Expressiveness in biologically inspired languages

A very recent and exciting new area of research is the application of Concurrency Theory tools to formalize and analyze biological systems and one of the most promising approach comes from the process algebras (process calculi). A process calculus is a formal language that allows to describe concurrent systems and comes with well-established techniques for quantitative and qualitative analysis. Biological systems can be regarded as concurrent systems and therefore modeled by means of process calculi. In this thesis we focus on the process calculi approach to the modeling of biological systems and investigate, mostly from a theoretical point of view, several promising bio-inspired formalisms: Brane Calculi and k-calculus family. We provide several expressiveness results mostly by means of comparisons between calculi. We provide a lower bound to the computational power of the non Turing complete MDB Brane Calculi by showing an encoding of a simple P-System into MDB. We address the issue of local implementation within the k-calculus family: whether n-way rewrites can be simulated by binary interactions only. A solution introducing divergence is provided and we prove a deterministic solution preserving the termination property is not possible. We use the symmetric leader election problem to test synchronization capabilities within the k-calculus family. Several fragments of the original k-calculus are considered and we prove an impossibility result about encoding n-way synchronization into (n-1)-way synchronization. A similar impossibility result is obtained in a pure computer science context. We introduce CCSn, an extension of CCS with multiple input prefixes and show, using the dining philosophers problem, that there is no reasonable encoding of CCS(n+1) into CCSn.

A dictionary of modular threefolds

The thesis deals with the modularity conjecture for three-dimensional Calabi-Yau varieties. This is a generalization of the work of A. Wiles and others on modularity of elliptic curves. Modularity connects the number of points on varieties with coefficients of certain modular forms. In chapter 1 we collect the basics on arithmetic on Calabi-Yau manifolds, including general modularity results and strategies for modularity proofs. In chapters 2, 3, 4 and 5 we investigate examples of modular Calabi-Yau threefolds, including all examples occurring in the literature and many new ones. Double octics, i.e. Double coverings of projective 3-space branched along an octic surface, are studied in detail. In chapter 6 we deal with examples connected with the same modular forms. According to the Tate conjecture there should be correspondences between them. Many correspondences are constructed explicitly. We finish by formulating conjectures on the occurring newforms, especially their levels. In the appendices we compile tables of coefficients of weight 2 and weight 4 newforms and many examples of double octics.

Theoretical and implementation aspects in the mechanization of the metatheory of programming languages

Interactive theorem provers are tools designed for the certification of formal proofs developed by means of man-machine collaboration. Formal proofs obtained in this way cover a large variety of logical theories, ranging from the branches of mainstream mathematics, to the field of software verification. The border between these two worlds is marked by results in theoretical computer science and proofs related to the metatheory of programming languages. This last field, which is an obvious application of interactive theorem proving, poses nonetheless a serious challenge to the users of such tools, due both to the particularly structured way in which these proofs are constructed, and to difficulties related to the management of notions typical of programming languages like variable binding. This thesis is composed of two parts, discussing our experience in the development of the Matita interactive theorem prover and its use in the mechanization of the metatheory of programming languages. More specifically, part I covers: - the results of our effort in providing a better framework for the development of tactics for Matita, in order to make their implementation and debugging easier, also resulting in a much clearer code; - a discussion of the implementation of two tactics, providing infrastructure for the unification of constructor forms and the inversion of inductive predicates; we point out interactions between induction and inversion and provide an advancement over the state of the art. In the second part of the thesis, we focus on aspects related to the formalization of programming languages. We describe two works of ours: - a discussion of basic issues we encountered in our formalizations of part 1A of the Poplmark challenge, where we apply the extended inversion principles we implemented for Matita; - a formalization of an algebraic logical framework, posing more complex challenges, including multiple binding and a form of hereditary substitution; this work adopts, for the encoding of binding, an extension of Masahiko Sato's canonical locally named representation we designed during our visit to the Laboratory for Foundations of Computer Science at the University of Edinburgh, under the supervision of Randy Pollack.

Structural design, manufacturing and testing of the new wing for the CSIR's Modular UAS in composite materials

In the framework of an international collaboration with South Africa CSIR, the structural design, manufacturing and testing of the new wing for the Modular UAS in composite materials has been performed.

