Transformation of UML Behavioral Diagrams to Support Software Model Checking

Unified Modeling Language (UML) is currently accepted as the standard for modeling (object-oriented) software, and its use is increasing in the aerospace industry. Verification and Validation of complex software developed according to UML is not trivial due to complexity of the software itself, and the several different UML models/diagrams that can be used to model behavior and structure of the software. This paper presents an approach to transform up to three different UML behavioral diagrams (sequence, behavioral state machines, and activity) into a single Transition System to support Model Checking of software developed in accordance with UML. In our approach, properties are formalized based on use case descriptions. The transformation is done for the NuSMV model checker, but we see the possibility in using other model checkers, such as SPIN. The main contribution of our work is the transformation of a non-formal language (UML) to a formal language (language of the NuSMV model checker) towards a greater adoption in practice of formal methods in software development.Comment: In Proceedings FESCA 2014, arXiv:1404.043

Descriptive Complexity of Deterministic Polylogarithmic Time and Space

We propose logical characterizations of problems solvable in deterministic polylogarithmic time (PolylogTime) and polylogarithmic space (PolylogSpace). We introduce a novel two-sorted logic that separates the elements of the input domain from the bit positions needed to address these elements. We prove that the inflationary and partial fixed point vartiants of this logic capture PolylogTime and PolylogSpace, respectively. In the course of proving that our logic indeed captures PolylogTime on finite ordered structures, we introduce a variant of random-access Turing machines that can access the relations and functions of a structure directly. We investigate whether an explicit predicate for the ordering of the domain is needed in our PolylogTime logic. Finally, we present the open problem of finding an exact characterization of order-invariant queries in PolylogTime.Comment: Submitted to the Journal of Computer and System Science

Stimulus-responsive Injectable Polysaccharide Scaffolds for Soft Tissue Engineering Prepared by O/W High Internal Phase Emulsion

This thesis describes work on the development of several novel stimuli-responsive porous hydrogels prepared from oil-in-water (o/w) high internal phase emulsion (HIPE) as injectable scaffolds for soft tissue engineering. Firstly, by copolymerising glycidyl methacrylate (GMA) derivatised dextran and N-isopropylacrylamide (NIPAAm) in the aqueous phase of a toluene-in-water HIPE, thermo-responsive polyHIPE hydrogels were obtained. The temperature depended modulus of these porous hydrogels, as revealed by oscillatory mechanical measurements, indicated improvements of the mechanical properties of these hydrogels when heated from room temperature to human body temperature, as the polyNIPAAm copolymer segments starts to phase separate from the aqueous phase and causes the hydrogel to form a more compact structure within the aqueous phase of the polyHIPE. Secondly ion responsive methacrylate modified alginate polyHIPE hydrogels were prepared. The physical dimensions, pore and pore throat sizes as well as water uptakes of these ion responsive hydrogels can be controllably decreased in the presence of Ca2+ ions and are fully recovered after disruption of the ionic crosslinking using a chelating agent (sodium citrate). These ion-responsive polyHIPE hydrogels also possess good mechanical properties (modulus up to 20 kPa). Both of these polyHIPE hydrogels could be easily extruded through a hypodermic needle while breaking into small fragments (about 0.5 to 3.0 mm in diameter), but the interconnected porous morphology was maintained after injection as revealed by SEM characterisation. Furthermore, the hydrogel fragments produced during injection can be crosslinked into a coherent scaffold under very mild condition using Ca2+ salts and alginate aqueous solution as the ionically crosslinkable adhesive. In order to increase the pore size of these covalently crosslinked polyHIPE hydrogels and also find a biocompatible nontoxic emulsifier as substitution to traditional surfactants, methyl myristate-in-water and soybean oil-in-water HIPEs solely stabilised by hydroxyapatite (HAp) nanoparticle were prepared. These Pickering- HIPEs were used as template to prepare polyHIPE hydrogels. Dextran-GMA, a water soluble monomer, was polymerised in the continuous phase of the HAp Pickering HIPEs leading to porous hydrogels with a tunable pore size varying from 1.5 μm to 41.0 μm. HAp is a nontoxic biocompatible emulsifier, which potentially provides extra functions, such as promoting hard tissue cell proliferation. HIPE-templated materials whose porous structure is maintained solely by the reversible physical aggregation between thermo-responsive dextran-b-polyNIPAAm block polymer chains in an aqueous environment (for this type of HIPE templated material we coined the name thermo-HIPEs) were prepared. No chemical reaction is required for the solidification of this porous material. This particular feature should provide a safer route to injectable scaffolds as issues of polymerisation/crosslinking chemistry or residual initiator fragments or monomers potentially being cytotoxic do not arise in our case, as all components are purified polymers prior to HIPE formation. Thermo-HIPEs with soybean oil or squalene as dispersed oil phase were prepared. Also in this HIPE system it was possible to replace the original surfactant Triton X405 with colloidal HAp nanoparticles or pH/thermo-responsive polyNIPAAm-co- AA microgel particles. The pore sizes and the mechanical properties of colloidal particles stabilised thermo-HIPEs showed improvement compared with thermo-HIPEs stabilised by Triton X405. In summary new injectable polyHIPEs have been prepared which retain their pore morphology during injection and can be solidified by either a thermal or ion (Ca2+) or chelating ion (Ca2+) stimulus. The materials used are intrinsically biocompatible and thus makes these porous injectable scaffolds excellent candidates for soft tissue engineering

