Proceedings of FORM 2022. Construction The Formation of Living Environment

This study examines the integration of building information modelling (BIM) technologies in operation & maintenance stage in the system of managing real estate that helps to reduce transaction costs. The approach and method are based on Digital Twin technology and Model Based System Engineering (MBSE) approach. The results of the development of a service for digital facility management and digital expertise are presented. The connection between physical and digital objects is conceptualized

Proceedings of the Fifth Mediterranean Conference on Information Systems: Professional Development Consortium

Collection of position statements of doctoral students and junior faculty in the Professional Development Consortium at the the Fifth Mediterranean Conference on Information Systems, Tel Aviv - Yafo

Infobiotics : computer-aided synthetic systems biology

Until very recently Systems Biology has, despite its stated goals, been too reductive in terms of the models being constructed and the methods used have been, on the one hand, unsuited for large scale adoption or integration of knowledge across scales, and on the other hand, too fragmented. The thesis of this dissertation is that better computational languages and seamlessly integrated tools are required by systems and synthetic biologists to enable them to meet the significant challenges involved in understanding life as it is, and by designing, modelling and manufacturing novel organisms, to understand life as it could be. We call this goal, where everything necessary to conduct model-driven investigations of cellular circuitry and emergent effects in populations of cells is available without significant context-switching, “one-pot” in silico synthetic systems biology in analogy to “one-pot” chemistry and “one-pot” biology. Our strategy is to increase the understandability and reusability of models and experiments, thereby avoiding unnecessary duplication of effort, with practical gains in the efficiency of delivering usable prototype models and systems. Key to this endeavour are graphical interfaces that assists novice users by hiding complexity of the underlying tools and limiting choices to only what is appropriate and useful, thus ensuring that the results of in silico experiments are consistent, comparable and reproducible. This dissertation describes the conception, software engineering and use of two novel software platforms for systems and synthetic biology: the Infobiotics Workbench for modelling, in silico experimentation and analysis of multi-cellular biological systems; and DNA Library Designer with the DNALD language for the compact programmatic specification of combinatorial DNA libraries, as the first stage of a DNA synthesis pipeline, enabling methodical exploration biological problem spaces. Infobiotics models are formalised as Lattice Population P systems, a novel framework for the specification of spatially-discrete and multi-compartmental rule-based models, imbued with a stochastic execution semantics. This framework was developed to meet the needs of real systems biology problems: hormone transport and signalling in the root of Arabidopsis thaliana, and quorum sensing in the pathogenic bacterium Pseudomonas aeruginosa. Our tools have also been used to prototype a novel synthetic biological system for pattern formation, that has been successfully implemented in vitro. Taken together these novel software platforms provide a complete toolchain, from design to wet-lab implementation, of synthetic biological circuits, enabling a step change in the scale of biological investigations that is orders of magnitude greater than could previously be performed in one in silico “pot”

Mechanisms for enhancing the optical transmission through a single

Este trabajo está dedicado al estudio teórico de las propiedades ópticas mediadas por ondas electromagnéticas superficiales en nanoestructuras metálicas perforadas con agujeros anulares. Con el método analítico de la Expansión Modal, se describen redes infinitas periódicas con agujeros y sistemas finitos (agujeros aislados o Geometrías Ojo de Buey: un agujero circular rodeado de surcos anulares concéntricos). Asimismo, las propiedades de transmisión en tiras de metal combinadas con dieléctricos no lineales de tipo Kerr se estudian usando el método numérico FDTD

Infobiotics : computer-aided synthetic systems biology

Until very recently Systems Biology has, despite its stated goals, been too reductive in terms of the models being constructed and the methods used have been, on the one hand, unsuited for large scale adoption or integration of knowledge across scales, and on the other hand, too fragmented. The thesis of this dissertation is that better computational languages and seamlessly integrated tools are required by systems and synthetic biologists to enable them to meet the significant challenges involved in understanding life as it is, and by designing, modelling and manufacturing novel organisms, to understand life as it could be. We call this goal, where everything necessary to conduct model-driven investigations of cellular circuitry and emergent effects in populations of cells is available without significant context-switching, “one-pot” in silico synthetic systems biology in analogy to “one-pot” chemistry and “one-pot” biology. Our strategy is to increase the understandability and reusability of models and experiments, thereby avoiding unnecessary duplication of effort, with practical gains in the efficiency of delivering usable prototype models and systems. Key to this endeavour are graphical interfaces that assists novice users by hiding complexity of the underlying tools and limiting choices to only what is appropriate and useful, thus ensuring that the results of in silico experiments are consistent, comparable and reproducible. This dissertation describes the conception, software engineering and use of two novel software platforms for systems and synthetic biology: the Infobiotics Workbench for modelling, in silico experimentation and analysis of multi-cellular biological systems; and DNA Library Designer with the DNALD language for the compact programmatic specification of combinatorial DNA libraries, as the first stage of a DNA synthesis pipeline, enabling methodical exploration biological problem spaces. Infobiotics models are formalised as Lattice Population P systems, a novel framework for the specification of spatially-discrete and multi-compartmental rule-based models, imbued with a stochastic execution semantics. This framework was developed to meet the needs of real systems biology problems: hormone transport and signalling in the root of Arabidopsis thaliana, and quorum sensing in the pathogenic bacterium Pseudomonas aeruginosa. Our tools have also been used to prototype a novel synthetic biological system for pattern formation, that has been successfully implemented in vitro. Taken together these novel software platforms provide a complete toolchain, from design to wet-lab implementation, of synthetic biological circuits, enabling a step change in the scale of biological investigations that is orders of magnitude greater than could previously be performed in one in silico “pot”