A study of two Languages for Active Objects with Futures

In computer systems, specifically in multithread, parallel and distributed systems, a deadlock is both a very subtle problem - because difficult to pre- vent during the system coding - and a very dangerous one: a deadlocked system is easily completely stuck, with consequences ranging from simple annoyances to life-threatening circumstances, being also in between the not negligible scenario of economical losses. Then, how to avoid this problem? A lot of possible solutions has been studied, proposed and implemented. In this thesis we focus on detection of deadlocks with a static program analysis technique, i.e. an analysis per- formed without actually executing the program. To begin, we briefly present the static Deadlock Analysis Model devel- oped for coreABS−− in chapter 1, then we proceed by detailing the Class- based coreABS−− language in chapter 2. Then, in Chapter 3 we lay the foundation for further discussions by ana- lyzing the differences between coreABS−− and ASP, an untyped Object-based calculi, so as to show how it can be possible to extend the Deadlock Analysis to Object-based languages in general. In this regard, we explicit some hypotheses in chapter 4 first by present- ing a possible, unproven type system for ASP, modeled after the Deadlock Analysis Model developed for coreABS−−. Then, we conclude our discussion by presenting a simpler hypothesis, which may allow to circumvent the difficulties that arises from the definition of the ”ad-hoc” type system discussed in the aforegoing chapter.

Engineering Agent-Oriented Technologies and Programming Languages for Computer Programming and Software Development

Mainstream hardware is becoming parallel, heterogeneous, and distributed on every desk, every home and in every pocket. As a consequence, in the last years software is having an epochal turn toward concurrency, distribution, interaction which is pushed by the evolution of hardware architectures and the growing of network availability. This calls for introducing further abstraction layers on top of those provided by classical mainstream programming paradigms, to tackle more effectively the new complexities that developers have to face in everyday programming. A convergence it is recognizable in the mainstream toward the adoption of the actor paradigm as a mean to unite object-oriented programming and concurrency. Nevertheless, we argue that the actor paradigm can only be considered a good starting point to provide a more comprehensive response to such a fundamental and radical change in software development. Accordingly, the main objective of this thesis is to propose Agent-Oriented Programming (AOP) as a high-level general purpose programming paradigm, natural evolution of actors and objects, introducing a further level of human-inspired concepts for programming software systems, meant to simplify the design and programming of concurrent, distributed, reactive/interactive programs. To this end, in the dissertation first we construct the required background by studying the state-of-the-art of both actor-oriented and agent-oriented programming, and then we focus on the engineering of integrated programming technologies for developing agent-based systems in their classical application domains: artificial intelligence and distributed artificial intelligence. Then, we shift the perspective moving from the development of intelligent software systems, toward general purpose software development. Using the expertise maturated during the phase of background construction, we introduce a general-purpose programming language named simpAL, which founds its roots on general principles and practices of software development, and at the same time provides an agent-oriented level of abstraction for the engineering of general purpose software systems.

Statistical analysis of written languages

La tesi presenta una serie di risultati dell'analisi quantitativa sulla linguistica. Inizialmente sono studiate due fra le leggi empiriche più famose di questo campo, le leggi di Zipf e Heaps, e vengono esposti vari modelli sullo sviluppo del linguaggio. Nella seconda parte si giunge alla discussione di risultati più specifici sulla presenza di fenomeni di burstiness e di correlazioni a lungo raggio nei testi. Tutti questi studi teorici sono affiancati da analisi sperimentali, svolte utilizzando varie traduzioni del libro "Guerra e pace" di Leo Tolstoj e concentrate principalmente sulle eventuali differenze riscontrabili tra le diverse lingue.

Extending Implicit Computational Complexity and Abstract Machines to Languages with Control

The Curry-Howard isomorphism is the idea that proofs in natural deduction can be put in correspondence with lambda terms in such a way that this correspondence is preserved by normalization. The concept can be extended from Intuitionistic Logic to other systems, such as Linear Logic. One of the nice conseguences of this isomorphism is that we can reason about functional programs with formal tools which are typical of proof systems: such analysis can also include quantitative qualities of programs, such as the number of steps it takes to terminate. Another is the possiblity to describe the execution of these programs in terms of abstract machines. In 1990 Griffin proved that the correspondence can be extended to Classical Logic and control operators. That is, Classical Logic adds the possiblity to manipulate continuations. In this thesis we see how the things we described above work in this larger context.