Visual and computational analysis of structure-activity relationships in high-throughput screening data

Novel analytic methods are required to assimilate the large volumes of structural and bioassay data generated by combinatorial chemistry and high-throughput screening programmes in the pharmaceutical and agrochemical industries. This paper reviews recent work in visualisation and data mining that can be used to develop structure-activity relationships from such chemical/biological datasets

Streamability of nested word transductions

We consider the problem of evaluating in streaming (i.e., in a single left-to-right pass) a nested word transduction with a limited amount of memory. A transduction T is said to be height bounded memory (HBM) if it can be evaluated with a memory that depends only on the size of T and on the height of the input word. We show that it is decidable in coNPTime for a nested word transduction defined by a visibly pushdown transducer (VPT), if it is HBM. In this case, the required amount of memory may depend exponentially on the height of the word. We exhibit a sufficient, decidable condition for a VPT to be evaluated with a memory that depends quadratically on the height of the word. This condition defines a class of transductions that strictly contains all determinizable VPTs

Using formal methods to support testing

Formal methods and testing are two important approaches that assist in the development of high quality software. While traditionally these approaches have been seen as rivals, in recent years a new consensus has developed in which they are seen as complementary. This article reviews the state of the art regarding ways in which the presence of a formal specification can be used to assist testing

Two-way automata and transducers with planar behaviours are aperiodic

We consider a notion of planarity for two-way finite automata and transducers, inspired by Temperley-Lieb monoids of planar diagrams. We show that this restriction captures star-free languages and first-order transductions.Comment: 18 pages, DMTCS submissio

05061 Abstracts Collection -- Foundations of Semistructured Data

From 06.02.05 to 11.02.05, the Dagstuhl Seminar 05061 ``Foundations of Semistructured Data\u27\u27 was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Towards Synthetic Life: Establishing a Minimal Segrosome for the Rational Design of Biomimetic Systems

DNA segregation is a fundamental life process, crucial for renewal, reproduction and propagation of all forms of life. Hence, a dedicated segregation machinery, a segrosome, must function reliably also in the context of a minimal cell. Conceptionally, the development of such a minimal cell follows a minimalistic approach, aiming at engineering a synthetic entity only consisting of the essential key elements necessary for a cell to survive. In this thesis, various prokaryotic segregation systems were explored as possible candidates for a minimal segrosome. Such a minimal segrosome could be applied for the rational design of biomimetic systems including, but not limited to, a minimal cell. DNA segregation systems of type I (ParABS) and type II (ParMRC) were compared for ensuring genetic stabilities in vivo using vectors derived from the natural secondary chromosome of Vibrio cholerae. The type II segregation system R1-ParMRC was chosen as the most promising candidate for a minimal segrosome, and it was characterized and reconstituted in vitro. This segregation system was encapsulated into biomimetic micro-compartments and its lifetime prolonged by coupling to ATP-regenerating as well as oxygen-scavenging systems. The segregation process was coupled to in vitro DNA replication using DNA nanoparticles as a mimic of the condensed state of chromosomes. Furthermore, another type II segregation system originating from the pLS20 plasmid from Bacillus subtilis (Alp7ARC) was reconstituted in vitro as a secondary orthogonal segrosome. Finally, a chimeric RNA segregation system was engineered that could be applied for an RNA-based protocell. Overall, this work demonstrates successful bottom-up assemblies of functional molecular machines that could find applications in biomimetic systems and lead to a deeper understanding of living systems