Simplifying and unifying composition for industrial component models

In a world of high productivity with a focus on maximizing profit, it becomes extremely important to produce new, reliable software as quickly and cheaply as possible. Compo- nent based software development (CBD) promised to reach this goal. By just composing prefabricated, reusable, well-tested components to new applications, application devel- opment should become much more productive and reliable. Application programmers should be able to select from a set of suitable components potentially produced by dif- ferent vendors. Industry contributed to this goal by introducing several different component mod- els as e.g. JavaBeans, Enterprise JavaBeans (EJBs), the Component Object Model (COM), the Corba Component Model (CCM), and most recently .NET. Each component model defines its own standard for component look up, instantiation, access to the functional- ity of the component, communication, composition techniques available etc. Although these component models already are a big step towards the goals of CBD, especially the composition techniques supported are still too restricted, not simple enough, and vary from component model to component model. Thus, the main goal of this thesis is to establish a basis and to develop techniques for simplifying and unifying the composition process for components belonging to in- dustrial component models. We introduce a unifying component model comprising the main features of current industrial component models. This model provides some additional, useful features, as e.g. the support of bi-directional connections which can be established by a certain composition mechanism. Components of this model can be composed to yield components of a higher level of abstraction. These composite com- ponents are described by a composition language which supports late binding mecha- nisms through strict interface based programming. As components of industrial compo- nent models can be integrated into our unifying model, all its features are also available for existing industrial component models. Compositions can be checked for consis- tency based on a type system we define for our component model. This type system respects amongst others conditions for bi-directional connections and a certain kind of alias control. Besides consistency checking, the type system is used to decide whether a component can be replaced by another one without invalidating any existing composite referring to the component to be replaced. To further simplify the composition process, we focus on tool support for visual composition. Some useful features are introduced, as e.g. the guided establishment of needed interconnections and the colored depiction of constituents of a composite causing incorrect composition

Program-level Specification and Deductive Verification of Security Properties

Programs with publicly accessible interfaces are increasingly used to process confidential data. This makes it all the more important to control the information flow within such applications. This thesis shows how highly precise specification and deductive verification of language-based secure information flow can be made feasible. The approach does not rely on fixed approximations, but makes use of the precision provided by the underlying calculus for Java Dynamic Logic

IC0701 verification competition 2011

Abstract. This paper reports on the experiences with the program verification competition held during the FoVeOOS conference in October 2011. There were 6 teams participating in this competition. We discuss the three different challenges that were posed and the solutions developed by the teams. We conclude with a discussion about the value of such competitions and lessons that can be learned from them.

Iterative Methods for Criticality Computations in Neutron Transport Theory

This thesis studies the so-called “criticality problem”, an important generalised eigenvalue problem arising in neutron transport theory. The smallest positive real eigenvalue of the problem contains valuable information about the status of the fission chain reaction in the nuclear reactor (i.e. the criticality of the reactor), and thus plays an important role in the design and safety of nuclear power stations. Because of the practical importance, efficient numerical methods to solve the criticality problem are needed, and these are the focus of this thesis. In the theory we consider the time-independent neutron transport equation in the monoenergetic homogeneous case with isotropic scattering and vacuum boundary conditions. This is an unsymmetric integro-differential equation in 5 independent variables, modelling transport, scattering, and fission, where the dependent variable is the neutron angular flux. We show that, before discretisation, the nonsymmetric eigenproblem for the angular flux is equivalent to a related eigenproblem for the scalar flux, involving a symmetric positive definite weakly singular integral operator(in space only). Furthermore, we prove the existence of a simple smallest positive real eigenvalue with a corresponding eigenfunction that is strictly positive in the interior of the reactor. We discuss approaches to discretise the problem and present discretisations that preserve the underlying symmetry in the finite dimensional form. The thesis then describes methods for computing the criticality in nuclear reactors, i.e. the smallest positive real eigenvalue, which are applicable for quite general geometries and physics. In engineering practice the criticality problem is often solved iteratively, using some variant of the inverse power method. Because of the high dimension, matrix representations for the operators are often not available and the inner solves needed for the eigenvalue iteration are implemented by matrix-free inneriterations. This leads to inexact iterative methods for criticality computations, for which there appears to be no rigorous convergence theory. The fact that, under appropriate assumptions, the integro-differential eigenvalue problem possesses an underlying symmetry (in a space of reduced dimension) allows us to perform a systematic convergence analysis for inexact inverse iteration and related methods. In particular, this theory provides rather precise criteria on how accurate the inner solves need to be in order for the whole iterative method to converge. The theory is illustrated with numerical examples on several test problems of physical relevance, using GMRES as the inner solver. We also illustrate the use of Monte Carlo methods for the solution of neutron transport source problems as well as for the criticality problem. Links between the steps in the Monte Carlo process and the underlying mathematics are emphasised and numerical examples are given. Finally, we introduce an iterative scheme (the so-called “method of perturbation”) that is based on computing the difference between the solution of the problem of interest and the known solution of a base problem. This situation is very common in the design stages for nuclear reactors when different materials are tested, or the material properties change due to the burn-up of fissile material. We explore the relation ofthe method of perturbation to some variants of inverse iteration, which allows us to give convergence results for the method of perturbation. The theory shows that the method is guaranteed to converge if the perturbations are not too large and the inner problems are solved with sufficiently small tolerances. This helps to explain the divergence of the method of perturbation in some situations which we give numerical examples of. We also identify situations, and present examples, in which the method of perturbation achieves the same convergence rate as standard shifted inverse iteration. Throughout the thesis further numerical results are provided to support the theory.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Single-cell genomic analysis in plants