Severe Accident Simulation of Small Modular Reactors

Since the Three Mile Island Unit 2 (TMI-2), accident in 1979 which led to the meltdown of about one half of the reactor core and to limited releases of radioactive materials to the environment, an important international effort has been made on severe accident research. The present work aims to investigate the behaviour of a Small Modular Reactor during severe accident conditions. In order to perform these analyses, a SMR has been studied for the European reference severe accident analysis code ASTEC, developed by IRSN and GRS. In the thesis will be described in detail the IRIS Small Modular Reactor; the reference reactor chosen to develop the ASTEC input deck. The IRIS model was developed in the framework of a research collaboration with the IRSN development team. In the thesis will be described systematically the creation of the ASTEC IRIS input deck: the nodalization scheme adopted, the solution used to simulate the passive safety systems and the strong interaction between the reactor vessel and the containment. The ASTEC SMR model will be tested against the RELAP-GOTHIC coupled code model, with respect to a Design Basis Accident, to evaluate the capability of the ASTEC code on reproducing correctly the behaviour of the nuclear system. Once the model has been validated, a severe accident scenario will be simulated and the obtained results along with the nuclear system response will be analysed.

The languages of postcolonial ireland and their potential for cultural expression

Ireland is a country in which two languages are spoken: English and Irish. This thesis analyzes the historical relationship between the languages, the cultural codes and meanings attached to each of them, as well as how much of the culture of its speakers each is able to carry. Beyond that, the influence the two languages have exercised on one another and their mutual entwinement is taken into closer examination.

Acknowledging linguistic diversity in a multicultural society: the issue of indigenous languages in Colombia.

Nowadays, modern society is gradually becoming multicultural. However, only in the last few years awareness on its importance has been raised. In the case of Colombia, multiculturalism has existed since the pre-Columbian period and today there are more than 80 ethnic groups and 65 indigenous languages in the country. The aim of this work is to illustrate the status of indigenous languages in Colombia and to enlighten about the importance of recognizing, protecting and strengthening the use of these native languages. Subsequent to this, it will be point out that linguistic diversity should be considered a resource and not a barrier to achieve unity in diversity. Finally, ethno-education will be presented as an adequate educational program that may guarantee an equal linguistic representation in the country.

Embedding Languages Without Breaking Tools

Domain-specific languages (DSLs) are increasingly used as embedded languages within general-purpose host languages. DSLs provide a compact, dedicated syntax for specifying parts of an application related to specialized domains. Unfortunately, such language extensions typically do not integrate well with the development tools of the host language. Editors, compilers and debuggers are either unaware of the extensions, or must be adapted at a non-trivial cost. We present a novel approach to embed DSLs into an existing host language by leveraging the underlying representation of the host language used by these tools. Helvetia is an extensible system that intercepts the compilation pipeline of the Smalltalk host language to seamlessly integrate language extensions. We validate our approach by case studies that demonstrate three fundamentally different ways to extend or adapt the host language syntax and semantics.

Practical Dynamic Grammars for Dynamic Languages

Grammars for programming languages are traditionally specified statically. They are hard to compose and reuse due to ambiguities that inevitably arise. PetitParser combines ideas from scannerless parsing, parser combinators, parsing expression grammars and packrat parsers to model grammars and parsers as objects that can be reconfigured dynamically. Through examples and benchmarks we demonstrate that dynamic grammars are not only flexible but highly practical.

Crystallization of Escherichia coli Catabolite Gene Activator Protein with its DNA Binding Site: The use of Modular DNA

To obtain crystals of the Escherichia coli catabolite gene activator protein (CAP) complexed with its DNA-binding site, we have searched for crystallization conditions with 26 different DNA segments ≥28 base-pairs in length that explore a variety of nucleotide sequences, lengths, and extended 5′ or 3′ termini. In addition to utilizing uninterrupted asymmetric lac site sequences, we devised a novel approach of synthesizing half-sites that allowed us to efficiently generate symmetric DNA segments with a wide variety of extended termini and lengths in the large size range (≥28 bp) required by this protein. We report three crystal forms that are suitable for X-ray analysis, one of which (crystal form III) gives measurable diffraction amplitudes to 3 Å resolution. Additives such as calcium, n-octyl-β-d-glucopyranoside and spermine produce modest improvements in the quality of diffraction from crystal form III. Adequate stabilization of crystal form III is unexpectedly complex, requiring a greater than tenfold reduction in the salt concentration followed by addition of 2-methyl-2,4-pentanediol and then an increase in the concentration of polyethylene glycol.