Aeronautical Engineering: A Continuing Bibliography with Indexes

This report lists reports, articles and other documents recently announced in the NASA STI Database

Formal computational framework for the study of molecular evolution

Over the past 10 years, multiple executable modelling formalisms for molecular biology have been developed in order to address the growing need for a system-level understanding of complex biological phenomena. An important class of these formalisms are biology-inspired process algebras, which offer-among other desirable properties - an almost complete separation of model specification (syntax) from model dynamics (semantics). In this thesis, the similarity between this separation and the genotype-phenotype duality in evolutionary biology is exploited to develop a process-algebraic approach to the study of evolution of biochemical systems. The main technical contribution of this thesis is the continuous π-calculus (cπ), a novel process algebra based on the classical π-calculus of Milner et. al. Its two defining characteristics are: continuous, compositional, computationally inexpensive semantics, and a exible interaction structure of processes (molecules). Both these features are conductive to evolutionary analysis of biochemical systems by, respectively, enabling many variants of a given model to be evaluated, and facilitating in silico evolution of new functional connections. A further major contribution is a collection of variation operators, syntactic model transformation schemes corresponding to common evolutionary events. When applied to a cπ model of a biochemical system, variation operators produce its evolutionary neighbours, yielding insights into the local fitness landscape and neutral neighbourhood. Two well-known biochemical systems are modelled in this dissertation to validate the developed theory. One is the KaiABC circadian clock in the cyanobacterium S. elongatus, the other is a mitogen-activated protein kinase cascade. In each case we study the system itself as well as its predicted evolutionary variants. Simpler examples, particularly that of a generic enzymatic reaction, are used throughout the thesis to illustrate important concepts as they are introduced

Thermo-hydro-mechanical simulation of a generic geological disposal facility for radioactive waste

Geological disposal is required for the safe and long-term disposal of legacy radioactive waste. High level waste and spent fuel generate significant heat that will cause thermo-hydro-mechanical coupled processes in the rock mass. The thermal expansion of the fluid will be greater than the grains causing a decrease in mean effective stress with the low permeability restricting Darcy flow and excess pore pressure equilibration. A decrease in mean effective stress can reduce material strength in granular materials, which may be significant near excavations where differential stress is increased. Microseismic monitoring provides cost effective, non-intrusive and three-dimensional data that can be calibrated with the stress and strain behaviour of a rock mass. However, there is no precedent for the microseismic monitoring of heat-producing radioactive waste. Generic concepts, analogue materials and data from in situ experiments are used to demonstrate the potential for the microseismic monitoring of heat-producing radioactive waste in lower strength sedimentary rocks. A mechanism for early post-closure microseismicity is demonstrated, whereby excess pore pressure decreases the mean effective stress towards yielding in shear. The rock and fluid property uncertainties are ranked according to their contribution to the excess pore pressure. Permeability is found to be important as expected, however, Biot's coefficient is demonstrably more important and yet often overlooked. Furthermore, the microseismic event locations, timings and pseudo scalar seismic moments are shown to have statistically significant relationships with the engineered backfill swelling pressure. Therefore, early post-emplacement microseismic monitoring could provide constraints for the engineered backfill swelling pressure and rock property uncertainties whilst the facility is still operational. Insights could prove timely for adapting the engineering designs, if they are not behaving as expected, in further high level waste and spent fuel tunnels

Multidimensional Context Modeling Applied to Non-Functional Analysis of Software

Context awareness is a first-class attribute of today software systems. Indeed, many applications need to be aware of their context in order to adapt their structure and behavior for offering the best quality of service even in case the software and hardware resources are limited. Modeling the context, its evolution, and its influence on the services provided by (possibly resource constrained) applications are becoming primary activities throughout the whole software life cycle, although it is still difficult to capture the multidimensional nature of context. We propose a framework for modeling and reasoning on the context and its evolution along multiple dimensions. Our approach enables (1) the representation of dependencies among heterogeneous context attributes through a formally defined semantics for attribute composition and (2) the stochastic analysis of context evolution. As a result, context can be part of a model-based software development process, and multidimensional context analysis can be used for different purposes, such as non-functional analysis. We demonstrate how certain types of analysis, not feasible with context-agnostic approaches, are enabled in our framework by explicitly representing the interplay between context evolution and non-functional attributes. Such analyses allow the identification of critical aspects or design errors that may not emerge without jointly taking into account multiple context attributes. The framework is shown at work on a case study in the eHealth domain