Individual cells in an organism are variable, which strongly impacts cellular processes. Advances in sequencing technologies have enabled single-cell genomic analysis to become widespread, addressing shortcomings of analyses conducted on populations of bulk cells. While the field of single-cell plant genomics is in its infancy, there is great potential to gain insights into cell lineage and functional cell types to help understand complex cellular interactions in plants. In this review, we discuss current approaches for single-cell plant genomic analysis, with a focus on single-cell isolation, DNA amplification, next-generation sequencing, and bioinformatics analysis. We outline the technical challenges of analysing material from a single plant cell, and then examine applications of single-cell genomics and the integration of this approach with genome editing. Finally, we indicate future directions we expect in the rapidly developing field of plant single-cell genomic analysis

The radiative transport equation with heterogeneous cross-sections

We consider the classical integral equation reformulation of the radiative transport equation (RTE) in a heterogeneous medium, assuming isotropic scattering. We prove an estimate for the norm of the integral operator in this formulation which is explicit in the (variable) coefficients of the problem (also known as the cross-sections). This result uses only elementary properties of the transport operator and some classical functional analysis. As a corollary, we obtain a bound on the convergence rate of source iteration (a classical stationary iterative method for solving the RTE). We also obtain an estimate for the solution of the RTE which is explicit in its dependence on the cross-sections. The latter can be used to estimate the solution in certain Bochner norms when the cross-sections are random fields. Finally we use our results to give an elementary proof that the generalised eigenvalue problem arising in nuclear reactor safety has only real and positive eigenvalues

Iterative methods for neutron transport eigenvalue problems

We discuss iterative methods for computing criticality in nuclear reactors. In general this requires the solution of a generalized eigenvalue problem for an unsymmetric integro-differential operator in six independent variables, modeling transport, scattering, and fission, where the dependent variable is the neutron angular flux. In engineering practice this problem is often solved iteratively, using some variant of the inverse power method. Because of the high dimension, matrix representations for the operators are often not available and the inner solves needed for the eigenvalue iteration are implemented by matrix-free inner iterations. This leads to technically complicated inexact iterative methods, for which there appears to be no published rigorous convergence theory. For the monoenergetic homogeneous model case with isotropic scattering and vacuum boundary conditions, we show that, before discretization, the general nonsymmetric eigenproblem for the angular flux is equivalent to a certain related eigenproblem for the scalar flux, involving a symmetric positive definite weakly singular integral operator (in space only). This correspondence to a symmetric problem (in a space of reduced dimension) permits us to give a convergence theory for inexact inverse iteration and related methods. In particular this theory provides rather precise criteria on how accurate the inner solves need to be in order for the whole iterative method to converge. We also give examples of discretizations which have a corresponding symmetric finite-dimensional reduced form. The theory is illustrated with numerical examples for several test problems of physical relevance, using GMRES as the inner solver

Molecular and Morphological Evidence Challenges the Records of the Extant Liverwort Ptilidium pulcherrimum in Eocene Baltic Amber

Preservation of liverworts in amber, a fossilized tree resin, is often exquisite. Twenty-three fossil species of liverworts have been described to date from Eocene (35-50 Ma) Baltic amber. In addition, two inclusions have been assigned to the extant species Ptilidium pulcherrimum (Ptilidiales or Porellales). However, the presence of the boreal P. pulcherrimum in the subtropical or warm-temperate Baltic amber forest challenges the phytogeographical interpretation of the Eocene flora. A re-investigation of one of the fossils believed to be P. pulcherrimum reveals that this specimen in fact represents the first fossil evidence of the genus Tetralophozia, and thus is re-described here as Tetralophozia groehnii sp. nov. A second fossil initially assigned to P. pulcherrimum is apparently lost, and can be reassessed only based on the original description and illustrations. This fossil is morphologically similar to the extant North Pacific endemic Ptilidium californicum, rather than P. pulcherrimum. Divergence time estimates based on chloroplast DNA sequences provide evidence of a Miocene origin of P. pulcherrimum, and thus also argue against the presence of this taxon in the Eocene. Ptilidium californicum originated 25-43 Ma ago. As a result, we cannot rule out that the Eocene fossil belongs to P. californicum. Alternatively, the fossil might represent a stem lineage element of Ptilidium or an early crown group species with morphological similarities to P. californicum