Stochastic simulations of the origins and implications of long-tailed distributions in gene expression

Gene expression noise results in protein number distributions ranging from long-tailed to Gaussian. We show how long-tailed distributions arise from a stochastic model of the constituent chemical reactions and suggest that, in conjunction with cooperative switches, they lead to more sensitive selection of a subpopulation of cells with high protein number than is possible with Gaussian distributions. Single-cell-tracking experiments are presented to validate some of the assumptions of the stochastic simulations. We also examine the effect of DNA looping on the shape of protein distributions. We further show that when switches are incorporated in the regulation of a gene via a feedback loop, the distributions can become bimodal. This might explain the bimodal distribution of certain morphogens during early embryogenesis.

Transverse momentum and pseudorapidity distributions of charged hadrons in pp collisions at sqrt(s) = 0.9 and 2.36 TeV

Measurements of inclusive charged-hadron transverse-momentum and pseudorapidity distributions are presented for proton-proton collisions at sqrt(s) = 0.9 and 2.36 TeV. The data were collected with the CMS detector during the LHC commissioning in December 2009. For non-single-diffractive interactions, the average charged-hadron transverse momentum is measured to be 0.46 +/- 0.01 (stat.) +/- 0.01 (syst.) GeV/c at 0.9 TeV and 0.50 +/- 0.01 (stat.) +/- 0.01 (syst.) GeV/c at 2.36 TeV, for pseudorapidities between -2.4 and +2.4. At these energies, the measured pseudorapidity densities in the central region, dN(charged)/d(eta) for |eta|

A Geometric Algorithm for Learning Oblique Decision Trees

In this paper we present a novel algorithm for learning oblique decision trees. Most of the current decision tree algorithms rely on impurity measures to assess goodness of hyperplanes at each node. These impurity measures do not properly capture the geometric structures in the data. Motivated by this, our algorithm uses a strategy, based on some recent variants of SVM, to assess the hyperplanes in such a way that the geometric structure in the data is taken into account. We show through empirical studies that our method is effective.

Behaviour of Bi-adhesive Joints

The use of relatively low modulus adhesive at the ends of overlap in a bi-adhesive bondline of a bonded joint can reduce the stress concentration significantly and, therefore, potentially lead to higher strength of the joint. This study presents the two-dimensional and three-dimensional nonlinear (geometric and material) finite element analyses of adhesively bonded single lap joints having modulus-graded bondline under monotonic loading conditions. The adhesives were modelled as an elasto-plastic multi-linear material, while the substrates were regarded as both linear elastic and bi-linear elasto-plastic material. The computational simulations have been performed to investigate the bondline behaviour by studying the stress and strain distributions both at the mid-plane as well as at the interface of the bondline. It has been observed that the static strength is higher for joints with bi-adhesive bondlines compared to those with single adhesives in bondline. Higher joint strength has also been observed for optimum bi-adhesive bondline ratio through parametric studies. Effects of load level, and bondline thickness on stress distribution in the bi-adhesive bondline have also been studied. 3D analysis results reveal the existence of complex multi-axial stress/strain state at the ends of the overlap in the bondline which cannot be observed in 2D plane strain analysis. About 1/3rd of the width of the joint from the free edge in the width direction has 3D stress state, especially in the compliant adhesive of the bondline. Magnitudes of longitudinal and lateral stress/strain components are comparable to peel stress/strain components. It has also been analytically shown that the in-plane global stiffness of the joint remains unaffected by modulus gradation of the bondline adhesive. (C) Koninklijke Brill NV, Leiden, 2010.

Evaluating the Predictability of the Volatility Smile Using Return Distributions

In this paper, we examine the predictability of observed volatility smiles in three major European index options markets, utilising the historical return distributions of the respective underlying assets. The analysis involves an application of the Black (1976) pricing model adjusted in accordance with the Jarrow-Rudd methodology as proposed in 1982. Thereby we adjust the expected future returns for the third and fourth central moments as these represent deviations from normality in the distributions of observed returns. Thus, they are considered one possible explanation to the existence of the smile. The obtained results indicate that the inclusion of the higher moments in the pricing model to some extent reduces the volatility smile, compared with the unadjusted Black-76 model. However, as the smile is partly a function of supply, demand, and liquidity, and as such intricate to model, this modification does not appear sufficient to fully capture the characteristics of the smile.

Geometric quantum computation using fictitious spin-1/2 subspaces of strongly dipolar coupled nuclear spins

Geometric phases have been used in NMR to implement controlled phase shift gates for quantum-information processing, only in weakly coupled systems in which the individual spins can be identified as qubits. In this work, we implement controlled phase shift gates in strongly coupled systems by using nonadiabatic geometric phases, obtained by evolving the magnetization of fictitious spin-1/2 subspaces, over a closed loop on the Bloch sphere. The dynamical phase accumulated during the evolution of the subspaces is refocused by a spin echo pulse sequence and by setting the delay of transition selective pulses such that the evolution under the homonuclear coupling makes a complete 2 pi rotation. A detailed theoretical explanation of nonadiabatic geometric phases in NMR is given by using single transition operators. Controlled phase shift gates, two qubit Deutsch-Jozsa algorithm, and parity algorithm in a qubit-qutrit system have been implemented in various strongly dipolar coupled systems obtained by orienting the molecules in liquid crystal media.

