Physics.