Simulation of structural and electronic properties of amorphous tungsten oxycarbides

Electron beam induced deposition with tungsten hexacarbonyl W(CO)6 as precursors leads to granular deposits with varying compositions of tungsten, carbon and oxygen. Depending on the deposition conditions, the deposits are insulating or metallic. We employ an evolutionary algorithm to predict the crystal structures starting from a series of chemical compositions that were determined experimentally. We show that this method leads to better structures than structural relaxation based on guessed initial structures. We approximate the expected amorphous structures by reasonably large unit cells that can accommodate local structural environments that resemble the true amorphous structure. Our predicted structures show an insulator to metal transition close to the experimental composition at which this transition is actually observed. Our predicted structures also allow comparison to experimental electron diffraction patterns.Comment: 17 Pages, 11 figure

On the joint security of signature and encryption schemes under randomness reuse: efficiency and security amplification

Lecture Notes in Computer Science, 7341We extend the work of Bellare, Boldyreva and Staddon on the systematic analysis of randomness reuse to construct multi-recipient encryption schemes to the case where randomness is reused across different cryptographic primitives. We find that through the additional binding introduced through randomness reuse, one can actually obtain a security amplification with respect to the standard black-box compositions, and achieve a stronger level of security. We introduce stronger notions of security for encryption and signatures, where challenge messages can depend in a restricted way on the random coins used in encryption, and show that two variants of the KEM/DEM paradigm give rise to encryption schemes that meet this enhanced notion of security. We obtain the most efficient signcryption scheme to date that is secure against insider attackers without random oracles.(undefined

Automating Program Verification and Repair Using Invariant Analysis and Test Input Generation

Software bugs are a persistent feature of daily life---crashing web browsers, allowing cyberattacks, and distorting the results of scientific computations. One approach to improving software uses program invariants---mathematical descriptions of program behaviors---to verify code and detect bugs. Current invariant generation techniques lack support for complex yet important forms of invariants, such as general polynomial relations and properties of arrays. As a result, we lack the ability to conduct precise analysis of programs that use this common data structure. This dissertation presents DIG, a static and dynamic analysis framework for discovering several useful classes of program invariants, including (i) nonlinear polynomial relations, which are fundamental to many scientific applications; disjunctive invariants, (ii) which express branching behaviors in programs; and (iii) properties about multidimensional arrays, which appear in many practical applications. We describe theoretical and empirical results showing that DIG can efficiently and accurately find many important invariants in real-world uses, e.g., polynomial properties in numerical algorithms and array relations in a full AES encryption implementation. Automatic program verification and synthesis are long-standing problems in computer science. However, there has been a lot of work on program verification and less so on program synthesis. Consequently, important synthesis tasks, e.g., generating program repairs, remain difficult and time-consuming. This dissertation proves that certain formulations of verification and synthesis are equivalent, allowing for direct applications of techniques and tools between these two research areas. Based on these ideas, we develop CETI, a tool that leverages existing verification techniques and tools for automatic program repair. Experimental results show that CETI can have higher success rates than many other standard program repair methods

Models for transcript quantification from RNA-Seq

RNA-Seq is rapidly becoming the standard technology for transcriptome analysis. Fundamental to many of the applications of RNA-Seq is the quantification problem, which is the accurate measurement of relative transcript abundances from the sequenced reads. We focus on this problem, and review many recently published models that are used to estimate the relative abundances. In addition to describing the models and the different approaches to inference, we also explain how methods are related to each other. A key result is that we show how inference with many of the models results in identical estimates of relative abundances, even though model formulations can be very different. In fact, we are able to show how a single general model captures many of the elements of previously published methods. We also review the applications of RNA-Seq models to differential analysis, and explain why accurate relative transcript abundance estimates are crucial for downstream analyses

Architectural Refinement in HETS

The main objective of this work is to bring a number of improvements to the Heterogeneous Tool Set HETS, both from a theoretical and an implementation point of view. In the first part of the thesis we present a number of recent extensions of the tool, among which declarative specifications of logics, generalized theoroidal comorphisms, heterogeneous colimits and integration of the logic of the term rewriting system Maude. In the second part we concentrate on the CASL architectural refinement language, that we equip with a notion of refinement tree and with calculi for checking correctness and consistency of refinements. Soundness and completeness of these calculi is also investigated. Finally, we present the integration of the VSE refinement method in HETS as an institution comorphism. Thus, the proof manangement component of HETS remains unmodified

Interaction Grammars

Interaction Grammar (IG) is a grammatical formalism based on the notion of polarity. Polarities express the resource sensitivity of natural languages by modelling the distinction between saturated and unsaturated syntactic structures. Syntactic composition is represented as a chemical reaction guided by the saturation of polarities. It is expressed in a model-theoretic framework where grammars are constraint systems using the notion of tree description and parsing appears as a process of building tree description models satisfying criteria of saturation and minimality