Optimum aperture distributions in the presence of blockage

A method is presented for optimising the performance indices of aperture antennas in the presence of blockage. An N-dimensional objective function is formed for maximising the directivity factor of a circular aperture with blockage under sidelobe-level constraints, and is minimised using the simplex search method. Optimum aperture distributions are computed for a circular aperture with blockage of circular geometry that gives the maximum directivity factor under sidelobe-level constraints.

Criticality of the exponential rate of decay for the largest nearest-neighbor link in random geometric graphs

Let n points be placed independently in d-dimensional space according to the density f(x) = A(d)e(-lambda parallel to x parallel to alpha), lambda, alpha > 0, x is an element of R-d, d >= 2. Let d(n) be the longest edge length of the nearest-neighbor graph on these points. We show that (lambda(-1) log n)(1-1/alpha) d(n) - b(n) converges weakly to the Gumbel distribution, where b(n) similar to ((d - 1)/lambda alpha) log log n. We also prove the following strong law for the normalized nearest-neighbor distance (d) over tilde (n) = (lambda(-1) log n)(1-1/alpha) d(n)/log log n: (d - 1)/alpha lambda <= lim inf(n ->infinity) (d) over tilde (n) <= lim sup(n ->infinity) (d) over tilde (n) <= d/alpha lambda almost surely. Thus, the exponential rate of decay alpha = 1 is critical, in the sense that, for alpha > 1, d(n) -> 0, whereas, for alpha <= 1, d(n) -> infinity almost surely as n -> infinity.

Methods and applications for improving parameter prediction models for stand structures in Finland

This thesis report attempts to improve the models for predicting forest stand structure for practical use, e.g. forest management planning (FMP) purposes in Finland. Comparisons were made between Weibull and Johnson s SB distribution and alternative regression estimation methods. Data used for preliminary studies was local but the final models were based on representative data. Models were validated mainly in terms of bias and RMSE in the main stand characteristics (e.g. volume) using independent data. The bivariate SBB distribution model was used to mimic realistic variations in tree dimensions by including within-diameter-class height variation. Using the traditional method, diameter distribution with the expected height resulted in reduced height variation, whereas the alternative bivariate method utilized the error-term of the height model. The lack of models for FMP was covered to some extent by the models for peatland and juvenile stands. The validation of these models showed that the more sophisticated regression estimation methods provided slightly improved accuracy. A flexible prediction and application for stand structure consisted of seemingly unrelated regression models for eight stand characteristics, the parameters of three optional distributions and Näslund s height curve. The cross-model covariance structure was used for linear prediction application, in which the expected values of the models were calibrated with the known stand characteristics. This provided a framework to validate the optional distributions and the optional set of stand characteristics. Height distribution is recommended for the earliest state of stands because of its continuous feature. From the mean height of about 4 m, Weibull dbh-frequency distribution is recommended in young stands if the input variables consist of arithmetic stand characteristics. In advanced stands, basal area-dbh distribution models are recommended. Näslund s height curve proved useful. Some efficient transformations of stand characteristics are introduced, e.g. the shape index, which combined the basal area, the stem number and the median diameter. Shape index enabled SB model for peatland stands to detect large variation in stand densities. This model also demonstrated reasonable behaviour for stands in mineral soils.

Toxicant distributions and impact models in environmental risk analysis of waste sites

Myrkyllisten aineiden jakaumat ja vaikutusmallit jätealueiden ympäristöriskien analyysissä.

Scaling theory of quantum resistance distributions in disordered systems

We have derived explicitly, the large scale distribution of quantum Ohmic resistance of a disordered one-dimensional conductor. We show that in the thermodynamic limit this distribution is characterized by two independent parameters for strong disorder, leading to a two-parameter scaling theory of localization. Only in the limit of weak disorder we recover single parameter scaling, consistent with existing theoretical treatments.

Properties of Toeplitz operators on analytic function spaces : from function symbols to distributions

Toeplitz operators are among the most important classes of concrete operators with applications to several branches of pure and applied mathematics. This doctoral thesis deals with Toeplitz operators on analytic Bergman, Bloch and Fock spaces. Usually, a Toeplitz operator is a composition of multiplication by a function and a suitable projection. The present work deals with generalizing the notion to the case where the function is replaced by a distributional symbol. Fredholm theory for Toeplitz operators with matrix-valued symbols is also considered. The subject of this thesis belongs to the areas of complex analysis, functional analysis and operator theory. This work contains five research articles. The articles one, three and four deal with finding suitable distributional classes in Bergman, Fock and Bloch spaces, respectively. In each case the symbol class to be considered turns out to be a certain weighted Sobolev-type space of distributions. The Bergman space setting is the most straightforward. When dealing with Fock spaces, some difficulties arise due to unboundedness of the complex plane and the properties of the Gaussian measure in the definition. In the Bloch-type spaces an additional logarithmic weight must be introduced. Sufficient conditions for boundedness and compactness are derived. The article two contains a portion showing that under additional assumptions, the condition for Bergman spaces is also necessary. The fifth article deals with Fredholm theory for Toeplitz operators having matrix-valued symbols. The essential spectra and index theorems are obtained with the help of Hardy space factorization and the Berezin transform, for instance. The article two also has a part dealing with matrix-valued symbols in a non-reflexive Bergman space, in which case a condition on the oscillation of the symbol (a logarithmic VMO-condition) must be added.